Three-Dimensional Imaging of Macrophages in Complete Organs

The introduction of the light-sheet microscope has facilitated the analysis of complete tissues for the presence of all cells and their location in relation to their niche. This contributes to a better understanding of cellular locations and interactions in organs. In the last decade, many new and improved protocols have been published which are essential to improve staining and visualization of the immune-fluorescence within different tissues. In this article, we will discuss two main protocols we have used to visualize tissue-resident macrophages.

Effects of butyl benzyl phthalate exposure during pregnancy and lactation on the post-involution mammary gland

The mammary gland undergoes comprehensive reorganization during pregnancy, lactation, and subsequent involution. Following involution, the mammary gland has structural and functional differences compared to the gland of a nulliparous female. These parity-associated changes are regulated by hormones and may be vulnerable to endocrine-disrupting chemicals (EDCs). In this study, we evaluated the long-term effects of butyl benzyl phthalate (BBP), an estrogenic plasticizer, on the parous mouse mammary gland. Pregnant BALB/c mice were treated with 0, 3, 500, or 18000 µg/kg/day BBP throughout both pregnancy and the lactational period. The litters born to these females were evaluated for litter size and growth. The parous females were then kept for five weeks following weaning of the pups, during which period there was no exposure to BBP. After five weeks of post-weaning, mammary glands were collected and assessed for changes in histomorphology, steroid receptor expression, innate immune cell number, and gene expression. An unexposed age-matched nulliparous control was also evaluated as a comparator group. BBP increased male and female pup weight at puberty and female offspring in adulthood. BBP also altered innate immune cells in the post-involution mammary gland, reducing the effect of parity on macrophages. Lastly, BBP modestly increased mammary gland ductal complexity and periductal structure, but had no effect on expression of estrogen receptor, progesterone receptor, or a marker of proliferation. These results suggest that BBP may interfere with some effects of parity on the mouse mammary gland and induce weight gain in exposed offspring.

Analyzing Lymphatic Vessel Patterning in Adult Tissue

Whole-mount immunostaining allows intact tissue to be surveyed in three dimensions, avoiding the more restricted fields of view provided by visualizing thin sections. This technique is particularly useful for imaging lymphatic and blood networks by high-resolution confocal microscopy, revealing how such vessels are spatially positioned, the subcellular arrangements of individual antigens, and interactions with individual cells within the interstitium or vessel lumen. The purpose of this chapter is to provide a practical guide for obtaining images of lymphatic vessels following immunofluorescence staining, primarily in mouse skin.

Studying Cell Division Plane Positioning in Early-Stage Embryos

Unraveling the mechanisms that govern division plane orientation is a major challenge to understand plant development. In this respect, the Arabidopsis early embryo is a model system of choice since embryogenesis is relatively simple and cell division planes orientation is highly predictable. Here we present an integrated set of protocols to study 3D cell division patterns in early-stage Arabidopsis embryos that combine both cellular and sub-cellular localization of selected protein markers with spatial organization of cells, cytoskeleton, and nuclei.

Whole mount staining of lenses for visualization of lens epithelial cell proteins

Whole mount imaging of the lens allows for high spatial resolution visualization of lens epithelial structures by using small molecule fluorescent probes. However, the visualization of specific proteins in lens epithelial cells within whole lenses remains a challenge as the capsule that surrounds the lens does not allow penetration of antibodies. Here we describe a whole mount imaging method that allows us to overcome this challenge by digesting the lens capsules of paraformaldehyde fixed lenses using collagenase. This method enables the penetration of antibodies for effective visualization of proteins in the epithelium of whole lenses.•

A limitation to lens whole mount imaging is the ability to visualize specific proteins as the collagen capsule surrounding the lens impedes the penetration of antibodies

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This protocol helps overcome this limitation by a light collagenase digestion of the capsule of fixed lenses prior to immunostaining

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This method allows for the imaging of specific proteins in the epithelium of the whole lens tissue

Endocrine disrupting chemicals and the mammary gland

Development of the mammary gland requires coordination of hormone signaling pathways including those mediated by estrogen, progesterone, androgen and prolactin receptors. These hormones play important roles at several distinct stages of life including embryonic/fetal development, puberty, pregnancy, lactation, and old age. This also makes the gland sensitive to perturbations from environmental agents including endocrine disrupting chemicals (EDCs). Although there is evidence from human populations of associations between EDCs and disruptions to breast development and lactation, these studies are often complicated by the timing of exposure assessments and the latency to develop breast diseases (e.g., years to decades). Rodents have been instrumental in providing insights-not only to the basic biology and endocrinology of the mammary gland, but to the effects of EDCs on this tissue at different stages of development. Studies, mostly but not exclusively, of estrogenic EDCs have shown that the mammary gland is a sensitive tissue, that exposures during perinatal development can produce abnormal mammary structures (e.g., alveolar buds, typically seen in pregnant females) in adulthood; that exposures during pregnancy can alter milk production; and that EDC exposures can enhance the response of the mammary tissue to hormones and chemical carcinogens. Other studies of persistent organic pollutants have shown that EDC exposures during critical windows of development can delay development of the gland, with lifelong consequences for the individual. Collectively, this work continues to support the conclusion that EDCs can harm the mammary gland, with effects that depend on the period of exposure and the period of evaluation.

Whole-Mount Immunofluorescence Staining of Early Mouse Embryos

Immunofluorescence staining enables the visualization of protein expression at a cellular or even sub-nuclear level. Whole-mount staining preserves the three-dimensional spatial information in biological samples allowing a comprehensive interpretation of expression domains. Here we describe the sample processing, protein detection using antibodies and confocal imaging of isolated preimplantation to early postimplantation mouse embryos up to Embryonic day 8.0 (E8.0).

Expression of Toll-like receptors 4 and 7 in murine peripheral nervous system development

BACKGROUND

Toll-Like Receptors (TLRs) play a critical role in the innate and adaptive immune system. They are the mammalian orthologs of Drosophila melanogaster protein Toll, which has been proved to have an early morphogenetic role in invertebrate embryogenesis that in the adult switches to an immune function.

AIM

The aim of this study was to evaluate the expression of TLR4 and TLR7 during dorsal root ganglia (DRG), paravertebral ganglia (PVG), and enteric nervous system (ENS) murine development.

METHODS

Mouse embryos from different stages (i.e. E12 to E18) were processed for immunolocalization analysis on formalin-fixed paraffin-embedded sections, and isolated intestine were processed for whole-mount preparations.

RESULTS

We observed a differentially regulated expression of TLR4 and TLR7 during embryogenesis and an overall increased expression of both receptors during development. While TLR4 was detectable in neurons of DRG and PVG starting from E14 and only from E18 in the ENS, TLR7 was already expressed in scattered neurons of all the investigated regions at E12.

CONCLUSIONS

TLR4 and TRL7 expression temporal patterns suggest a morphogenetic role for these receptors in the development of neural crest derivatives in mammals.

Alizarin Red and Alcian Blue Preparations to Visualize the Skeleton

Understanding proteolytic remodeling of extracellular matrix involves the generation of global or conditional knockout mice by homologous recombination in embryonic stem cells or their manipulation through new advanced technologies such as CRISPR-Cas9. These models provide opportunities to understand the roles of ADAMTS genes in skeletogenesis. Whole-mount skeletal preparations are necessary for assessment of the skeletal phenotype. They allow for facile visualization of skeletal patterning, size and shape of skeletal elements, and skeletal structure. This protocol describes the staining of the murine skeleton using Alcian blue to identify cartilage and alizarin red to identify bone.

Single-Molecule RNA FISH in Whole-Mount Organoids

Single-molecule RNA fluorescent in situ hybridization (smFISH) enables the detection and quantification of single RNA molecules. Three-dimensional organoid cultures have emerged as versatile in vitro primary culture models that recapitulate many physiological features of their tissue of origin. Here we describe a protocol to visualize single RNA molecules in organoid cultures. Our method accommodates both a whole-mount staining workflow which requires spinning disk confocal microscopy, and a cryosectioning workflow which is compatible with widefield microscopy. Organoid smFISH enables to address various biological problems that range from the identification of cell types (e.g., via the intestinal stem cell marker Lgr5) to the quantification of RNA localization in an epithelium.

Whole-Mount Immunolocalization Procedure for Plant Female Meiocytes

Here we present an optimized protocol for immunolocalization of meiotic proteins during female meiosis in whole mount tissues. It ensures ovule morphology integrity and homogeneous reagent penetration. The method relies on paraformaldehyde tissue fixation, polyacrylamide embedding, tissue permeabilization, antibody incubation, counterstaining, and confocal microscopy analysis. This protocol has been used in diverse Arabidopsis ecotypes and in the legume Vigna unguiculata.

Morphological Analysis of Lacteal Structure in the Small Intestine of Adult Mice

The lacteal is a blunt-ended lymphatic capillary located at the center of a villus in the small intestine that plays multifaceted roles under both physiologic and pathologic conditions. However, studies of its biology are limited by the lack of a feasible method to visualize all the relevant components for its regulation. Here, we describe an efficient whole-mount protocol to visualize the intact structure of lacteals and surrounding cells in villi of the small intestine of adult mouse.

Whole-Mount In Situ Hybridization of Mouse Embryos Using DIG-Labeled RNA Probes

Whole-mount in situ hybridization (WMISH) is a commonly used technique for visualizing the expression profile of mRNAs in embryos. Unlike traditional in situ hybridization techniques, which require thin tissue sections, the WMISH technique allows gene expression patterns to be assessed over the entire embryo and structure. Here, we describe the detailed procedural steps of WMISH, including probe production, embryo fixation and staining, and post-hybridization signal detection. Using this protocol, we visualized highly specific expression patterns of Sonic hedgehog and Bmp4 mRNAs in E12.5 mouse embryos.

Silencing cuticular pigmentation genes enables RNA FISH in intact insect appendages

Optical imaging of gene expression by fluorescence in situ hybridisation (FISH) in insects is often impeded by their pigmented cuticle. As most chemical bleaching agents are incompatible with FISH, we developed an RNA interference (RNAi)-based method for clearing cuticular pigmentation which enables the use of whole-mount body appendages for RNA FISH (termed RNA-i-FISH). Silencing laccase2 or tyrosine hydroxylase in two leaf beetles species (Chrysomela populi and Phaedon cochleariae) cleared their pigmented cuticle and decreased light absorbance. Subsequently, intact appendages (palps, antennae, legs) from RNAi-cleared individuals were used to image the expression and spatial distribution of antisense mRNA of two chemosensory genes encoding gustatory receptor and odorant-binding protein. Imaging did not work for RNAi controls because the pigmentation was retained, or for FISH controls (sense mRNA). Several bleaching agents were incompatible with FISH, because of degradation of RNA, lack of clearing efficacy or long incubation times. Overall, silencing pigmentation genes is a significant improvement over bleaching agents, enabling FISH in intact insect appendages.

Whole-Mount and Section In Situ Hybridization in Mouse Embryos for Detecting mRNA Expression and Localization

In situ hybridization is defined as one of the most useful and powerful methods to know where genes (e.g., mRNA, ncRNA) of interest are expressed in tissues. Expression of mRNA can be detected as blue or dark purple signals though hybridization, immunoreaction and coloring steps. Genome-wide approaches in various model animals have been conducted thoroughly, and have led to new research areas aimed at uncovering novel gene functions in cell differentiation and development. To elucidate gene function, spatiotemporal gene expression analysis is very important. Here I describe protocols of whole-mount and section in situ hybridization, and emphasize the relevance of optimizing temperature, and sodium concentration, in hybridization buffer and substrate to improve signal.

Dorsal Ear Skin Window for Intravital Imaging and Functional Analysis of Lymphangiogenesis

Postdevelopmental lymphangiogenesis occurs in chronic inflammation and wound healing, and here we describe a window preparation in the mouse ear in which lymphangiogenesis can be observed and manipulated. This model has many advantages, including access for intravital immunostaining and imaging to assess morphological features and regeneration kinetics, as well as functional assays such as lymphatic clearance. We describe five procedures: (1) the creation of a collagen-fibrin-filled window in the mouse ear as a model for regenerative lymphangiogenesis, (2) intravital immunostaining for live analysis of morphology and structure, (3) lymphatic clearance assay for functional quantification, (4) whole-mount imaging with tissue clearing for confocal imaging, and (5) postmortem lymphangiography. These procedures allow for identification of morphological and functional abnormalities in both preexisting and newly formed lymphatic vessels.

Whole-Mount BrdU Staining with Fluorescence In Situ Hybridization in Planarians

Detection of cell proliferation based on the incorporation of 5'-bromo-2'-deoxyuridine (BrdU) has become a standard approach for studying stem cell and progenitor cell populations in developing and adult tissue. In this chapter, we describe three BrdU administration methods for planarians and a staining protocol combining BrdU detection with whole-mount fluorescence in situ hybridization (FISH). Collectively, these protocols enable the combined analysis of BrdU-incorporation and endogenous gene expression, as for example during lineage tracing applications.

An improved method for in vitro morphofunctional analysis of mouse dorsal root ganglia

Sensory neurons in dorsal root ganglia (DRGs) are the first-order neurons along the pathway conveying sensory information from the periphery to the central nervous system. The analysis of the morphological and physiological features of these neurons and their alterations in pathology is the necessary prerequisite to understand pain encoding mechanisms. Here, we describe an in vitro procedure for combined morphofunctional analysis of mouse DRGs. Freshly excised DRGs obtained from adult mice were incubated in collagenase to dissolve the ensheathing connective capsule. The degradation of the connective tissue facilitates both access to the neurons by classical recording glass pipettes and the penetration of primary antibodies for immunohistochemical procedures. The entire DRGs were then imaged using a confocal microscope obtaining a fine 3D representation of their cytoarchitecture without requiring tissue sectioning. Thus, our proposed whole-mount preparation represents a flexible in vitro approach for both functional and phenotypic analysis of DRG neurons by at the same time preserving their neuroanatomical relationships.

Studying Cell Division Plane Positioning in Early-Stage Embryos

Unraveling the mechanisms that govern division plane orientation is a major challenge to understand plant development. In this respect, the Arabidopsis early embryo is a model system of choice since embryogenesis is relatively simple and cell division planes orientation is highly predictable. Here, we present an integrated set of protocols to study 3D cell division patterns in early-stage Arabidopsis embryos that combine both cellular and sub-cellular localization of selected protein markers with spatial organization of cells, cytoskeleton, and nuclei.

Protocol: an improved and universal procedure for whole-mount immunolocalization in plants

Rapid advances in microscopy have boosted research on cell biology. However sample preparation enabling excellent reproducible tissue preservation and cell labeling for in depth microscopic analysis of inner cell layers, tissues and organs still represents a major challenge for immunolocalization studies. Here we describe a protocol for whole-mount immunolocalization of proteins which is applicable to a wide range of plant species. The protocol is improved and robust for optimal sample fixation, tissue clearing and multi-protein staining procedures and can be used in combination with simultaneous detection of specific sequences of nucleic acids. In addition, cell wall and nucleus labelling can be implemented in the protocol, thereby allowing a detailed analysis of morphology and gene expression patterns with single-cell resolution. Besides enabling accurate, high resolution and reproducible protein detection in expression and localization studies, the procedure takes a single working day to complete without the need for robotic equipment.

Studying apoptosis in the Zebrafish

Zebrafish (Danio rerio) have been extensively used to study apoptotic cell death during normal development and under a wide range of experimental manipulations. A number of features make zebrafish a particularly powerful model organism: (1) embryos are small in size, develop rapidly outside the mother, and are optically transparent; (2) tools are readily available for rapid knockdown and overexpression of genes; and (3) embryos can be arrayed into multiwell plates and are permeable to a wide range of drugs and small molecules. The molecular machinery underlying the intrinsic and extrinsic apoptosis pathways appears to be highly conserved between zebrafish and mammals. In this chapter, techniques are described for detecting apoptotic cells in situ in both fixed and live zebrafish embryos. Methods for inducing and inhibiting apoptosis and for functionally manipulating genes involved in apoptotic signaling are also discussed.