Aqueous-based tissue clearing in crustaceans

Breaking Biomphalaria black box by in situ revelation of fluorescent Schistosoma mansoni parasites

Tissue clearing is an old-fashioned method developed in the 1900's and used to turn an opaque biological object into a 3D visualizable transparent structure. Developed and diversified over the last decade, this method is most of the time applied to mammals' tissues, and especially mouse and human tissues for cytological, histological and pathophysiological studies. Through autofluorescence, immunofluorescence, in situ hybridization, intercalating agents, fluorescent transfection markers or fluorescent particle uptake, optically cleared samples can be monitored to discover new biological structures and cellular interactions through 3D-visualization, which can be more challenging in some extend through classical histological methods. Most of the tissue clearing procedures have been developed for specific applications like endogenous fluorescence visualization, immunolabeling or for revealing specific organs. Thus, choosing the adapted protocol may be empirical for non-model species, especially for mollusks for which very little related literature is available. Herein, we suggest an effective optical tissue clearing procedure for the freshwater snail Biomphalaria glabrata, known as the intermediate host of the human parasite Schistosoma mansoni. This clearing procedure involves solvents with a minimal toxicity, preserves the endogenous fluorescence of labeled parasites inside snail tissues and is compatible with an immunolabeling procedure.

See-Star: a versatile hydrogel-based protocol for clearing large, opaque and calcified marine invertebrates

Studies of morphology and developmental patterning in adult stages of many invertebrates are hindered by opaque structures, such as shells, skeletal elements, and pigment granules that block or refract light and necessitate sectioning for observation of internal features. An inherent challenge in studies relying on surgical approaches is that cutting tissue is semi-destructive, and delicate structures, such as axonal processes within neural networks, are computationally challenging to reconstruct once disrupted. To address this problem, we developed See-Star, a hydrogel-based tissue clearing protocol to render the bodies of opaque and calcified invertebrates optically transparent while preserving their anatomy in an unperturbed state, facilitating molecular labeling and observation of intact organ systems. The resulting protocol can clear large (> 1 cm3) specimens to enable deep-tissue imaging, and is compatible with molecular techniques, such as immunohistochemistry and in situ hybridization to visualize protein and mRNA localization. To test the utility of this method, we performed a whole-mount imaging study of intact nervous systems in juvenile echinoderms and molluscs and demonstrate that See-Star allows for comparative studies to be extended far into development, facilitating insights into the anatomy of juveniles and adults that are usually not amenable to whole-mount imaging.

CRISPR-clear imaging of melanin-rich B16-derived solid tumors

Tissue clearing combined with deep imaging has emerged as a powerful technology to expand classical histological techniques. Current techniques have been optimized for imaging sparsely pigmented organs such as the mammalian brain. In contrast, melanin-rich pigmented tissue, of great interest in the investigation of melanomas, remains challenging. To address this challenge, we have developed a CRISPR-based gene editing approach that is easily incorporated into existing tissue-clearing workflows such the PACT clearing method. We term this method CRISPR-Clear. We demonstrate its applicability to highly melanin-rich B16-derived solid tumors, including one made transgenic for HER2, constituting one of very few syngeneic mouse tumors that can be used in immunocompetent models. We demonstrate the utility in detailed tumor characterization by staining for targeting antibodies and nanoparticles, as well as expressed fluorescent proteins. With CRISPR-Clear we have unprecedented access to optical interrogation in considerable portions of intact melanoma tissue for stained surface markers, expressed fluorescent proteins, of subcellular compartments, and of the vasculature.

MAX: a simple, affordable, and rapid tissue clearing reagent for 3D imaging of wide variety of biological specimens

Transparency of biological specimens is crucial to obtaining detailed 3-dimensional images and understanding the structure and function of biological specimens. This transparency or tissue clearing can be achieved by adjusting the refractive index (RI) with embedding media and removing light barriers such as lipids, inorganic deposits, and pigments. Many currently available protocols consist of multiple steps to achieve sufficient transparency, making the process complex and time-consuming. Thus, in this study, we tailored the recipe for RI adjustment media named MAX based on the recently reported MACS protocol to achieve a single-step procedure, especially for ECM-rich tissues. This was achieved by the improvement of the tissue penetrability of the RI-matching reagent by combining MXDA with sucrose or iodixanol. While this was sufficient for the 3D imaging in many applications, MAX can also be combined with modular processes for de-lipidation, de-coloration, and de-calcification to further maximize the transparency depending on the special features of the tissues. Our approach provides an easy alternative for tissue clearing and 3D imaging.

Taking advantage of transparency: A proof-of-principle for the analysis of the uptake of labeled microplastic particles by organisms of different functional feeding guilds using an adapted CUBIC protocol

The analysis of the ingestion of microplastics (MP) by biota is frequently performed through invasive procedures such as chemical digestion protocols or by histological analysis of thin sections. Different, promising approaches for the observation of ingested MP particles pose so called tissue clearing methods. They are currently applied to organs, tissue samples, or whole organisms, rendering the sample transparent and enable to look inside an otherwise opaque environment. To date, there is a lack of methods to detect labeled MP inside an opaque organism's digestive tract without interfering with the sample's integrity. Therefore, our goal was to adapt the CUBIC tissue clearing protocol (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational Analysis) for aquatic and terrestrial organisms of various functional feeding groups for the analysis of the uptake of fluorescent labeled microplastic (MP) particles. We included the buff-tailed bumblebee Bombus terrestris, the compost worm Eisenia fetida, the woodlouse Porcellio scaber, the freshwater shrimp Gammarus roeselii, and the quagga mussel Dreissena bugensis in the analysis. The adapted CUBIC method has led to transparency in all normally opaque organisms. It further offers a simple way of locating fluorescent labeled MP inside the digestive system of the different organisms while leaving them intact.

Observing silkworm embryos at the fertilization stage using a tissue clearing reagent

There are various reports on embryogenesis in silkworm, Bombyx mori, a model organism for lepidopteran insects. New tissue observation methods have been developed with the development of biological science. Applying these methods to silkworm eggs makes it possible to capture morphological and histological features that have not been observed until now. Tissue transparency technology is a method of observation that has advanced remarkably recently. This study emphasized the CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis) method. The tissue clearing reagent used in CUBIC is water-soluble, containing urea and amino alcohol, which easily and effectively clears animal tissue by immersing the sample in the reagent. This study showed that silkworm eggs are made transparent using the modified CUBIC method at the fertilization stage. Furthermore, we observed the behavior of egg nucleus, polar body nuclei, and sperm nuclei at the fertilization stage.

TISSUE CLEARING

Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.

Tissue clearing and 3D imaging in developmental biology

Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.

Physical and chemical mechanisms of tissue optical clearing

Advanced optical methods combined with various probes pave the way toward molecular imaging within living cells. However, major challenges are associated with the need to enhance the imaging resolution even further to the subcellular level for the imaging of larger tissues, as well as for in vivo studies. High scattering and absorption of opaque tissues limit the penetration of light into deep tissues and thus the optical imaging depth. Tissue optical clearing technique provides an innovative way to perform deep-tissue imaging. Recently, various optical clearing methods have been developed, which provide tissue clearing based on similar physical principles via different chemical approaches. Here, we introduce the mechanisms of the current clearing methods from fundamental physical and chemical perspectives, including the main physical principle, refractive index matching via various chemical approaches, such as dissociation of collagen, delipidation, decalcification, dehydration, and hyperhydration, to reduce scattering, as well as decolorization to reduce absorption.

Pathological application of carbocyanine dye-based multicolour imaging of vasculature and associated structures

Simultaneous visualisation of vasculature and surrounding tissue structures is essential for a better understanding of vascular pathologies. In this work, we describe a histochemical strategy for three-dimensional, multicolour imaging of vasculature and associated structures, using a carbocyanine dye-based technique, vessel painting. We developed a series of applications to allow the combination of vessel painting with other histochemical methods, including immunostaining and tissue clearing for confocal and two-photon microscopies. We also introduced a two-photon microscopy setup that incorporates an aberration correction system to correct aberrations caused by the mismatch of refractive indices between samples and immersion mediums, for higher-quality images of intact tissue structures. Finally, we demonstrate the practical utility of our approach by visualising fine pathological alterations to the renal glomeruli of IgA nephropathy model mice in unprecedented detail. The technical advancements should enhance the versatility of vessel painting, offering rapid and cost-effective methods for vascular pathologies.

Research Techniques Made Simple: Optical Clearing and Three-Dimensional Volumetric Imaging of Skin Biopsies

Skin histology is traditionally carried out using two-dimensional tissue sections, which allows for rapid staining, but these sections cannot accurately represent three-dimensional structures in skin such as nerves, vasculature, hair follicles, and sebaceous glands. Although it may be ideal to image skin in a three-dimensional manner, it is technically challenging to image deep into tissue because of light scattering from collagen fibrils in the dermis and refractive index mismatch owing to the presence of differing biological materials such as cytoplasm, and lipids in the skin. Different optical clearing methods have been developed recently, making it possible to render tissues transparent using different approaches. Here, we discuss the steps involved in tissue preparation for three-dimensional volumetric imaging and provide a brief overview of the different optical clearing methods as well as different imaging modalities for three-dimensional imaging.

A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity

Tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. Whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. We have developed a fast DEpigmEntation-Plus-Clearing method (DEEP-Clear) that is easily incorporated in existing workflows and combines whole system labeling with a spectrum of detection techniques, ranging from immunohistochemistry to RNA in situ hybridization, labeling of proliferative cells (EdU labeling) and visualization of transgenic markers. With light-sheet imaging of whole animals and detailed confocal studies on pigmented organs, we provide unprecedented insight into eyes, whole nervous systems, and subcellular structures in animal models ranging from worms and squids to axolotls and zebrafish. DEEP-Clear thus paves the way for the exploration of species-rich clades and developmental stages that are largely inaccessible by regular imaging approaches.

See-through observation of malaria parasite behaviors in the mosquito vector

Although it is known that malaria parasites proliferate in the midgut of mosquito vector, their detailed behaviors, from gamete maturation to formation of next generation sporozoite, have not been fully understood at cellular or molecular level. This is mainly attributed to technical difficulties of dissection and whole-mount observation, of delicate and opaque mosquito body contents. In addition, blood pigment surrounding parasites immediately after blood meal also complicates tracing mosquito-stage parasites. Recent revolutionary studies have overcome such negative factors in tissue observation by clearing organisms. CUBIC reagents succeeded to remove both light scattering and blood pigment from various mouse tissues, and to whole-organ image fluorescence-labeled cell structures. In this study, we utilized the advanced version of CUBIC technology and high sensitivity fluorescent markers for see-through observation of mosquito vector after engulfment of rodent malaria parasites to clarify their behaviors during mosquito stage. As a result, we succeeded to visualize oocysts, sporozoites, female gametes and ookinetes in the mosquito bodies without any dissection.