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This review summarizes the current state of methods and results achievable by cryo-electron microscopy (cryo-EM) imaging for molecular, cell, and structural biologists who wish to understand what is required and how it might help to address their research questions. It covers some of the main issues in sample preparation, microscopes and data collection, image processing, three-dimensional (3D) reconstruction, and validation and interpretation of the resulting EM density maps and atomic models.

Tissue clearing is one of the most powerful strategies for a comprehensive analysis of disease progression. Here, we established an integrated pipeline that combines tissue clearing, 3D imaging, and machine learning and applied to a mouse tumour model of experimental lung metastasis using human lung adenocarcinoma A549 cells. This pipeline provided the spatial information of the tumour microenvironment. We further explored the role of transforming growth factor-β (TGF-β) in cancer metastasis. TGF-β-stimulated cancer cells enhanced metastatic colonization of unstimulated-cancer cells in vivo when both cells were mixed. RNA-sequencing analysis showed that expression of the genes related to coagulation and inflammation were up-regulated in TGF-β-stimulated cancer cells. Further, whole-organ analysis revealed accumulation of platelets or macrophages with TGF-β-stimulated cancer cells, suggesting that TGF-β might promote remodelling of the tumour microenvironment, enhancing the colonization of cancer cells. Hence, our integrated pipeline for 3D profiling will help the understanding of the tumour microenvironment., Shimpei Kubota et al. describe a pipeline for quantitative whole-organ analysis that that combines tissue clearing, 3D imaging, and machine learning for analysis of the tumour microenvironment. The authors apply this in a mouse model of lung tumour and reveal the role of TGF-β in remodelling the cellular microenvironment favouring metastatic invasion.

Context.— Postmortem evaluation for neurodegenerative disease is expensive in time and materials. These challenges can be met by implementing simpler sampling protocols while preserving anatomic relations. Objective.— To determine the diagnostic effectiveness and cost-effectiveness of a simplified brain blocking protocol compared with the standard blocking protocol used in our Alzheimer's Disease Research Center (ADRC). Design.— We prospectively compared the neuropathologic diagnoses established from our standard 19-cassette/19 brain sites ADRC protocol to a simplified 6-cassette/12 brain sites protocol in 52 consecutive cases. The simplified protocol generated 14 slides for comparison to 52 slides from our standard protocol. Results.— Compared with the ADRC protocol the simplified protocol produced Alzheimer Disease Neuropathologic Changes probability scores that were the same in 50 of 52 cases (r = 0.99). Staging for Lewy pathology was equivalent in 45 of 52 (r = 0.98), scoring for cerebral amyloid angiopathy was equivalent in 48 of 52 (r = 0.97), and grading for arteriolosclerosis was the same in 45 of 52 cases (r = 0.92). Progressive supranuclear palsy (n = 4), multiple system atrophy (n = 2), and corticobasal degeneration (n = 1) could be diagnosed by either protocol independently. The estimated savings per case was 72% or $1744.89 ($2436.37 [ADRC] versus $691.48 [simplified]). Conclusions.— The diagnosis of neurodegenerative disease at autopsy can be done accurately with a less expensive, simplified protocol. Our protocol is similar to those of previously published approaches, but it has a simpler organization scheme. This method should be valuable to institutions where autopsy cost considerations may be important.

Aims A variety of tissue clearing techniques have been developed to render intact tissue transparent. For thicker samples, additional partial tissue delipidation is required before immersion into the final refractive index (RI)‐matching solution, which alone is often inadequate to achieve full tissue transparency. However, it is difficult to determine a sufficient degree of tissue delipidation, excess of which can result in tissue distortion and protein loss. Here, we aim to develop a clearing strategy that allows better monitoring and more precise determination of delipidation progress. Methods We combined the detergent sodium dodecyl sulphate (SDS) with OPTIClear, a RI‐matching solution, to form a strategy termed Accurate delipidation with Optimal Clearing (Accu‐OptiClearing). Accu‐OptiClearing allows for a better preview of the final tissue transparency achieved when immersed in OPTIClear alone just before imaging. We assessed for the changes in clearing rate, protein loss, degree of tissue distortion, and preservation of antigens. Results Partial delipidation using Accu‐OptiClearing accelerated tissue clearing and better preserved tissue structure and antigens than delipidation with SDS alone. Despite achieving similar transparency in the final OPTIClear solution, more lipids were retained in samples cleared with Accu‐OptiClearing compared to SDS. Conclusions Combining the RI‐matching solution OPTIClear with detergents, Accu‐OptiClearing, can avoid excessive delipidation, leading to accelerated tissue clearing, less tissue damage and better preserved antigens., Our new strategy of using Accurate dilapidation with Optimal Clearing combines SDS, OPTIClear and refractive index‐matching solution. The new strategy provides fast, non‐swell/shrink, and no protein loss protocol for making the brain to be semi‐transparent. This opens a new avenue of fast pathological analysis of the brain without many thin tissue sectioning.

Objectives. The criteria for “active surveillance” depend in part on quantification of tumor extent and grade on prostate biopsies. It is known that false-negative biopsies may occur from incomplete sectioning of cores within the paraffin blocks. Methods. We retrospectively analyzed a prostate biopsy series, which were subjected to a second round of sections, in order to determine the rate of missed cancers. Results. Of 1324 sets of prostate biopsies, 4.5% (60) showed additional involved cores or higher grade tumor on recut sections. In 27 patients (2.0%), the changed diagnosis resulted in a potential mild increase in National Comprehensive Cancer Network (NCCN) risk, from negative to very low (12), very low to low (12), and low to favorable intermediate (3). In 3 patients (0.2%), the changed diagnosis resulted in a significant increase in NCCN risk. Comparison of the initial sets of slides to the recuts demonstrated areas of absent tissue in many of the cases in which tumor segments were missed. In 2/3 cases with the significant grade increase, gaps were present in one that should have alerted the pathologist to incomplete sections, and the tumor was fragmented at the edge of the core appearing incompletely sampled. Conclusions. A significant increase in risk was seen in this study in 0.2% of patients when blocks were recut for further sampling, with minor increases in 2%. While embedding issues only rarely resulted in clinically significant sampling error, the 3 significantly underdiagnosed cases underscore the need for pathologists to be alert to incomplete sections of prostate cores.

Structural elucidation and molecular scrutiny of cerebral vasculature is crucial for understanding the functions and diseases of the brain. Here, we introduce SeeNet, a method for near-complete three-dimensional visualization of cerebral vascular networks with high signal-to-noise ratios compatible with molecular phenotyping. SeeNet employs perfusion of a multifunctional crosslinker, vascular casting by temperature-controlled polymerization of hybrid hydrogels, and a bile salt-based tissue-clearing technique optimized for observation of vascular connectivity. SeeNet is capable of whole-brain visualization of molecularly characterized cerebral vasculatures at the single-microvessel level. Moreover, SeeNet reveals a hitherto unidentified vascular pathway bridging cerebral and hippocampal vessels, thus serving as a potential tool to evaluate the connectivity of cerebral vasculature., Structural and molecular elucidation of cerebrovascular network is promising for understanding energy supply system in the brain. Here, the authors describe labeling and tissue clearing techniques that visualize the whole-brain vasculature in a molecularly characterizable manner.

Aims: The mechanisms underlying the selective degeneration of motor neurones in amyotrophic lateral sclerosis (ALS) are poorly understood. The aim of this study was to implement spatially resolved RNA sequencing in human post mortem cortical tissue from an ALS patient harbouring the C9orf72 hexanucleotide repeat expansion to identify dysregulated transcripts that may account for differential vulnerabilities of distinct (i) cell types and (ii) brain regions in the pathogenesis of ALS.Methods: Using spatial transcriptomics (ST) we analysed the transcriptome of post mortem brain tissue, with spatial resolution down to 100 μm. Validation of these findings was then performed using BaseScope, an adapted, in situ hybridization technique with single‐transcript single‐cell‐resolution, providing extensive regional and cell‐type specific confirmation of these dysregulated transcripts. The validation cohort was then extended to include multiple post mortem brain regions and spinal cord tissue from an extended cohort of C9orf72, sporadic ALS (sALS) and SOD1 ALS cases.Results: We identified sixteen dysregulated transcripts of proteins that have roles within six disease‐related pathways. Furthermore, these complementary molecular pathology techniques converged to identify two spatially dysregulated transcripts, GRM3 and USP47, that are commonly dysregulated across sALS, SOD1 and C9orf72 cases alike.Conclusions: This study presents the first description of ST in human post mortem cortical tissue from an ALS patient harbouring the C9orf72 hexanucleotide repeat expansion. These data taken together highlight the importance of preserving spatial resolution, facilitating the identification of genes whose dysregulation may in part underlie regional susceptibilities to ALS, crucially highlighting potential therapeutic and diagnostic targets.

Risk evaluation of lymph node metastasis (LNM) for endoscopically resected submucosal invasive (T1) colorectal cancers (CRC) is critical for determining therapeutic strategies, but interobserver variability for histologic evaluation remains a major problem. To address this issue, we developed a machine-learning model for predicting LNM of T1 CRC without histologic assessment. A total of 783 consecutive T1 CRC cases were randomly split into 548 training and 235 validation cases. First, we trained convolutional neural networks (CNN) to extract cancer tile images from whole-slide images, then re-labeled these cancer tiles with LNM status for re-training. Statistical parameters of the tile images based on the probability of primary endpoints were assembled to predict LNM in cases with a random forest algorithm, and defined its predictive value as random forest score. We evaluated the performance of case-based prediction models for both training and validation datasets with area under the receiver operating characteristic curves (AUC). The accuracy for classifying cancer tiles was 0.980. Among cancer tiles, the accuracy for classifying tiles that were LNM-positive or LNM-negative was 0.740. The AUCs of the prediction models in the training and validation sets were 0.971 and 0.760, respectively. CNN judged the LNM probability by considering histologic tumor grade.

India is known for its diverse cultivated and wild rice germplasm. In today's crop improvement programmes, wild relatives are much-needed genetic repository of valuable traits. Analysis of genetic diversity at the chromosomal level is one cost-effective tool to unlock foundational information related to genetics and plant breeding. Presently, enzymatic maceration and air-drying method (EMA) has been applied for the first time in six cultivated and nine wild Indian rice (diploid and tetraploid). EMA method following Giemsa staining has yielded large numbers of cytoplasm free metaphase plates with distinct chromosome morphology. Detailed analysis has revealed karyotype diversities in terms of total chromatin length (TCL), chromosome morphology and location of sat chromosomes within and between the studied species. Most of the cultivated rice has gained additional amount in TCL during the period of domestication in comparison to their progenitor Oryza nivara. Morphological clarity of the small chromosomes of rice was much required and has helped to identify individual chromosomes in the diverse karyotypes. Diversity in landmark SAT chromosomes is another important observation, not reported previously in Indian rice. Present study has shown that in most of the O. sativa members, the 10th pair contains SAT except one where 6th pair is satellited. On the other hand, diversity of SAT in diploid and tetraplod wild species has been recorded on 5th, 7th and 8th chromosome pairs and on 9th, 12th, 22nd and 23rd chromosome pairs, respectively. Karyomorphometric indices has helped to construct dendrogram to elucidate intraspecies and interspecies relationships. Untapped genetic diversity recorded in Indian rice through chromosomal analysis will be useful to the breeders and genome researchers.

Summary This protocol is intended as a guide for implementing or refining the usage of the air-liquid interface (ALI) model system to generate airway mucociliary tissue in vitro. We present a streamlined protocol for isolating the stem cells from inferior nasal turbinates of donors, allowing for a simple and low-cost supply of primary cells for research. We also provide our detailed protocols for ALI tissue processing and immunofluorescence to aid in the standardization of these techniques between research groups. For complete details on the use and execution of this protocol, please refer to Hussain et al., (2014)Yang et al., (2016)Im et al., (2019)., Graphical abstract, Highlights • Rapid isolation of human nasal epithelial cells via nasal brushing • Generation of airway mucociliary tissue in vitro using the air-liquid interface • Detailed description of formalin fixation and paraffin embedding procedures • Antigen retrieval and immunohistochemistry of in vitro-generated airway tissue, This protocol is intended as a guide for implementing or refining the usage of the air-liquid interface (ALI) model system to generate airway mucociliary tissue in vitro. We present a streamlined protocol for isolating the stem cells from inferior nasal turbinates of donors, allowing for a simple and low-cost supply of primary cells for research. We also provide our detailed protocols for ALI tissue processing and immunofluorescence to aid in the standardization of these techniques between research groups.

The evolution of the diagnosis of infectious diseases began with the observation of the morphological characteristics of organisms such as ascaris and whipworms, followed by the use of the microscope and haematoxylin and eosin stains, which allowed recognition of microscopic characteristics undetectable with the naked eye, such as the viral cytopathic changes of herpes and the presence of fungi. Patterns of acute and chronic granulomatous inflammation were also observed; these were not specific to the exact aetiology of the disease, which led to the introduction of special methenamine stains for fungi and Ziehl-Neelsen for fungi and mycobacteria. Later, the use of immunohistochemistry was introduced, which acknowledged the use of antibodies to classify microorganisms and detect cases that were either difficult to interpret or in the midst of severe inflammatory processes. Currently, the use of molecular biology has made it possible to reach diagnoses that would have been very difficult to obtain through traditional methods; these techniques show key specific characteristics and facilitate the diagnosis of various infectious pathologies. These new techniques are based on the detection of antigens and nucleic acids of microorganisms, an important advance in the diagnosis of infectious diseases.

Background The Paris System for Reporting Urinary Cytology (TPS) defines clear morphologic criteria to classify urinary specimens into 7 diagnostic categories. According to TPS, a nuclear-to-cytoplasmic ratio (N:C ratio) >0.7 and hyperchromasia must be observed to render a diagnosis of high-grade urothelial carcinoma (HGUC). TPS was established using only liquid-based preparation techniques, and to the authors' knowledge it is unknown whether TPS can be applied using other preparation methods. Methods In the current prospective study, voided urine samples from patients with HGUC and negative for HGUC (NHGUC) were prepared using both ThinPrep and cytospin methods. ImageJ image processing software was used to measure the N:C ratio and hyperchromasia. For each patient, the N:C ratio and degree of hyperchromasia of urothelial cells present in both cytopreparations were compared. Results A total of 10 HGUC cases and 9 NHGUC cases, represented by a total of 688 cells (mean, 36.7 cells in HGUC cases; and mean, 35.8 cells in NHGUC cases), were evaluated in the current study. An overall comparison of HGUC cells with NHGUC cells demonstrated that HGUC cells had a higher average N:C ratio (0.5465 vs 0.2846) and greater hyperchromasia as measured by the average nuclear pixel gray value (100.8 vs 120.7). The N:C ratio was statistically different in 4 NHGUC cases, demonstrating higher N:C ratios in the ThinPrep preparations. Hyperchromasia was found to be statistically different in 6 cases, 5 of which demonstrated increased hyperchromasia in the ThinPrep specimens. Conclusions The morphologic features of HGUC cells appear to be similar in samples prepared using the ThinPrep and cytospin methods, and therefore TPS criteria may be applied successfully in laboratories that use these methods.

Our current knowledge of the properties of renal ion channels responsible for electrolytes and cell energy homeostasis mainly relies on rodent studies. However, it has not been established yet to what extent their characteristics can be generalized to those of humans. The present study was designed to develop a standardized protocol for the isolation of well-preserved glomeruli and renal tubules from rodent and human kidneys and to assess the functional suitability of the obtained materials for physiological studies. Separation of nephron segments from human and rodent kidneys was achieved using a novel vibrodissociation technique. The integrity of isolated renal tubules and glomeruli was probed via electrophysiological analysis and fluorescence microscopy, and the purity of the collected fractions was confirmed using quantitative RT-PCR with gene markers for specific cell types. The developed approach allows rapid isolation of well-preserved renal tubules and glomeruli from human and rodent kidneys amenable for electrophysiological, Ca2+ imaging, and omics studies. Analysis of the basic electrophysiological parameters of major K+ and Na+ channels expressed in human cortical collecting ducts revealed that they exhibited similar biophysical properties as previously reported in rodent studies. Using vibrodissociation for nephron segment isolation has several advantages over existing techniques: it is less labor intensive, requires little to no enzymatic treatment, and produces large quantities of well-preserved experimental material in pure fractions. Applying this method for the separation of nephron segments from human and rodent kidneys may be a powerful tool for the indepth assessment of kidney function in health and disease.

Traditional two-dimensional histological sections and microcomputed tomography remain to be the major tools for studying craniofacial bones despite the complicated spatial organization of craniofacial organs. Recently, our laboratory developed the Poly(Ethylene Glycol) Associated Solvent System (PEGASOS) tissue clearing method, which can efficiently render hard tissues, including bones and teeth fully transparent without losing endogenous fluorescent signals. Complete tissue transparency enables us to acquire three-dimensional (3D) images of craniofacial bone vasculature, osteogenesis utilizing various labeling strategies, thus to investigate the spatial relationship among different tissues during postnatal craniofacial development. We found out that during the early stage of postnatal development, craniofacial osteogenesis occurs throughout the entire craniofacial bones, including the periosteum, dura, bone marrow, and suture. After 3–4 weeks, craniofacial osteogenesis is gradually restricted to the suture region and remaining bone marrow space. Similarly, craniofacial bone vasculature gradually restricts to the suture region. Osteogenesis is spatially associated with vasculature during the entire postnatal development. Importantly, we demonstrated that in adult calvarial bones, Gli1+ mesenchymal stem cells were also spatially associated with the vasculature. These findings indicate that craniofacial bones share similar osteogenesis mechanism as the long bone despite their distinct osteogenic mechanisms. In addition, the PEGASOS tissue clearing method-based 3D imaging technique is a useful new tool for craniofacial research.

Electron microscopy (EM) provides the necessary resolution to visualize the finer structures of nervous tissue morphology, which is important to understand healthy and pathological conditions in the brain. However, for the interpretation of the micrographs the tissue preservation is crucial. The quality of the tissue structure is mostly influenced by the post mortem interval (PMI), the time of death until the preservation of the tissue. Therefore, the aim of this study was to optimize the preparation-procedure for the human frontal lobe to preserve the ultrastructure as well as possible despite the long PMIs. Combining chemical pre- and post-fixation with cryo-fixation and cryo-substitution (“hybrid freezing”), it was possible to improve the preservation of the neuronal profiles of human brain samples compared to the “standard” epoxy resin embedding method. In conclusion short PMIs are generally desirable but up to a PMI of 16 h the ultrastructure can be preserved on an acceptable level with a high contrast using the “hybrid freezing” protocol described here.

Background:Current clinical practice calls for pulse lavage of fresh osteochondral allografts (OCAs) to reduce immunogenicity; however, there is limited evidence of its effectiveness in reducing allogenic bone marrow elements.Purpose:To evaluate the effectiveness of pulse lavage in removing marrow elements from trabecular bone in fresh OCA transplantation.Study Design:Controlled laboratory study.Methods:The authors evaluated 48 fresh OCA plugs with 4 different common sizes (14- and 24-mm diameter, 6- and 10-mm thickness). Within each size group, half of the samples underwent pulse lavage (n = 6) with saline solution and half were left untreated (no lavage; control group, n = 6). For each treatment and size group, 3 samples were analyzed for DNA content as an indicator of the number of residual nucleated cells; the other 3 samples were histologically analyzed to assess the presence and distribution of cells within subchondral bone pores in 3 specific locations within the plug: peripheral, intermediate, and core.Results:Osteochondral plugs treated with pulse lavage did not show a significant decrease in DNA content in comparison with untreated plugs. Overall, histological analysis did not show a significant difference between the treated and untreated groups ( P = .23). Subgroup analysis by size demonstrated decreased marrow content in treated versus untreated groups in the thinner plug sizes (14 × 6 mm and 24 × 6 mm). Histological evaluation by zone demonstrated a significant difference between groups only in the peripheral zone ( P = .04).Conclusion:Pulse lavage has limited effectiveness in removing marrow elements, in particular in plugs that are larger in diameter and, more importantly, in thickness. Better techniques for subchondral bone treatment are required for more thorough removal of potentially immunogenic marrow elements.Clinical Relevance:OCA transplantation has become an established treatment modality. Unfortunately, OCA is not without limitations, chiefly its mode of failure through inadequate integration of the allograft subchondral bone with subsequent collapse. In an effort to improve integration, current clinical practice calls for pulse lavage to remove allogenic bone marrow from the subchondral bone in hopes of decreasing the immunogenicity of the graft and facilitating revascularization.

The development of precision testing for disease diagnosis has advanced medicine by specifically matching patients with drugs to treat specific diseases. High-quality diagnostics start with high-quality tissue specimens. The development and optimization of tissue handling and processing have lagged behind bioassay development. Ultrasound time-of-flight (TOF) technology has been successfully used to monitor the critical processing step of tissue fixation with formalin. In this study, we expand the use of this technology to monitor tissue dehydration and clearing by analyzing TOF signals from 270 different specimens, representing 13 different tissue types obtained through surgical resections. We determined the time constant τ90 for each tissue type for the following tissue processing solvents: 70% ethanol, 90% ethanol, 100% ethanol, and xylene. The TOF signals were correlated with tissue morphology to ensure that high-quality tissue was produced. Tissues can be grouped into those exhibiting fast and slow reagent diffusion. We monitored incomplete dehydration of tissue by skipping a key processing step, dehydration in absolute ethanol, and then correlated the τ90 with poor histomorphology, demonstrating that the technique can detect significant processing errors. Ultrasound TOF technology can therefore be used to monitor all phases of tissue processing cycle and yields an important preanalytical quality metric.

Recently, deep learning frameworks have been shown to be successful and efficient in processing digital histology images for various detection and classification tasks. Among these tasks, cell detection and classification are key steps in many computer-assisted diagnosis systems. Traditionally, cell detection and classification is performed as a sequence of two consecutive steps by using two separate deep learning networks, one for detection and the other for classification. This strategy inevitably increases the computational complexity of the training stage. In this paper, we propose a synchronized deep autoencoder network for simultaneous detection and classification of cells in bone marrow histology images. The proposed network uses a single architecture to detect the positions of cells and classify the detected cells, in parallel. It uses a curve-support Gaussian model to compute probability maps that allow detecting irregularly-shape cells precisely. Moreover, the network includes a novel neighborhood selection mechanism to boost the classification accuracy. We show that the performance of the proposed network is superior than traditional deep learning detection methods and very competitive compared to traditional deep learning classification networks. Runtime comparison also shows that our network requires less time to be trained.\ud

Background The basic rhythmicity underlying stepping in mammals is generated by a neural network, situated in the spinal cord, known as the locomotor central pattern generator (CPG). While a molecular approach has provided information regarding neuronal populations that participate in locomotor activity and their specific function, the distributed nature of the locomotor CPG has made it difficult to identify and characterize the specific neurons belonging to each population that are rhythmically-active during stepping. New Method We describe a preparation in which we isolate the spinal cord from a neonatal mouse, section it at a lumbar segment, situate it in an upright orientation under the objective lens of a 2- photon microscope, and evoke fictive locomotion. Results This preparation allows us to image rhythmic Ca2+ oscillations in spinal neurons, and visually identify those that are involved in fictive locomotor activity. We can then characterize unique features of these neurons. Comparison with Existing Methods This builds on existing fictive locomotor preparations and is the first which allows for the visual identification of locomotor related neurons spanning the transverse plane of the spinal cord, facilitating their electrophysiological and anatomical characterization Conclusions This approach promises to provide new information regarding the distribution of the locomotor CPG in the transverse plane, the characteristics of its component interneurons, as well as the cellular mechanisms and network properties which underlie rhythm generation. By altering the location of Ca2+ indicator application it can also be used to identify and characterize neurons involved in other facets of sensorimotor processing.

While epiglottis is essentially a mammalian structure, studying its microstructure in any placental model will add an important information to the field of comparative anatomy and the related branches of biology. The aim of this study was to describe the structure of the epiglottis in dromedary camels using light and scanning electron microscopy (SEM), with reference to the possible functions. A total of 11 epiglottis cartilages from 11 larynges were used. The study revealed unusual, deeply situated glands just beneath the cartilage plate. They have unusually, wide surface-openings, while their ducts were partly located within the cartilage. This is presumed to be an adaptation to the need for rapid and efficient mucosal surface hydration in the arid conditions. The possible secretion transport mechanisms in these glands were also discussed. Furthermore, the SEM revealed for the first time, the presence of taste buds in camel epiglottis. However, in histological sections, visibility of taste buds was dependent upon the staining techniques. The taste buds were not seen with standard H& E stain, as they blended imperceptibly with the surrounding epithelium. Conversely, Mallory's trichrome showed contrasting colors, and taste buds were visible. In conclusion, camel epiglottis has an unusual structure, which may be correlated to environmental adaptation and important for the general health of upper respiratory tract in this species.

Microscopy is widely used for brain research because of its high resolution and ability to stain for many different biomarkers. Since whole brains are usually sectioned for tissue staining and imaging, reconstruction of 3D brain volumes from these sections is important for visualization and analysis. Recently developed tissue clearing techniques and advanced confocal microscopy enable multilayer sections to be imaged without compromising the resolution. However, noticeable structure inconsistence occurs if surface layers are used to align these sections. In this paper, a structure-based intensity propagation method is designed for the robust representation of multilayer sections. The 3D structures in reconstructed brains are more consistent using the proposed methods. Experiments are conducted on 367 multilayer sections from 20 mouse brains. The average reconstruction quality measured by the structure consistence index increases by 45% with the tissue flattening method, and 29% further with the structure-based intensity propagation.

Background Traditional methods for mounting tissue sections onto slides are suboptimal as the amount of labor required quickly multiplies with increasing number of samples. Methods to accelerate the tissue mounting process while reducing the associated risk of tissue damage are needed. New Method We designed and 3D printed a mechanized device with an inclined platform used to mount tissue sections onto slides in buffer solution. The main advantage of this design is to reduce the time required for mounting sections as well as minimize the possibility of damaging delicate or thin tissue sections. Results Using our device, we illustrate and describe in detail the steps required to mount smaller coronally cut mouse brain sections, as well as bigger tangentially cut ferret brain sections. This method's efficiency was assessed by comparing the time required to mount an entire slide of ferret brain sections using our method and the conventional method. Using our device reduced the tissue mounting time by 60%. Comparison with Existing Method(s) Compared to existing conventional tissue mounting methods, our device is a simple and user friendly alternative that substantially reduces the time required to mount tissue sections while preserving tissue section quality. Conclusions Using our device can streamline histological processing and prove to be especially useful for a variety of tissue types as the platform was designed to accommodate different size microscope slides, and thus use for varying tissue section sizes.

Background: Although the liver is the primary organ of drug metabolism, the lungs also contain drug-metabolizing enzymes and may, therefore, contribute to the elimination of drugs. In this investigation, the Precision-cut Lung Slice (PCLS) technique was standardized with the aims of characterizing and comparing rat and human pulmonary drug metabolizing activity. Method: Due to the limited availability of human lung tissue, standardization of the PCLS method was performed with rat lung tissue. Pulmonary enzymatic activity was found to vary significantly with rat age and rat strain. The Dynamic Organ Culture (DOC) system was superior to well-plates for tissue incubations, while oxygen supply appeared to have a limited impact within the 4h incubation period used here. Results: The metabolism of a range of phase I and phase II probe substrates was assessed in rat and human lung preparations. Cytochrome P450 (CYP) activity was relatively low in both species, whereas phase II activity appeared to be more significant.Conclusion:PCLS is a promising tool for the investigation of pulmonary drug metabolism. The data indicates that pulmonary CYP activity is relatively low and that there are significant differences in enzyme activity between rat and human lung.

Immunological methods, which have been widely used in autoimmune blistering diseases (AIBDs) of the oral mucosa, can also be adopted as auxiliary diagnostic tools in oral lichen planus (OLP) and discoid lupus erythematosus (DLE). AIBDs, characterized by autoantibodies against structural proteins of keratinocytes or the basement membrane zone, clinically present as blisters and erosions of the oral mucosa. When atypical lesions occur, OLP or DLE may be confused with AIBDs. The improvement of diagnostic accuracy is necessary due to the significant differences in treatment and prognosis among these diseases. A variety of immunological methods are used for qualitative and quantitative detection of target antigens and autoantibodies. These methods can evaluate efficacy of treatment, monitor diseases and guide treatment decisions. In this review, we discuss the application of immunofluorescence, biochemical tests, and protein microarrays for AIBDs, OLP and DLE, as well as the differential diagnostic methods using immunological tests.

Background Cell blocks and immunohistochemistry (IHC) are increasingly recognized as being complementary tools for cytologic diagnostics, especially for neoplastic diseases. Objectives The study aimed to evaluate the utility of cell tube block (CTB) IHC for refining the diagnosis of effusions in dogs and cats. Methods Cavitary effusions (n = 25) from dogs and cats classified by cytology as reactive, neoplastic, borderline (suspicious of neoplasia), and chylous were studied. CTB sections were stained with H&E, and immunostained with PAX-5, CD3, pancytokeratin (CK), vimentin, and Wilms tumor 1 protein (WT1) antibodies, according to the cytologic diagnoses. A histologic case series of confirmed normal, reactive, and neoplastic mesothelium and several different carcinomas were included to test the utility of WT1 as a marker of mesothelial cells. Results CTBs had a layered appearance with reduced background staining. CD3 and PAX5 immunolabeling allowed immunophenotype assessment in all of the lymphoma cases. In carcinomatous effusions, neoplastic cells were CK-positive, WT1-negative, and vimentin-negative (except for two cases). Wilms tumor 1 protein was positive in the nuclei of normal, reactive, and neoplastic mesothelial cells, and ovarian carcinomatous cells. Other carcinomas and lymphomas were negative. Conclusions CTBs are valuable tools to assist in making a diagnosis of cavitary effusions in dogs and cats, and WT1 is a promising marker to differentiate mesothelial from carcinomatous cells.

Macrocyclic lactone-resistant Parascaris have been reported throughout the world. In part, the drug resistant phenotype is hypothesized to be associated with ATP-binding cassette transporters known as P-glycoproteins. In many systems, P-glycoproteins efflux drugs out of cells thereby precluding drug binding to target receptors. Parascaris may evade macrocyclic lactone-mediated death by effluxing drugs away from target receptors in the nervous system. Alternatively, P-glycoprotein expression in the gut or body wall could prevent penetration of drugs into the body of the parasite altogether. In the present study, we evaluate expression of Peq-pgp-11 and Peq-pgp-16 using a novel multiple nucleic acid hybridization method. This method allowed for visualization of individual mRNA transcripts within fixed tissue sections of Parascaris adults. Our investigation revealed expression of Peq-pgp-11 and Peq-pgp-16 in the intestine, body wall, nerves, lateral cords, and reproductive tissues of male and female parasites. These results suggest that Pgp could efflux drugs locally at the level of parasite neuronal tissue as well as at sites of entry for drugs such as the hypodermis and intestine. The multiple nucleic acid hybridization method could be useful for providing tissue context for gene expression in a variety of nematode parasites.

For the validation of optical diagnostic technologies, experimental results need to be benchmarked against the gold standard. Currently, the gold standard for tissue characterization is assessment of hematoxylin and eosin (H&E)-stained sections by a pathologist. When processing tissue into H&E sections, the shape of the tissue deforms with respect to the initial shape when it was optically measured. We demonstrate the importance of accounting for these tissue deformations when correlating optical measurement with routinely acquired histopathology. We propose a method to register the tissue in the H&E sections to the optical measurements, which corrects for these tissue deformations. We compare the registered H&E sections to H&E sections that were registered with an algorithm that does not account for tissue deformations by evaluating both the shape and the composition of the tissue and using microcomputer tomography data as an independent measure. The proposed method, which did account for tissue deformations, was more accurate than the method that did not account for tissue deformations. These results emphasize the need for a registration method that accounts for tissue deformations, such as the method presented in this study, which can aid in validating optical techniques for clinical use. (C) The Authors. Published by SPIE under a Creative Commons Attribution 4.0 Unported License.

The renal pelvis (RP) is a funnel-shaped, smooth muscle structure that facilitates normal urine transport from the kidney to the ureter by regular, propulsive contractions. Regular RP contractions rely on pacemaker activity, which originates from the most proximal region of the RP at the pelvis-kidney junction (PKJ). Due to the difficulty in accessing and preserving intact preparations of the PKJ, most investigations on RP pacemaking have focused on single-cell electrophysiology and Ca2+ imaging experiments. Although important revelations on RP pacemaking have emerged from such work, these experiments have several intrinsic limitations, including the inability to accurately determine cellular identity in mixed suspensions and the lack of in situ imaging of RP pacemaker activity. These factors have resulted in a limited understanding of the mechanisms that underlie normal rhythmic RP contractions. In this paper, a protocol is described to prepare intact segments of mouse PKJ using a vibratome sectioning technique. By combining this approach with mice expressing cell-specific reporters and genetically encoded Ca2+ indicators, investigators may be able to more accurately study the specific cell types and mechanisms responsible for peristaltic RP contractions that are vital for normal urine transport.

Introduction Whether cardiac mucosa at the esophagogastric junction is normal or metaplastic is controversial. Studies attempting to resolve this issue have been limited by the use of superficial pinch biopsies, abnormal esophagi resected typically because of cancer, or autopsy specimens in which tissue autolysis in the stomach obscures histologic findings. Methods We performed histologic and immunohistochemical studies of the freshly fixed esophagus and stomach resected from 7 heart-beating, deceased organ donors with no history of esophageal or gastric disease and with minimal or no histologic evidence of esophagitis and gastritis. Results All subjects had cardiac mucosa, consisting of a mixture of mucous and oxyntic glands with surface foveolar epithelium, at the esophagogastric junction. All also had unique structures we termed compact mucous glands (CMG), which were histologically and immunohistochemically identical to the mucous glands of cardiac mucosa, under esophageal squamous epithelium and, hitherto undescribed, in uninflamed oxyntic mucosa throughout the gastric fundus. Discussion These findings support cardiac mucosa as a normal anatomic structure and do not support the hypothesis that cardiac mucosa is always metaplastic. However, they do support our novel hypothesis that in the setting of reflux esophagitis, reflux-induced damage to squamous epithelium exposes underlying CMG (which are likely more resistant to acid-peptic damage than squamous epithelium), and proliferation of these CMG as part of a wound-healing process to repair the acid-peptic damage could result in their expansion to the mucosal surface to be recognized as cardiac mucosa of a columnar-lined esophagus.

Cryo-electron tomography (cryo-ET) is a powerful technique to examine cellular structures as they exist in situ. However, direct imaging by TEM for cryo-ET is limited to specimens up to ~400 nm in thickness, narrowing its applicability to areas such as cellular projections or small bacteria and viruses. Cryo-focused-ion-beam (cryo-FIB) milling has emerged in recent years as a method to generate thin specimens from cellular samples in preparation for cryo-ET. In this technique, specimens are thinned with a beam of gallium ions to gradually ablate cellular material in order to leave a thin, electron-transparent section (a lamella) through the bulk material. The lamella can be used for high-resolution cryo-ET to visualize cells in 3D in a near-native state. This approach has proved to be robust and relatively simple for new users, and exhibits minimal sectioning artifacts. In this chapter, we describe a general approach to cryo-FIB milling for users with prior cryo-EM experience, with extensive notes on operation and troubleshooting.

Organisms are inherently three dimensional, thus comprehensive understanding of the complicated biological system requires analysis of organs or even whole bodies in the context of three dimensions. However, this is a tremendous task since the biological specimens are naturally opaque, a major obstacle in whole-body and whole-organ imaging. Tissue clearing technique provides a prospective solution and has become a powerful tool for three-dimensional imaging and quantification of organisms. Tissue clearing technique aims to make tissue transparent by minimizing light scattering and light absorption, thus allowing deep imaging of large volume samples. When combined with diverse molecular labeling methods and high-throughput optical sectioning microscopes, tissue clearing technique enables whole-body and whole-organ imaging at cellular or subcellular resolution, providing detailed and comprehensive information about the intact biological systems. Here, we give an overview of recent progress and biomedical applications of tissue clearing technique. We introduce the mechanisms and basic principles of tissue clearing, and summarize the current tissue clearing methods. Moreover, the available imaging techniques and software packages for data processing are also presented. Finally, we introduce the recent advances in applications of tissue clearing in biomedical fields. Tissue clearing contributes to the investigation of structure-function relationships in intact mammalian organs, and opens new avenues for cellular and molecular mapping of intact human organs. We hope this review contributes to a better understanding of tissue clearing technique and can help researchers to select the best-suited clearing protocol for their experiments.

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Tissue clearing has become a powerful technique for studying anatomy and morphology at scales ranging from entire organisms to subcellular features. With the recent proliferation of tissue-clearing methods and imaging options, it can be challenging to determine the best clearing protocol for a particular tissue and experimental question. The fact that so many clearing protocols exist suggests there is no one-size-fits-all approach to tissue clearing and imaging. Even in cases where a basic level of clearing has been achieved, there are many factors to consider, including signal retention, staining (labeling), uniformity of transparency, image acquisition and analysis. Despite reviews citing features of clearing protocols, it is often unknown a priori whether a protocol will work for a given experiment, and thus some optimization is required by the end user. In addition, the capabilities of available imaging setups often dictate how the sample needs to be prepared. After imaging, careful evaluation of volumetric image data is required for each combination of clearing protocol, tissue type, biological marker, imaging modality and biological question. Rather than providing a direct comparison of the many clearing methods and applications available, in this tutorial we address common pitfalls and provide guidelines for designing, optimizing and imaging in a successful tissue-clearing experiment with a focus on light-sheet fluorescence microscopy (LSFM). This tutorial provides guidance for selecting and optimizing tissue-clearing protocols for specific samples and biological questions. In addition, instructions are provided for developing an imaging strategy and processing the resulting data.

The cell block (CB) technique is a generalized method utilized for the diagnostic evaluation of body cavity fluids. Ascites cytology is one of the most important diagnostic processes for epithelial ovarian cancer. However, in clinical practice, the usefulness of the CB method to diagnose this tumor remains unelucidated. Between 2008 and 2017, 15 peritoneal or pleural fluid samples obtained from patients with ovarian or peritoneal carcinoma or other gastrointestinal malignancies were preoperatively subjected to a diagnostic evaluation to predict the histological type and original organ. The CBs were made from 10% formalin neutral buffer solution fixed sediments of fluid samples after cytological smears were made by conventional method. Four-μm thickness sections were prepared from the cell blocks and stained with immunohistochemical method, using 16 kinds of antibodies and hematoxylin eosin staining method. The cellularity, architectural patterns, and morphological details were also studied. The median (range) age of patients was 73 (35–87) years. The clinical features were identified as follows: pleural effusion in 4, ovarian mass in 7, peritoneal dissemination in 12, para-aortic nodal swelling in one, and liver tumor in one (some overlapping). Five patients had a history of prior malignancy. Finally, we could accurately diagnose the histological type in 9 patients based on subsequent biopsy, surgery, and autopsy. In all 9 women, the clinical diagnosis, CB diagnosis and final pathological diagnosis were consistent. The CB technique may be a helpful modality for evaluating fluid cytology to obtain a final histopathologic diagnosis.

Studies on islet of Langerhans physiology are crucial to understand the role of the endocrine pancreas in diabetes pathogenesis and the development of new therapeutic approaches. However, so far most research addressing islet of Langerhans biology relies on islets obtained via enzymatic isolation from the pancreas, which is known to cause mechanical and chemical stress, thus having a major impact on islet cell physiology. To circumvent the limitations of islet isolation, we have pioneered a platform for the study of islet physiology using the pancreas tissue slice technique. This approach allows to explore the detailed three-dimensional morphology of intact pancreatic tissue at a cellular level and to investigate islet cell function under near-physiological conditions. The described procedure is less damaging and faster than alternative approaches and particularly advantageous for studying infiltrated and structurally damaged islets. Furthermore, pancreas tissue slices have proven valuable for acute studies of endocrine as well as exocrine cell physiology in their conserved natural environment. We here provide a detailed protocol for the preparation of mouse pancreas tissue slices, the assessment of slice viability, and the study of pancreas cell physiology by hormone secretion and immunofluorescence staining.

Pancreatic beta cells have a significant remodeling capacity which plays an essential role in the maintenance of glucose homeostasis. Beta cell apoptosis, replication, size, dedifferentiation, and (neo)generation contribute to the beta cell mass regulation. However, the extent of their respective contribution varies significantly depending on the specific condition, and it is the balance among them that determines the eventual change in beta cell mass. Thus, the study of the pancreatic beta cell mass regulation requires the determination of all these factors. In this chapter, we describe the quantification of beta cell replication based on the incorporation of thymidine analogs into replicated DNA strands and on the expression of Ki67 antigen and phosphorylation of histone H3. Beta cell apoptosis is analyzed by the TUNEL technique, and beta cell mass and cross-sectional area of individual beta cells are determined by computerized image processing methods.