Visualising the effect of freezing on the vascular system of wheat in three dimensions by in-block imaging of dye-infiltrated plants.

Infrared thermography has shown after roots of grasses freeze, ice spreads into the crown and then acropetally into leaves initially through vascular bundles. Leaves freeze singly with the oldest leaves freezing first and the youngest freezing later. Visualising the vascular system in its native 3-dimensional state will help in the understanding of this freezing process. A 2 cm section of the crown that had been infiltrated with aniline blue was embedded in paraffin and sectioned with a microtome. A photograph of the surface of the tissue in the paraffin block was taken after the microtome blade removed each 20 µm section. Two hundred to 300 images were imported into Adobe After Effects and a 3D volume of the region infiltrated by aniline blue dye was constructed. The reconstruction revealed that roots fed into what is functionally a region inside the crown that could act as a reservoir from which all the leaves are able to draw water. When a single root was fed dye solution, the entire region filled with dye and the vascular bundles of every leaf took up the dye; this indicated that the vascular system of roots was not paired with individual leaves. Fluorescence microscopy suggested the edge of the reservoir might be composed of phenolic compounds. When plants were frozen, the edges of the reservoir became leaky and dye solution spread into the mesophyll outside the reservoir. The significance of this change with regard to freezing tolerance is not known at this time. Thermal cameras that allow visualisation of water freezing in plants have shown that in crops like wheat, oats and barley, ice forms first at the bottom of the plant and then moves upwards into leaves through water conducting channels. Leaves freeze one at a time with the oldest leaves freezing first and then younger ones further up the stem freeze later. To better understand why plants freeze like this, we reconstructed a 3-dimensional view of the water conducting channels. After placing the roots of a wheat plant in a blue dye and allowing it to pull the dye upwards into leaves, we took a part of the stem just above the roots and embedded it in paraffin. We used a microtome to slice a thin layer of the paraffin containing the plant and then photographed the surface after each layer was removed. After taking about 300 images, we used Adobe After Effects software to re-construct the plant with the water conducting system in three dimensions. The 3D reconstruction showed that roots fed into a roughly spherical area at the bottom of the stem that could act as a kind of tank or reservoir from which the leaves pull up water. When we put just one root in dye, the entire reservoir filled up and the water conducting channels in every leaf took up the dye. This indicates that the water channels in roots were not directly connected to specific leaves as we had thought. When plants were frozen, the dye leaked out of the reservoir and spread into cells outside. Research is continuing to understand the significance of this change during freezing. It is possible that information about this effect can be used to help breeders develop more winter-hardy crop plants.

[Wilhelm His, Sr., and the development of paraffin embedding. German version]. / Wilhelm His Senior und die Entwicklung der Paraffineinbettung.

Paraffin histology is one of the most important and commonly used laboratory techniques in diagnostic histopathology. The discovery of paraffin embedding is often attributed to the pathologist Edwin Klebs. Klebs was following the lead of Stricker, who embedded embryos in a mixture of hot stearin and white beeswax. We show that Klebs experimented with paraffin wax for embedding tumour tissue. But he quickly rejected it as unsuitable because paraffin wax did not infiltrate the tissue. One of Klebs' correspondents, embryologist Wilhelm His, Sr., learned of Klebs' experiments and decided to try paraffin embedding. His dehydrated chicken embryos in alcohol, cleared them in lavender oil, and dripped hot paraffin wax onto them. This process allowed His to cut good sections. Here, we have replicated His's paraffin embedding protocol in order to determine whether His had indeed made the landmark discovery of infiltration embedding with paraffin wax. We followed the protocol that he gives in his 1868 monograph on the early development of the chicken. The protocol described by His failed, in our hands, to yield sections of the quality that he illustrates in his monograph. Typically, the tissue disintegrated when sectioned due to poor infiltration of the wax. Usable sections could only be obtained if His's protocol was modified by melting the embedded embryos in fresh paraffin wax. One explanation for our findings is that we failed to faithfully replicate His's protocol. Another is that his protocol was incomplete. We suggest that His is likely to have discovered and perfected infiltration embedding with paraffin wax but did not publish a complete protocol.

Wilhelm His Sr. and the development of paraffin embedding.

Paraffin histology is one of the most important and commonly-used laboratory techniques in diagnostic histopathology. The discovery of paraffin embedding is often attributed to the pathologist Edwin Klebs. Klebs was following the lead of Stricker, who embedded embryos in a mixture of hot stearin and white beeswax. We show that Klebs experimented with paraffin wax for embedding tumour tissue. But he quickly rejected it as unsuitable because paraffin wax did not infiltrate the tissue. One of Klebs' correspondents, embryologist Wilhelm His, Sr., learned of Klebs' experiments and decided to try paraffin embedding. His dehydrated chicken embryos in alcohol, cleared them in lavender oil, and dripped hot paraffin wax onto them. This process allowed His to cut good sections. Here, we have replicated His's paraffin embedding protocol in order to determine whether His had indeed made the landmark discovery of infiltration embedding with paraffin wax. We followed the protocol that he gives in his 1868 monograph on the early development of the chicken. The protocol described by His failed, in our hands, to yield sections of the quality that he illustrates in his monograph. Typically, the tissue disintegrated when sectioned due to poor infiltration of the wax. Usable sections could only be obtained if His's protocol was modified by melting the embedded embryos in fresh paraffin wax. One explanation for our findings is that we failed to faithfully replicate His's protocol. Another is that his protocol was incomplete. We suggest that His is likely to have discovered and perfected infiltration embedding with paraffin wax but did not publish a complete protocol.

Multimodal Characterization of Resin Embedded and Sliced Polymer Nanoparticles by Means of Tip-Enhanced Raman Spectroscopy and Force-Distance Curve Based Atomic Force Microscopy.

Understanding the property-function relation of nanoparticles in various application fields involves determining their physicochemical properties, which is still a remaining challenge to date. While a multitude of different characterization tools can be applied, these methods by themselves can only provide an incomplete picture. Therefore, novel analytical techniques are required, which can address both chemical functionality and provide structural information at the same time with high spatial resolution. This is possible by using tip-enhanced Raman spectroscopy (TERS), but due to its limited depth information, TERS is usually restricted to investigations of the nanoparticle surface. Here, TERS experiments are established on polystyrene nanoparticles (PS NPs) after resin embedding and microtome slicing. With that, unique access to their internal morphological features is gained, and thus, enables differentiation between information obtained for core- and shell-regions. Complementary information is obtained by means of transmission electron microscopy (TEM) and from force-distance curve based atomic force microscopy (FD-AFM). This multimodal approach achieves a high degree of discrimination between the resin and the polymers used for nanoparticle formulation. The high potential of TERS combined with advanced AFM spectroscopy tools to probe the mechanical properties is applied for quality control of the resin embedding procedure.

Ultra-Microtome for the Preparation of TEM Specimens from Battery Cathodes.

With the wide application of ultra-microtome sectioning in the preparation of transmission electron microscopy (TEM) specimens with bio- and organic materials, here, we report an ultra-microtome-based method for the preparation of TEM specimens from cathodes of Li-ion batteries. The ultra-microtome sectioning reduces the sample thickness to tens of nanometers and yields atomic resolution from the core region of particles of hundreds of nanometers. Analysis indicates that the mechanical cross-sectioning introduces no observable microstructural artifacts or structural damage, such as microcracking and nanoporosity. These results demonstrate the high efficiency of the ultra-microtome approach in preparing well-thinned specimens of particulate materials that allow for atomic-scale TEM imaging of a large number of sectioned particles in one single TEM specimen, thereby providing statistically significant results of the TEM analysis.

Electron Microscopy Imaging of Zinc Soaps Nucleation in Oil Paint.

Using the recently developed techniques of electron tomography, we have explored the first stages of disfiguring formation of zinc soaps in modern oil paintings. The formation of complexes of zinc ions with fatty acids in paint layers is a major threat to the stability and appearance of many late 19th and early 20th century oil paintings. Moreover, the occurrence of zinc soaps in oil paintings leading to defects is disturbingly common, but the chemical reactions and migration mechanisms leading to large zinc soap aggregates or zones remain poorly understood. State-of-the-art scanning (SEM) and transmission (TEM) electron microscopy techniques, primarily developed for biological specimens, have enabled us to visualize the earliest stages of crystalline zinc soap growth in a reconstructed zinc white (ZnO) oil paint sample. In situ sectioning techniques and sequential imaging within the SEM allowed three-dimensional tomographic reconstruction of sample morphology. Improvements in the detection and discrimination of backscattered electrons enabled us to identify local precipitation processes with small atomic number contrast. The SEM images were correlated to low-dose and high-sensitivity TEM images, with high-resolution tomography providing unprecedented insight into the structure of nucleating zinc soaps at the molecular level. The correlative approach applied here to study phase separation, and crystallization processes specific to a problem in art conservation creates possibilities for visualization of phase formation in a wide range of soft materials.

Chemically and thermally stable silica nanowires with a ß-sheet peptide core for bionanotechnology.

BACKGROUND: A series of amyloidogenic peptides based on the sequence KFFEAAAKKFFE template the silica precursor, tetraethyl orthosilicate to form silica-nanowires containing a cross-ß peptide core. RESULTS: Investigation of the stability of these fibres reveals that the silica layers protect the silica-nanowires allowing them to maintain their shape and physical and chemical properties after incubation with organic solvents such as 2-propanol, ethanol, and acetonitrile, as well as in a strong acidic solution at pH 1.5. Furthermore, these nanowires were thermally stable in an aqueous solution when heated up to 70 °C, and upon autoclaving. They also preserved their conformation following incubation up to 4 weeks under these harsh conditions, and showed exceptionally high physical stability up to 1000 °C after ageing for 12 months. We show that they maintain their ß-sheet peptide core even after harsh treatment by confirming the ß-sheet content using Fourier transform infrared spectra. The silica nanowires show significantly higher chemical and thermal stability compared to the unsiliconised fibrils. CONCLUSIONS: The notable chemical and thermal stability of these silica nanowires points to their potential for use in microelectromechanics processes or fabrication for nanotechnological devices.

Challenges of microtome-based serial block-face scanning electron microscopy in neuroscience.

Serial block-face scanning electron microscopy (SBEM) is becoming increasingly popular for a wide range of applications in many disciplines from biology to material sciences. This review focuses on applications for circuit reconstruction in neuroscience, which is one of the major driving forces advancing SBEM. Neuronal circuit reconstruction poses exceptional challenges to volume EM in terms of resolution, field of view, acquisition time and sample preparation. Mapping the connections between neurons in the brain is crucial for understanding information flow and information processing in the brain. However, information on the connectivity between hundreds or even thousands of neurons densely packed in neuronal microcircuits is still largely missing. Volume EM techniques such as serial section TEM, automated tape-collecting ultramicrotome, focused ion-beam scanning electron microscopy and SBEM (microtome serial block-face scanning electron microscopy) are the techniques that provide sufficient resolution to resolve ultrastructural details such as synapses and provides sufficient field of view for dense reconstruction of neuronal circuits. While volume EM techniques are advancing, they are generating large data sets on the terabyte scale that require new image processing workflows and analysis tools. In this review, we present the recent advances in SBEM for circuit reconstruction in neuroscience and an overview of existing image processing and analysis pipelines.

Serial section histopathology image dataset of colon and pancreas tissue captured through light microscope.

Till date, histopathological examination of concerned tissue by light microscopy is considered to be the gold standard and most acceptable method for the final diagnosis of disease processes. Sometimes, examination of serial sections, i.e., consecutive sections obtained from a histopathologically processed tissue specimen using a microtome, plays a very vital role in comprehensive understanding of the tissue details, aiding in treatment planning, prognosis, and final diagnosis. In this study, the histopathological dataset showcased, focuses on images of serial sections from colonic and pancreatic tissues, captured through light microscopy. These sequential images might serve as a valuable resource for generating a three-dimensional representation of histological tissue samples. The resulting 3D reconstructed data obtained from the serial sections will provide detailed structural information at a high resolution. Although whole-slide imaging is considered a better option to get images of all sections on one slide at multiple desired magnifications and is obviously a more wanted option for 3D reconstruction of an entire tissue, its high cost poses a significant barrier. In this study, the dataset is prepared and collected from the histopathology division of the Department of Pathology, North Bengal Medical College, near Siliguri. It consisted of 168 serial section images of colon and pancreatic tissue captured at different magnifications. This comprehensive dataset will aid biomedical researchers in the field of histopathology analysis, an area that still holds potential for recent advancements, particularly in 3D reconstruction.

Human Precision-Cut Lung Slices: Generation of and Measurement of Contractility and Relaxation of Small Airways.

Lung slices have been used since the mid-1990's to study various aspects of lung biology that include, but are not limited to, mechanisms of airway contraction and relaxation; the pulmonary immune response in the context of inflammatory diseases of the lung like asthma and chronic obstructive pulmonary disease; mast cell-mediated airway contractility and inflammation; modulation of airway cells following pathogen exposure; and consequences of environmental toxicant exposure. Here we describe the generation of human precision-cut lung slices (hPCLS) and measurement of contraction and relaxation of small airways within the slices.

Microscopic characterization of petiole anatomy of Asteraceous taxa of Western Himalaya-Pakistan.

Petiole anatomy of 15 species of family Asteraceae was examined which aimed to investigate petiolar anatomical structures for species level identification. Shandon Microtome was used for petiole histological preparations. Both qualitative and quantitative features were studied under microscope which showed significant variation in petiole, collenchyma, parenchyma shape/size, vascular bundles arrangement/size, and vessel elements quantity. Artemisia japonica Thunb., Cirsium vulgare (Savi) Ten., Myriactis nepalensis Less., Seriphidium brevifolium Ling & Y.R.Ling, Taraxacum officinale (L.) Weber ex F.H.Wigg., and Xanthium strumarium L. showed winged petioles. Maximum length and width of upper and lower epidermis was found in Tagetes erecta L. which is 23.05 ± 0.89 µm, 24.9 ± 1.257 µm length and 21.75 ± 1.38067 µm, 22.75 ± 0.467 µm width, respectively. Petioles of Parthenium hysterophorus L. was longest one with 9.85 ± 10.45 µm while A. japonica Thunb. showed highest number of vessel elements. Maximum size of vascular bundles was found in T. erecta L. with 5.05 ± 14.25 µm. Artemisia annua L., C. vulgare (Savi) Ten, Cyanthillium cinereum (L.) H.Rob., Helianthus annus L., M. nepalensis Less., P. hysterophorus L., Senecio chrysanthemoides DC. have trichomes while Tussilago farfara L. has highest number of vascular bundles. All species have angular collenchyma type except M. nepalensis Less., P. hysterophorus L., S. brevifolium Ling & Y.R.Ling, Tagetes minuta L., T. officinale L., S. chrysanthemoides DC., and T. farfara L. Cluster analysis implemented that distinct plant species in cluster. Petiolar anatomical structures and taxonomic key will helpful for distinguishing Asteraceous taxa at genus and species level. This taxonomic significant investigation will also provide baseline to taxonomists for other Asteraceae studies and phylogenetic research.

Experimental Techniques to Obtain the Cross-Sectional Images of Textile Yarns.

In the fabric industry, textile yarns are the fundamental building blocks. Hence, visualizing and studying yarn structure is essential to understand the structure and behavior of the fibers. Obtaining the yarn's cross-section images is crucial in the calculations of yarn's porosity; furthermore, a more precise expansion for the fiber's migration can be concluded from the cross-sectional images. In this paper, three different methods (microtome, micro-computed tomography, and epoxy grinding-polishing methods) to image and visualize the yarn's cross-section are presented. The experimental techniques are compared in terms of result useability, time of preparation, and overall outcome of the cross-sectional image. The images can be used for fiber distribution, air gap calculation, and twist analysis as well. The fiber diameter distribution of polyester yarn was measured based on the images obtained by the three different methods; the average fiber diameter measured based on the combined data from the three different methods was found to be 10.90 ± 0.30 µm.

Preparation of Immunofluorescently Labeled Tissue Sections for Imaging at Low and High Magnifications in the Confocal Microscope.

The confocal laser scanning microscope allows us to examine tissue sections in greater detail than a widefield fluorescence microscope. However, this requires samples to be better preserved than standard cryostat sections, which are not usually aldehyde-fixed. Thick sections (approximately 70 µm) of formaldehyde-fixed tissue can be cut using a vibrating microtome and subsequently labeled with primary and secondary fluorescent antibodies and/or fluorescent stains. When imaged in the confocal microscope, these samples allow us to collect high-resolution images, detailing the intracellular location of multiple proteins and structures. In this chapter, we describe the technique used to prepare vibrating microtome sections, using porcine tissue infected with African swine fever virus as an example. This technique can easily be applied to any animal tissue with any suitable combination of antibodies, depending on the hypothesis.

Targeted 2D histology and ultrastructural bone analysis based on 3D microCT anatomical locations.

Histological processing of mineralised tissue (e.g. bone) allows examining the anatomy of cells and tissues as well as the material properties of the tissue. However, resin-embedding offers limited control over the specimen position for cutting. Moreover, specific anatomical planes (coronal, sagittal) or defined landmarks are often missed with standard microtome sectioning. Here we describe a method to precisely locate a specific anatomical 2D plane or any anatomical feature of interest (e.g. bone lesions, newly formed bone, etc.) using 3D micro computed tomography (microCT), and to expose it using controlled-angle microtome cutting. The resulting sections and corresponding specimen's block surface offer correlative information of the same anatomical location, which can then be analysed using multiscale imaging. Moreover, this method can be combined with immunohistochemistry (IHC) to further identify any component of the bone microenvironment (cells, extracellular matrix, proteins, etc.) and guide subsequent in-depth analysis. Overall, this method allows to:•Cut your specimens in a consistent position and precise manner using microCT-based controlled-angle microtome sectioning.•Locate and expose a specific anatomical plane (coronal, sagittal plane) or any other anatomical landmarks of interest based on microCT.•Identify any cell or tissue markers based on IHC to guide further in-depth examination of those regions of interest.

Oncolytic Immunotherapy for Bladder Cancer Using Coxsackie A21 Virus: Using a Bladder Tumor Precision-Cut Slice Model System to Assess Viral Efficacy.

Oncolytic viruses are anticancer agents that selectively target and kill cancer cells by direct lysis, while at the same time stimulating a tumor antigen-specific adaptive immune response. These promising therapeutic agents target multiple cancers and have already proven to be an effective treatment option for solid malignancies. One such agent, T-Vec (Talimogene laherparepvec) has been licensed and is in routine clinical use for treatment of malignant melanoma.Non-muscle invasive bladder cancer (NMIBC) is an ideal potential target for oncolytic immunotherapy as locally instilled live biological therapy using Bacille Calmette-Guerin (BCG) is already well established in the clinical setting. Coxsackievirus A21 (CVA21) is a novel intercellular adhesion molecule-1 (ICAM-1)-targeted immunotherapeutic virus. We have investigated CVA21-induced cytotoxicity in a panel of human bladder cancer cell lines, revealing a range of sensitivities largely correlating with expression of the viral receptor ICAM-1. CVA21 in combination with low doses of mitomycin-C enhanced CVA21 viral replication and oncolysis by increasing surface expression levels of ICAM-1. In addition to cell lines and an animal model a key component of our studies into oncolytic immunotherapy for bladder cancer was the use of a bladder tumor precision slice preclinical model system which represents tumor architecture, heterogeneity, and the complexity of a tumor in vitro. Results seen in cell lines were reflected in the tumor slice model whereby levels of virus protein expression and induction of apoptosis were enhanced with prior exposure to mitomycin-C. In this chapter we demonstrate the utility of the precision cut tumor slice model as a unique organotypic model to test oncolytic viruses. We will describe how to prepare and slice the tumor using a vibrating microtome together with the optimum culture and conditions for treatment.

Basic Neuroanatomical Methods.

This unit covers some basic procedures that are common to a wide range of neuroanatomical protocols for brain tissue. Procedures are provided for preparation of unfixed fresh brain tissue as well as for perfusion fixation of animals to obtain fixed neural tissue. A variety of methods for sectioning are described, including frozen sectioning using a cryostat or microtome and sectioning with a vibratome. The choice of sectioning method depends on how the brain has been prepared and what histochemical method is to be used. A fluorescent immunohistochemical method to localize endogenous molecules as well as induced markers such as green fluorescent protein and red fluorescent protein is also provided. Additionally, three post-sectioning procedures are described: defatting of slide-mounted sections, fluorescent Nissl staining, and thionin staining of sections. Finally, support protocols are provided, describing a method for maintaining the correct order of cut tissue, whether rostral to caudal or lateral to medial; a procedure for subbing slides with gelatin, which is necessary in some protocols in order for sections to adhere to slides; and preparation of custom 3D-printed 10- or 20-well tissue plates and trays for subsequent immunostaining. Published 2019. U.S. Government. Basic Protocol 1: Preparation of unfixed fresh-frozen brain tissue Basic Protocol 2: Perfusion fixation Basic Protocol 3: Cryostat sectioning of frozen brain tissue Basic Protocol 4: Sliding-microtome sectioning of fixed brain tissue Basic Protocol 5: Vibratome and Compresstome sectioning Support Protocol 1: Tissue collection in a 1-in-10 series Support Protocol 2: Preparation of gelatin-subbed microscope slides Support Protocol 3: Custom 3D-printed 10- and 20-well tissue plates Basic Protocol 6: Post-sectioning procedures I: Fluorescent immunohistochemical localization Basic Protocol 7: Post-sectioning procedures II: Defatting Basic Protocol 8: Post-sectioning procedures III: Nissl staining Basic Protocol 9: Post-sectioning procedures IV: Thionin staining.

Essential Methods of Plant Sample Preparation for Light Microscopy.

There are various preparatory techniques for light microscopy permitting access to the inner structure of plant body and its development. Minute objects might be processed as whole-mount preparations, while voluminous ones should be separated into smaller pieces. Here we summarize some of the "classical" techniques to cut more voluminous objects into slices and access their inner structure either for simple anatomical analysis or for further processing (e.g., histochemistry, immunohistochemistry, in situ hybridization, enzyme histochemistry).

A review of artifacts in histopathology.

Histopathological examination is considered as gold standard procedure for arriving at a final diagnosis of various lesions of the human body. However, it is limited by a number of alterations of normal morphologic and cytological features that occur as a result of presence of artifacts. These artifacts may occur during surgical removal, fixation, tissue processing, embedding and microtomy and staining and mounting procedures. They can even lead to complete uselessness of the tissue. It is therefore essential to identify the commonly occurring artifacts during histopathological interpretations of tissue sections. This article reviews the common artifacts encountered during slide examination alongside the remedial measures which can be undertaken to differentiate between an artifact and tissue constituent.

SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy.

We present SBEMimage, an open-source Python-based application to operate serial block-face electron microscopy (SBEM) systems. SBEMimage is designed for complex, challenging acquisition tasks, such as large-scale volume imaging of neuronal tissue or other biological ultrastructure. Advanced monitoring, process control, and error handling capabilities improve reliability, speed, and quality of acquisitions. Debris detection, autofocus, real-time image inspection, and various other quality control features minimize the risk of data loss during long-term acquisitions. Adaptive tile selection allows for efficient imaging of large tissue volumes of arbitrary shape. The software's graphical user interface is optimized for remote operation. In its user-friendly viewport, tile grids covering the region of interest to be acquired are overlaid on previously acquired overview images of the sample surface. Images from other sources, e.g., light microscopes, can be imported and superimposed. SBEMimage complements existing DigitalMicrograph (Gatan Microscopy Suite) installations on 3View systems but permits higher acquisition rates by interacting directly with the microscope's control software. Its modular architecture and the use of Python/PyQt make SBEMimage highly customizable and extensible, which allows for fast prototyping and will permit adaptation to a wide range of SBEM systems and applications.

Western Blot Analysis and Immunostaining for Prediction of Embryotoxicity in Mus musculus.

A broad range of research must be answered in order to gain a complete understanding of the histological and histochemical profile of teratological exposure in Mus musculus. Continued research is needed to track patterns of teratogen effects on the DNA expression of the embryonic brain and its variation impact. An important technique used in cell and molecular biology is Western blotting. By using a Western blot analysis and immunostaining, researchers are able to predict embryotoxicity in Mus musculus. The method uses three elements to accomplish this task: (1) Nonspecific antibody binding to a nitrocellulose membrane, (2) an incubation using a primary antibody, and (3) the antigen-antibody reaction using a secondary antibody. The proteins are further stained with a substrate/chromogen. In this chapter, the electrophoresis-based protein detection following mice embryonic exposure to a teratogen, 2-methoxyethanol, is described.