Characterization of a peg-like terminal NOR structure with light microscopy and high-resolution scanning electron microscopy

Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations

In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.

FluoroNanogold: an important probe for correlative microscopy

Correlative microscopy is a powerful imaging approach that refers to observing the same exact structures within a specimen by two or more imaging modalities. In biological samples, this typically means examining the same sub-cellular feature with different imaging methods. Correlative microscopy is not restricted to the domains of fluorescence microscopy and electron microscopy; however, currently, most correlative microscopy studies combine these two methods, and in this review, we will focus on the use of fluorescence and electron microscopy. Successful correlative fluorescence and electron microscopy requires probes, or reporter systems, from which useful information can be obtained with each of the imaging modalities employed. The bi-functional immunolabeling reagent, FluoroNanogold, is one such probe that provides robust signals in both fluorescence and electron microscopy. It consists of a gold cluster compound that is visualized by electron microscopy and a covalently attached fluorophore that is visualized by fluorescence microscopy. FluoroNanogold has been an extremely useful labeling reagent in correlative microscopy studies. In this report, we present an overview of research using this unique probe.

Current SEM techniques for de- and re-construction of centromeres to determine 3D CENH3 distribution in barley mitotic chromosomes

Combined light microscopic (LM) and field emission scanning electron microscopic (FESEM) techniques with FluoroNanogold labelling allowed quantification and high resolution analysis of 3D distribution of the centromere-specific histone H3 variant CENH3 in barley mitotic chromosomes. Chromosomes were investigated with fluorescence LM, conventional FESEM, low-voltage FESEM and combined FIB/FESEM techniques for unprecedented comprehensive analysis to determine chromatin distribution patterns in the centromere. Using data from FIB/FESEM sectioning of centromeric regions of chromosomes, it was possible to render 3D reconstruction of the CENH3 distribution with highest resolution achieved to date. Complementary data derived from each approach show that CENH3 localizes not only to the primary constriction, but also in the pericentric regions and is distributed exclusively in the interior, rather than on the surface, of the centromere. This is relevant for understanding kinetochore assembly and digresses from current models of centromere structure. We emphasize here this broad microscopic approach, focusing on technical aspects of combined FESEM techniques, for which advantages and limitations are discussed, providing a relevant example--in the field of centromeric research--for application to investigations of other subcellular biological structures.

Correlative microscopy: providing new understanding in the biomedical and plant sciences

Correlative microscopy is the application of two or more distinct microscopy techniques to the same region of a sample, generating complementary morphological, structural and chemical information that exceeds what is possible with any single technique. As a variety of complementary microscopy approaches rather than a specific type of instrument, correlative microscopy has blossomed in recent years as researchers have recognised that it is particularly suited to address the intricate questions of the modern biological sciences. Specialised technical developments in sample preparation, imaging methods, visualisation and data analysis have also accelerated the uptake of correlative approaches. In light of these advances, this critical review takes the reader on a journey through recent developments in, and applications of, correlative microscopy, examining its impact in biomedical research and in the field of plant science. This twin emphasis gives a unique perspective into use of correlative microscopy in fields that often advance independently, and highlights the lessons that can be learned from both fields for the future of this important area of research.

Analysis of the ultrastructure of archaea by electron microscopy

The ultrastructural characterization of archaeal cells is done with both types of electron microscopy, transmission electron microscopy, and scanning electron microscopy. Depending on the scientific question, different preparation methods have to be employed and need to be optimized, according to the special cultivation conditions of these-in many cases extreme-microorganisms. Recent results using various electron microscopy techniques show that archaeal cells have a variety of cell appendages, used for motility as well as for establishing cell-cell and cell-surface contacts. Cryo-preparation methods, in particular high-pressure freezing and freeze-substitution, are crucial for obtaining results: (1) showing the cells in ultrathin sections in a good structural preservation, often with unusual shapes and subcellular complexity, and (2) enabling us to perform immunolocalization studies. This is an important tool to make a link between biochemical and ultrastructural studies.

Scanning electron microscopy of chromosomes

Scanning electron microscopic analysis is an indispensable tool for high-resolution visualization of chromosomes and their ultrastructural details. It allows a three-dimensional structural approach for elucidating higher-order chromatin structure and chromosome architecture. Artificial decondensation under a variety of conditions shows that structural elements of chromosomes are composed of matrix fibers and chromomeres. Currently, chromosome labeling methods include DNA contrasting with platinum blue, silver contrasting of proteins, and immunolabeling with Nanogold. With these techniques, DNA and protein distribution can be determined, and functionally relevant elements (e.g., epigenetic modifications, specific proteins, DNA sequences) can be located to structural elements of chromosomes with, at present, local resolution of approximately 30 nm.

Topology of the mammalian cell via cryo-FIB etching

Mapping of a mammalian cell down to a feature size of 20-30 nm in 3D is a goal that will answer many questions concerning the connectivity (topology) of a Eukaryotic cell's traffic routes. These routes are defined and separated from one another by the protein-impregnated lipid membrane barrier of the endoplasmic reticulum (ER). We trace the routes from outside a live flash frozen buccal epithelial cell via gold (Au) labelled pores in the plasma membrane to the ER below and then through the cell as isosurfaces in 3D maps. The outer tubular ER with three-way branching changes to a sheet-like ER nearer the nucleus, and the cytoplasmic space between the ER membranes continues as a volume into the nuclear interior via the nuclear pores. We find some evidence that the last layer of the cytoplasmic ER membrane, also termed the outer nuclear membrane, has discrete gaps, so the ER lumen in these areas is continuous with the nuclear luminal domain and further, the inner nuclear membrane has small protrusions into the nucleus. The routes were established in live, unstained, unfixed, cells etched with a pAmp current of a focused ion beam (cryo-FIB) dual beam electron microscope, at -150 degrees C, 1e-4Pa, and confirmed at 37 degrees C in lipid-dye stained cells. The cryo-FIB etch of a cuboid of 2D planes, and its reconstruction into many 3D maps, takes only hours, facilitating the execution of experiments with comparative conditions in a few days.