Electron microscopy (EM) techniques play a vital role in virology research including phage discovery and their identification. The use of different staining protocols based on the concept of negative staining is one of the most important steps in the EM processing. This chapter will summarize the widely used EM protocols in phage research, their advantages, and limitations. Phage-based therapy, especially recently developed nanoparticle-phage conjugates, are expected to find clinical significance in the antimicrobial resistance (AMR) epidemic. EM techniques are important to characterize these conjugates and we will also discuss the methods here.

Hydraulic fracking exposes shale plays to acidic hydraulic fracking fluid (HFF), releasing toxic uranium (U) along with the desired oil and gas. With no existing methods to ensure U remains sequestered in the shale, this study sought to add organic ligands to HFF to explore potential U retention in shale plays. To test this possibility, incubations were set up in which uranyl acetate and one organic bipyridine ligand (either 2,2\'-, 2,3\'-, 2,4\'-, or 4,4\'-bipyridine) were added to pristine HFF as the crystallization medium. After several months and complete evaporation of all volatiles, bulk yellow crystalline material was obtained from the incubations, three of which yielded crystals suitable for single-crystal analysis, resulting in two novel structures and a high-quality structure of a previously described compound. The UO2VI acetate complexes bis(acetato-κ2O,O\')(2,2\'-bipyridine-κ2N,N\')dioxidouranium(VI), [U(C2H3O2)2O2(C10H8N2)2] or [2,2\'-bipyridine]UVIO2(CH3CO2)2, (I), and bis(acetato-κ2O,O\')(2,4\'-bipyridine-κN1\')dioxidouranium(VI), [U(C2H3O2)2O2(C10H8N2)2] or [2,4\'-bipyridine]2UVIO2(CH3CO2)2, (III), contain eight-coordinate UVI in a pseudo-hexagonal bipyramidal coordination geometry and are molecular, packing via weak C-H...O/N interactions, whereas catena-poly[bis(2,3\'-bipyridinium) [di-μ-acetato-μ3-hydroxido-μ-hydroxido-di-μ3-oxido-hexaoxidotriuranium(VI)]-2,3\'-bipyridine-water (1/1/1)], (C10H9N2)2[U3(C2H3O2)2O8(OH)2]·C10H8N2·H2O or {[2,3\'-bipyridinium]2[2,3\'-bipyridine][(UVIO2)3(O)2(OH)2(CH3CO2)2·H2O]}n, (II), forms an ionic one-dimensional polymer with seven-coordinate pentagonal bipyramidal UVI centers and hydrogen-bonding interactions within each chain. The formation of these crystals could indicate the potential for bipyridine to bind with U in shale during fracking, which will be explored in a future study via ICP-MS (inductively coupled plasma mass spectrometry) analyses of U concentration in HFF/bipyridine/shale incubations. The variation seen here between the molecular structures may indicate variance in the ability of bipyridine isomers to form complexes with U, which could impact their ability to retain U within shale in the context of fracking.

BACKGROUND: The liver was identified as a primary target organ for the chemo-radiological effects of uranyl acetate (UA). Although the anti-oxidant and anti-apoptotic properties of gallic acid (GA) make it a promising phytochemical to resist its hazards, there is no available data in this area of research.
METHODS: To address this issue, eighteen rats were randomly and equally divided into three groups. One group was received carboxymethyl cellulose (vehicle of GA) and kept as a control. The UA group was injected intraperitoneally with UA at a single dose of 5 mg/kg body weight. The third group (GA + UA group) was treated with GA orally at a dose of 100 mg/kg body weight for 14 days before UA exposure. UA was injected on the 15th day of the experiment in either the UA group or the GA + UA group. The biochemical, histological, and immunohistochemical findings in the GA + UA group were compared to both control and UA groups.
RESULTS: The results showed that UA exposure led to a range of adverse effects. These included elevated plasma levels of aspartate aminotransferase, lactate dehydrogenase, total protein, globulin, glucose, total cholesterol, triglycerides, low-density lipoprotein cholesterol, and very-low-density lipoprotein and decreased plasma levels of high-density lipoprotein cholesterol. The exposure also disrupted the redox balance, evident through decreased plasma total antioxidant capacity and hepatic nitric oxide, superoxide dismutase, reduced glutathione, glutathione-S-transferase, glutathione reductase, and glutathione peroxidase and increased hepatic oxidized glutathione and malondialdehyde. Plasma levels of albumin and alanine aminotransferase did not significantly change in all groups. Histopathological analysis revealed damage to liver tissue, characterized by deteriorations in tissue structure, excessive collagen accumulation, and depletion of glycogen. Furthermore, UA exposure up-regulated the immuno-expression of cleaved caspase-3 and down-regulated the immuno-expression of nuclear factor-erythroid-2-related factor 2 in hepatic tissues, indicating an induction of apoptosis and oxidative stress response. However, the pre-treatment with GA proved to be effective in mitigating these negative effects induced by UA exposure, except for the disturbances in the lipid profile.
CONCLUSIONS: The study suggests that GA has the potential to act as a protective agent against the adverse effects of UA exposure on the liver. Its ability to restore redox balance and inhibit apoptosis makes it a promising candidate for countering the harmful effects of chemo-radiological agents such as UA.

Biological nanoparticles, such as bacterial outer membrane vesicles (OMVs), are routinely characterized through transmission electron microscopy (TEM). In this study, we report a novel method to prepare OMVs for TEM imaging. To preserve vesicular shape and structure, we developed a dual fixation protocol involving osmium tetroxide incubation prior to negative staining with uranyl acetate. Combining osmium tetroxide with uranyl acetate resulted in preservation of sub-50 nm vesicles and improved morphological stability, enhancing characterization of lipid-based nanoparticles by TEM.

Sample preparation protocols for conventional high voltage transmission electron microscopy (TEM) heavily rely on the usage of staining agents containing various heavy metals, most commonly uranyl acetate and lead citrate. However high toxicity, rising legal regulations, and problematic waste disposal of uranyl acetate have increased calls for the reduction or even complete replacement of this staining agent. One of the strategies for uranyless imaging is the employment of low-voltage transmission electron microscopy. To investigate the influence of different imaging and staining strategies on the final image of cyanobacterial cells, samples stained by uranyl acetate with lead citrate, as well as unstained samples, were observed using TEM and accelerating voltages of 200 kV or 25 kV. Moreover, to examine the possibilities of reducing chromatic aberration, which often causes issues when imaging using electrons of lower energies, samples were also imaged using a scanning transmission electron microscopy at 15 kV accelerating voltages. The results of this study demonstrate that low-voltage electron microscopy offers great potential for uranyless electron microscopy.

High-pressure freezing followed by freeze-substitution is a valuable method for ultrastructural analyses of resin-embedded biological samples. The visualization of lipid membranes is one of the most critical aspects of any ultrastructural study and can be especially challenging in high-pressure frozen specimens. Historically, osmium tetroxide has been the preferred fixative and staining agent for lipid-containing structures in freeze-substitution solutions. However, osmium tetroxide is not only a rare and expensive material, but also volatile and toxic. Here, we introduce the use of a combination of potassium permanganate, uranyl acetate, and water in acetone as complementing reagents during the freeze-substitution process. This mix imparts an intense en bloc stain to cellular ultrastructure and membranes, which makes poststaining superfluous and is well suited for block-face imaging. Thus, potassium permanganate can effectively replace osmium tetroxide in the freeze-substitution solution without sacrificing the quality of ultrastructural preservation.

Primary ciliary dyskinesia (PCD) is a disorder affecting motile cilia. An early accurate diagnosis helps prevent lung damage and preserve lung function. To make a diagnostic assessment, one of the commonly used methods that allows for the examination of ciliary ultrastructure is transmission electron microscopy (TEM). This allows for a quantitative assessment of ciliary components to identify defects associated with PCD. Heavy metal staining is required to provide a contrast when imaging cilia in the TEM. One of the most commonly used stains is uranyl acetate (UA). UA can be applied to cellular material before embedding (en bloc), or to ultrathin sections of embedded samples (grid staining). UA is radioactive and, due to growing safety concerns and restrictions by government bodies, universities and hospitals, it is essential to find a suitable alternative. We show UA-zero (UAZ), when used en bloc, provides a high contrast and is a suitable replacement for UA. PCD diagnostic experts, having reviewed ciliary cross-sections stained with UAZ en bloc, are confident that the staining and PCD defects are readily detectable similar to samples that have been stained with UA.

In recent years, electron cryo-microscopy (CryoEM) has become a powerful method for the high-resolution studies of biological macromolecules. While CryoEM experiments can begin without additional microscopy steps, negative-stain EM can tremendously minimize CryoEM screening. Negative-stain is a quick method that can be used to screen for robust biochemical conditions, the integrity, binding, and composition of samples and to get an estimation of sample grid concentration. For some applications, the map resolutions potentially afforded by stain may be as biologically informative as in CryoEM. Here, I describe the benefits and pitfalls of negative-stain EM, with particular emphasis on Uranyl stains with the main goal of screening in advance of CryoEM. In addition, I provide a materials list, detailed protocol and possible adjustments for the use of stains for biological samples requiring imaging and/or diffraction-based methods of EM.

Structural DNA nanotechnology can produce a wide range of 3D nanostructures with programmable structure and size at <5 nm resolution. However, it is challenging to dry these structures without capillary force-induced damage. As a result, the applications of 3D DNA nanostructures have long been limited in aqueous environments. Ready access to free-standing 3D DNA nanostructures in the dry state could revolutionize many research areas, especially in the development of low-density, high-strength materials. Here we report a method to obtain free-standing wireframe 3D DNA tetrahedra in air on a solid substrate, such as SiO2 and mica, by absorbing uranyl acetate and lyophilization. The dried DNA tetrahedron structure, 93 ± 2 nm in height, withstands 42 ± 22 nN of loading force. The effective hardness (9.1 ± 5.1 MPa) and Young\'s modulus (77 ± 48 MPa) of this low-density (70.7 kg/m3) DNA-inorganic hybrid nanostructure are comparable to other reported low-density high-strength materials.

The aim of this study is to characterize the genotoxicity of depleted uranium (DU) in Chinese Hamster Ovary cells (CHO) with mutations in various DNA repair pathways. CHO cells were exposed to 0-300 μM of soluble DU as uranyl acetate (UA) for 0-48 h. Intracellular UA concentrations were measured via inductively coupled mass spectrometry (ICP-MS) and visualized by transmission electron microscopy (TEM). Cytotoxicity was assessed in vitro by clonogenic survival assay. DNA damage response was assessed via Fast Micromethod® to determine UA-induced DNA single strand breaks. Results indicate that UA is entering the CHO cells, with the highest concentration localizing in the nucleus. Clonogenic assays show that UA is cytotoxic in each cell line with the greatest cytotoxicity in the base excision repair deficient EM9 cells and the nuclear excision repair deficient UV5 cells compared to the non-homologous end joining deficient V3.3 cells and the parental AA8 cells after 48 h. This indicates that UA is producing single strand breaks and forming UA-DNA adducts rather than double strand breaks in CHO cells. Fast Micromethod® results indicate an increased amount of single strand breaks in the EM9 cells after 48 h UA exposure compared to the V3.3 and AA8 cells. These results indicate that DU induces DNA damage via strand breaks and uranium-DNA adducts in treated cells. These results suggest that: (1) DU is genotoxic in CHO cells, and (2) DU is inducing single strand breaks rather than double strand breaks in vitro.