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Concept: Electron microscopy


Those investigators who study the morphology of Legionella and Legionella-infected cells have greatly benefited from the superior resolution afforded by electron microscopy (EM). It can also be said with confidence that EM will continue to reveal as yet to be discovered features of this fascinating intracellular pathogen. In this chapter we detail our practical experience in the application of three transmission electron microscopy (TEM) techniques to the study of Legionella: conventional ultrastructural analysis, immuno-gold labeling, and negative staining. Each of these techniques has particular, well-defined applications, which are discussed in the context of our in-house developed methods. We invite researchers to try the methods given here in the study of Legionella, and adopt TEM as part of their research tools arsenal.

Concepts: Electron, Biology, Microscope, Transmission electron microscopy, Scanning electron microscope, Staining, Electron microscopy, Negative stain


In bacteria Selenocysteyl-tRNA(sec) (SelC) is synthesized by Selenocysteine Synthase (SelA). Here we show by fluorescence anisotropy binding assays and electron microscopical symmetry analysis that the SelA- tRNA(sec) binding stoichiometry is of one tRNA(sec) molecule per SelA monomer (1:1) rather than the 1:2 value proposed previously. Negative stain transmission electron microscopy revealed a D5 pointgroup symmetry for the SelA- tRNA(sec) assembly both with and without tRNA(sec) bound. Furthermore, SelA can associate forming a supramolecular complex of stacked decamer rings, which does not occur in the presence of tRNA(sec). We discuss the structure-function relationships of these assemblies and their regulatory role in bacterial Selenocysteyl-tRNA(sec) synthesis.

Concepts: Electron, Oxygen, Microscope, Atom, Transmission electron microscopy, Staining, Electron microscopy, Negative stain


A method that enables high precision extraction of transmission electron microscope (TEM) specimens in low contrast materials has been developed. The main idea behind this work is to produce high contrast markers on both sides of and close to the area of interest. The markers are filled during the depositing of the protective layer. The marker material can be of either Pt or C depending on which one gives the highest contrast. It is thereby possible to distinguish the location of the area of interest during focused ion beam (FIB) milling and ensure that the TEM sample is extracted precisely at the desired position. This method is generally applicable and enables FIB/scanning electron microscope users to make high quality TEM specimens from small features and low contrast materials without a need for special holders. We explain the details of this method and illustrate its potential by examples from three different types of materials.

Concepts: Electron, Electron microscope, Scientific techniques, Transmission electron microscopy, Marker, Scanning electron microscope, Electron microscopy, Focused ion beam


Abstract A conspicuous biomorphic ovoid structure has been discovered in the Nakhla martian meteorite, made of nanocrystalline iron-rich saponitic clay and amorphous material. The ovoid is indigenous to Nakhla and occurs within a late-formed amorphous mesostasis region of rhyolitic composition that is interstitial to two clinopyroxene grains with Al-rich rims, and contains acicular apatite crystals, olivine, sulfides, Ti-rich magnetite, and a new mineral of the rhoenite group. To infer the origin of the ovoid, a large set of analytical tools was employed, including scanning electron microscopy and backscattered electron imaging, wavelength-dispersive X-ray analysis, X-ray mapping, Raman spectroscopy, time-of-flight secondary ion mass spectrometry analysis, high-resolution transmission electron microscope imaging, and atomic force microscope topographic mapping. The concentric wall of the ovoid surrounds an originally hollow volume and exhibits internal layering of contrasting nanotextures but uniform chemical composition, and likely inherited its overall shape from a preexisting vesicle in the mesostasis glass. A final fibrous layer of Fe-rich phases blankets the interior surfaces of the ovoid wall structure. There is evidence that the parent rock of Nakhla has undergone a shock event from a nearby bolide impact that melted the rims of pyroxene and the interstitial matter and initiated an igneous hydrothermal system of rapidly cooling fluids, which were progressively mixed with fluids from the melted permafrost. Sharp temperature gradients were responsible for the crystallization of Al-rich clinopyroxene rims, rhoenite, acicular apatites, and the quenching of the mesostasis glass and the vesicle. During the formation of the ovoid structure, episodic fluid infiltration events resulted in the precipitation of saponite rinds around the vesicle walls, altered pyrrhotite to marcasite, and then isolated the ovoid wall structure from the rest of the system by depositing a layer of iron oxides/hydroxides. Carbonates, halite, and sulfates were deposited last within interstitial spaces and along fractures. Among three plausible competing hypotheses here, this particular abiotic scenario is considered to be the most reasonable explanation for the formation of the ovoid structure in Nakhla, and although compelling evidence for a biotic origin is lacking, it is evident that the martian subsurface contains niche environments where life could develop. Key Words: Biomorph-Clays-Search for life (biosignatures)-Martian meteorites-Hydrothermal systems. Astrobiology 14, xxx-xxx.

Concepts: Electron, Electron microscope, Mass spectrometry, X-ray crystallography, Scientific techniques, Transmission electron microscopy, Scanning electron microscope, Electron microscopy


Although gilt silver threads were widely used for decorating historical textiles, their manufacturing techniques have been elusive for centuries. Contemporary written sources give only limited, sometimes ambiguous information, and detailed cross-sectional study of the microscale soft noble metal objects has been hindered by sample preparation. In this work, to give a thorough characterization of historical gilt silver threads, nano- and microscale textural, chemical and structural data on cross sections, prepared by focused ion beam milling, were collected, using various electron-optical methods (high-resolution scanning electron microscopy (SEM), wavelength-dispersive electron probe microanalysis (EPMA), electron back-scattered diffraction (EBSD) combined with energy-dispersive electron probe microanalysis (EDX), transmission electron microscopy (TEM) combined with EDX, and micro-Raman spectroscopy. The thickness of the gold coating varied between 70-400 nm. Data reveal nano- and microscale metallurgy-related, gilding-related and corrosion-related inhomogeneities in the silver base. These inhomogeneities account for the limitations of surface analysis when tracking gilding methods of historical metal threads, and explain why chemical information has to be connected to 3D texture on submicrometre scale. The geometry and chemical composition (lack of mercury, copper) of the gold/silver interface prove that the ancient gilding technology was diffusion bonding. The observed differences in the copper content of the silver base of the different thread types suggest intentional technological choice. Among the examined textiles of different ages (13th-17th centuries) and provenances narrow technological variation has been found.

Concepts: Electron, Spectroscopy, Gold, Scientific techniques, Transmission electron microscopy, Silver, Scanning electron microscope, Electron microscopy


Pioneered by Lehn, Cram, Peterson and Breslow, supramolecular chemistry concepts have evolved providing fundamental knowledge of the relationships between the structures and reactivities of organized molecules. A particular fascinating class of metallo-supramolecular molecules are hollow coordination cages that provide cavities of molecular dimensions promoting applications in diverse areas including catalysis, enzyme mimetics and material science. Here we report the synthesis of coordination cages with exceptional cross-sectional diameters that are composed of multiple sub-cages providing numerous distinctive binding sites through labile coordination solvent molecules. The building principles, involving Archimedean and Platonic bodies, renders these supramolecular keplerates as a class of cages whose composition and topological aspects compare to characteristics of edge-transitive {Cu2} MOFs with A3X4 stoichiometry. The nature of the cavities in these double-shell metal-organic polyhedra and their inner/outer binding sites provide perspectives for post-synthetic functionalizations, separations and catalysis. Transmission electron microscopy studies demonstrate that single molecules are experimentally accessible.

Concepts: DNA, Electron, Molecule, Chemistry, Atom, Chemical equilibrium, Nanotechnology, Electron microscopy


Estimating motion is a fundamental task for the visual system of sighted animals. In Drosophila, direction-selective T4 and T5 cells respond to moving brightness increments (ON) and decrements (OFF), respectively. Current algorithmic models of the circuit are based on the interaction of two differentially filtered signals. However, electron microscopy studies have shown that T5 cells receive their major input from four classes of neurons: Tm1, Tm2, Tm4, and Tm9. Using two-photon calcium imaging, we demonstrate that T5 is the first direction-selective stage within the OFF pathway. The four cells provide an array of spatiotemporal filters to T5. Silencing their synaptic output in various combinations, we find that all input elements are involved in OFF motion detection to varying degrees. Our comprehensive survey challenges the simplified view of how neural systems compute the direction of motion and suggests that an intricate interplay of many signals results in direction selectivity.

Concepts: Nervous system, Electron, Neuron, Microscope, Synapse, Major, The Circuit, Electron microscopy


Nanoscale metal inclusions in or on solid-state dielectrics are an integral part of modern electrocatalysis, optoelectronics, capacitors, metamaterials and memory devices. The properties of these composite systems strongly depend on the size, dispersion of the inclusions and their chemical stability, and are usually considered constant. Here we demonstrate that nanoscale inclusions (for example, clusters) in dielectrics dynamically change their shape, size and position upon applied electric field. Through systematic in situ transmission electron microscopy studies, we show that fundamental electrochemical processes can lead to universally observed nucleation and growth of metal clusters, even for inert metals like platinum. The clusters exhibit diverse dynamic behaviours governed by kinetic factors including ion mobility and redox rates, leading to different filament growth modes and structures in memristive devices. These findings reveal the microscopic origin behind resistive switching, and also provide general guidance for the design of novel devices involving electronics and ionics.

Concepts: Electron, Maxwell's equations, Nitrogen, Metal, Uranium, Electrolysis, Heavy metal music, Electron microscopy


Groundbreaking advances in volume electron microscopy and specimen preparation are enabling the 3-dimensional visualisation of specimens with unprecedented detail, and driving a gratifying resurgence of interest in the ultrastructural examination of cellular systems. Serial section techniques, previously the domain of specialists, are becoming increasingly automated with the development of systems such as the automatic tape-collecting ultramicrotome, and serial blockface and focused ion beam scanning electron microscopes. These changes are rapidly broadening the scope of biomedical studies to which volume electron microscopy techniques can be applied beyond the brain. Further innovations in microscope design are also in the pipeline, which have the potential to enhance the speed and quality of data collection. The recent introduction of integrated light and electron microscopy systems will revolutionise correlative light and volume electron microscopy studies, by enabling the sequential collection of data from light and electron imaging modalities without intermediate specimen manipulation. In doing so, the acquisition of comprehensive functional information and direct correlation with ultrastructural details within a 3-dimensional reference space will become routine. The prospects for volume electron microscopy are therefore bright, and the stage is set for a challenging and exciting future.

Concepts: Electron, Electron microscope, Microscope, Dimension, Microscopy, Scanning electron microscope, Optical microscope, Electron microscopy


Composites incorporating two-dimensional nanostructures within polymeric matrices have potential as functional components for several technologies, including gas separation. Prospectively, employing metal-organic frameworks (MOFs) as versatile nanofillers would notably broaden the scope of functionalities. However, synthesizing MOFs in the form of freestanding nanosheets has proved challenging. We present a bottom-up synthesis strategy for dispersible copper 1,4-benzenedicarboxylate MOF lamellae of micrometre lateral dimensions and nanometre thickness. Incorporating MOF nanosheets into polymer matrices endows the resultant composites with outstanding CO2 separation performance from CO2/CH4 gas mixtures, together with an unusual and highly desired increase in the separation selectivity with pressure. As revealed by tomographic focused ion beam scanning electron microscopy, the unique separation behaviour stems from a superior occupation of the membrane cross-section by the MOF nanosheets as compared with isotropic crystals, which improves the efficiency of molecular discrimination and eliminates unselective permeation pathways. This approach opens the door to ultrathin MOF-polymer composites for various applications.

Concepts: Electron, Electron microscope, Atom, Composite material, Scanning electron microscope, Carbon fiber, Electron microscopy, Focused ion beam