Reconstructing 3D digital model without distortion for poorly conductive porous rock by nanoprobe-assisted FIB-SEM tomography

Oil and natural gas prospecting requires precise pore characterisation of insulating rock samples, which involves severe charging problems in the state-of-art FIB-SEM tomography, such as overexposure, drift and distortion. For weak cemented samples with very poor conductivity, the conventional ways such as decreasing accelerating voltage or current as well as coating a thin layer of carbon or gold fail to eliminate all the detrimental effect, leading to image distortion in the form of lateral shift and longitudinal stretching. A new nanoprobe-assisted method is explored in FIB-SEM tomography to address this problem and improve image quality. To be specific, a metallic nanoprobe is induced and attached on the sample surface to create an express path for the export of excess electrons near the region of interest, which effectively removes distortion and drift when imaging. Two adjacent areas were characterised and reconstructed into 3D digital models by FIB-SEM tomography with nanoprobe-assisted method applied to one region only. The lateral shift creates zigzag feature for distorted region and the longitudinal stretching of undistorted object can reach 14%. Average pore size of distorted region is larger than that of the undistorted region, however considering the longitudinal stretching, the average pore size of distorted region can be corrected to the same level as the undistorted region. The systematic error caused by distortion for poorly conductive porous rock is hazardous for digital rock physics analysis. Therefore, the nanoprobe-assisted FIB-SEM tomography should be regarded as a one of the optional and feasible procedures in case decreasing accelerating voltage or current as well as coating a thin layer of conductive material does not work.

Multifaceted Study of the Interactions between CPO-27-Ni and Polyurethane and Their Impact on Nitric Oxide Release Performance

A multifaceted study involving focused ion beam scanning electron microscopy techniques, mechanical analysis, water adsorption measurements, and molecular simulations is employed to rationalize the nitric oxide release performance of polyurethane films containing 5, 10, 20, and 40 wt % of the metal-organic framework (MOF) CPO-27-Ni. The polymer and the MOF are first demonstrated to exhibit excellent compatibility. This is reflected in the even distribution and encapsulation of large wt % MOF loadings throughout the full thickness of the films and by the rather minimal influence of the MOF on the mechanical properties of the polymer at low wt %. The NO release efficiency of the MOF is attenuated by the polymer and found to depend on wt % of MOF loading. The formation of a fully connected network of MOF agglomerates within the films at higher wt % is proposed to contribute to a more complex guest transport in these formulations, resulting in a reduction of NO release efficiency and film ductility. An optimum MOF loading of 10 wt % is identified for maximizing NO release without adversely impacting the polymer properties. Bactericidal efficacy of released NO from the films is demonstrated against Pseudomonas aeruginosa, with a >8 log₁₀ reduction in cell density observed after a contact period of 24 h.

In vivo aging of zirconia dental ceramics - Part I: Biomedical grade 3Y-TZP

OBJECTIVE

In vivo aging of biomedical grade 3Y-TZP ceramics in the oral environment was assessed and compared to artificially accelerated in vitro hydrothermal aging extrapolations at 37°C.

METHODS

88 discs were pressed and sintered (1450-1500°C) from two commercial 3Y-TZP compositions containing 0.25% Al₂O₃ to generate finer- and coarser-grained specimens. As-sintered (AS) and airborne-particle abraded (APA; 50μm Al₂O₃) surfaces were investigated. In vivo aging was performed by incorporating specimens in lingual flanges of complete dentures of 12 edentulous volunteers who wore them continuously for up to 24 months. For comparison, in vitro hydrothermal aging at 134°C was also performed and analysed by XRD and (FIB)-SEM. Data was statistically analysed with linear regression models.

RESULTS

Finer and coarser-grained specimens exhibited statistically insignificant differences in aging in vivo. The monoclinic fraction (X_m) on AS surfaces abruptly increased to ∼8% after 6 months. The aging process then proceeded with slower linear kinetics (∼0.24%/month). After 24 months, X_m reached ∼12%. The calculated maximum transformed layer was 0.385μm representing one layer of transformed grains. APA surfaces were highly aging resistant. The initial X_m of ∼4.0% linearly increased by 0.03%/month in vivo. In vitro aging exhibited an initial induction period, followed by linear aging kinetics. Coarser-grained AS surfaces aged significantly faster than fine-grained (2.41%/h compared to 2.16%/h). APA discs aged at a rate of 0.3%/h in vitro. Microcracking within a single grain and pull-out of grain clusters were observed on aged AS surfaces.

SIGNIFICANCE

Biomedical grade 3Y-TZP was susceptible to in vivo aging. After 2 years in vivo, the aging kinetics were almost 3-times faster than the generally accepted in vitro-in vivo extrapolation.

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies

Pathogenesis induced by SARS-CoV-2 is thought to result from both an inflammation-dominated cytokine response and virus-induced cell perturbation causing cell death. Here, we employ an integrative imaging analysis to determine morphological organelle alterations induced in SARS-CoV-2-infected human lung epithelial cells. We report 3D electron microscopy reconstructions of whole cells and subcellular compartments, revealing extensive fragmentation of the Golgi apparatus, alteration of the mitochondrial network and recruitment of peroxisomes to viral replication organelles formed by clusters of double-membrane vesicles (DMVs). These are tethered to the endoplasmic reticulum, providing insights into DMV biogenesis and spatial coordination of SARS-CoV-2 replication. Live cell imaging combined with an infection sensor reveals profound remodeling of cytoskeleton elements. Pharmacological inhibition of their dynamics suppresses SARS-CoV-2 replication. We thus report insights into virus-induced cytopathic effects and provide alongside a comprehensive publicly available repository of 3D datasets of SARS-CoV-2-infected cells for download and smooth online visualization.

Fusion of Mitochondria to 3-D Networks, Autophagy and Increased Organelle Contacts are Important Subcellular Hallmarks during Cold Stress in Plants

Low temperature stress has a severe impact on the distribution, physiology, and survival of plants in their natural habitats. While numerous studies have focused on the physiological and molecular adjustments to low temperatures, this study provides evidence that cold induced physiological responses coincide with distinct ultrastructural alterations. Three plants from different evolutionary levels and habitats were investigated: The freshwater alga Micrasterias denticulata, the aquatic plant Lemna sp., and the nival plant Ranunculus glacialis. Ultrastructural alterations during low temperature stress were determined by the employment of 2-D transmission electron microscopy and 3-D reconstructions from focused ion beam–scanning electron microscopic series. With decreasing temperatures, increasing numbers of organelle contacts and particularly the fusion of mitochondria to 3-dimensional networks were observed. We assume that the increase or at least maintenance of respiration during low temperature stress is likely to be based on these mitochondrial interconnections. Moreover, it is shown that autophagy and degeneration processes accompany freezing stress in Lemna and R. glacialis. This might be an essential mechanism to recycle damaged cytoplasmic constituents to maintain the cellular metabolism during freezing stress.

Cryo-fluorescence microscopy of high-pressure frozen C. elegans enables correlative FIB-SEM imaging of targeted embryonic stages in the intact worm

Rapidly changing features in an intact biological sample are challenging to efficiently trap and image by conventional electron microscopy (EM). For example, the model organism C. elegans is widely used to study embryonic development and differentiation, yet the fast kinetics of cell division makes the targeting of specific developmental stages for ultrastructural study difficult. We set out to image the condensed metaphase chromosomes of an early embryo in the intact worm in 3-D. To achieve this, one must capture this transient structure, then locate and subsequently image the corresponding volume by EM in the appropriate context of the organism, all while minimizing a variety of artifacts. In this methodological advance, we report on the high-pressure freezing of spatially constrained whole C. elegans hermaphrodites in a combination of cryoprotectants to identify embryonic cells in metaphase by in situ cryo-fluorescence microscopy. The screened worms were then freeze substituted, resin embedded and further prepared such that the targeted cells were successfully located and imaged by focused ion beam scanning electron microscopy (FIB-SEM). We reconstructed the targeted metaphase structure and also correlated an intriguing punctate fluorescence signal to a H2B-enriched putative polar body autophagosome in an adjacent cell undergoing telophase. By enabling cryo-fluorescence microscopy of thick samples, our workflow can thus be used to trap and image transient structures in C. elegans or similar organisms in a near-native state, and then reconstruct their corresponding cellular architectures at high resolution and in 3-D by correlative volume EM.

Globular structure of the hypermineralized tissue in human femoral neck

Bone becomes more fragile with ageing. Among many structural changes, a thin layer of highly mineralized and brittle tissue covers part of the external surface of the thin femoral neck cortex in older people and has been proposed to increase hip fragility. However, there have been very limited reports on this hypermineralized tissue in the femoral neck, especially on its ultrastructure. Such information is critical to understanding both the mineralization process and its contributions to hip fracture. Here, we use multiple advanced techniques to characterize the ultrastructure of the hypermineralized tissue in the neck across various length scales. Synchrotron radiation micro-CT found larger but less densely distributed cellular lacunae in hypermineralized tissue than in lamellar bone. When examined under FIB-SEM, the hypermineralized tissue was mainly composed of mineral globules with sizes varying from submicron to a few microns. Nano-sized channels were present within the mineral globules and oriented with the surrounding organic matrix. Transmission electron microscopy showed the apatite inside globules were poorly crystalline, while those at the boundaries between the globules had well-defined lattice structure with crystallinity similar to the apatite mineral in lamellar bone. No preferred mineral orientation was observed both inside each globule and at the boundaries. Collectively, we conclude based on these new observations that the hypermineralized tissue is non-lamellar and has less organized mineral, which may contribute to the high brittleness of the tissue.

Ellipsoidal mesoscale mineralization pattern in human cortical bone revealed in 3D by plasma focused ion beam serial sectioning

Visualizing bone mineralization and collagen fibril organization at intermediate scales between the nanometer and the hundreds of microns range, is still an important challenge. Similarly, visualizing cellular components which locally affect the tissue structure requires a precision of a few tens of nanometers at maximum while spanning several tens of micrometers. In the last decade, gallium focused ion beam (FIB) equipped with a scanning electron microscope (SEM) proved to be an extremely valuable structural tool to meet those ends. In this study, we assess the capability of a recent plasma FIB-SEM technology which provides a potential increase in measurement speed over gallium FIB-SEM, thus paving the way to larger volume analysis. Nanometer-scale layers of demineralized and mineralized unstained human femoral lamellar bone were sequentially sectioned over volumes of 6-16,000 μm³. Analysis of mineralized tissue revealed prolate ellipsoidal mineral clusters measuring approximately 1.1 µm in length by 700 nm at their maximum diameter. Those features, suggested by others in high resolution studies, appear here as a ubiquitous motif in mineralized lamellar bone over thousands of microns cubed, suggesting a heterogeneous and yet regular pattern of mineral deposition past the single collagen fibril level. This large scale view retained sufficient resolution to visualize the collagen fibrils while also partly visualizing the lacuno-canalicular network in three-dimensions. These findings are strong evidence for suitability of PFIB as a bone analysis tool and the need to revisit bone mineralization over multi-length scales with mineralized tissue.

The LaserFIB: new application opportunities combining a high-performance FIB-SEM with femtosecond laser processing in an integrated second chamber

The development of the femtosecond laser (fs laser) with its ability to provide extremely rapid athermal ablation of materials has initiated a renaissance in materials science. Sample milling rates for the fs laser are orders of magnitude greater than that of traditional focused ion beam (FIB) sources currently used. In combination with minimal surface post-processing requirements, this technology is proving to be a game changer for materials research. The development of a femtosecond laser attached to a focused ion beam scanning electron microscope (LaserFIB) enables numerous new capabilities, including access to deeply buried structures as well as the production of extremely large trenches, cross sections, pillars and TEM H-bars, all while preserving microstructure and avoiding or reducing FIB polishing. Several high impact applications are now possible due to this technology in the fields of crystallography, electronics, mechanical engineering, battery research and materials sample preparation. This review article summarizes the current opportunities for this new technology focusing on the materials science megatrends of engineering materials, energy materials and electronics.

The Physical Role of Mesenchymal Cells Driven by the Actin Cytoskeleton Is Essential for the Orientation of Collagen Fibrils in Zebrafish Fins

Fibrous collagen imparts physical strength and flexibility to tissues by forming huge complexes. The density and orientation of collagen fibers must be correctly specified for the optimal physical property of the collagen complex. However, little is known about its underlying cellular mechanisms. Actinotrichia are collagen fibers aligned at the fin-tip of bony fish and are easily visible under the microscope due to their thick, linear structure. We used the actinotrichia as a model system to investigate how cells manipulate collagen fibers. The 3D image obtained by focused ion beam scanning electron microscopy (FIB-SEM) showed that the pseudopodia of mesenchymal cells encircle the multiple actinotrichia. We then co-incubated the mesenchymal cells and actinotrichia in vitro, and time-lapse analysis revealed how cells use pseudopods to align collagen fiber orientation. This in vitro behavior is dependent on actin polymerization in mesenchymal cells. Inhibition of actin polymerization in mesenchymal cells results in mis-orientation of actinotrichia in the fin. These results reveal how mesenchymal cells are involved in fin formation and have important implications for the physical interaction between cells and collagen fibers.

Two-Stage Alignment of FIB-SEM Images of Rock Samples

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography provides a stack of images that represent serial slices of the sample. These images are displaced relatively to each other, and an alignment procedure is required. Traditional methods for alignment of a 3D image are based on a comparison of two adjacent slices. However, such algorithms are easily confused by anisotropy in the sample structure or even experiment geometry in the case of porous media. This may lead to significant distortions in the pore space geometry, if there are no stable fiducial marks in the frame. In this paper, we propose a new method, which meaningfully extends existing alignment procedures. Our technique allows the correction of random misalignments between slices and, at the same time, preserves the overall geometrical structure of the specimen. We consider displacements produced by existing alignment algorithms as a signal and decompose it into low and high-frequency components. Final transformations exclude slow variations and contain only high frequency variations that represent random shifts that need to be corrected. The proposed algorithm can operate with not only translations but also with arbitrary affine transformations. We demonstrate the performance of our approach on a synthetic dataset and two real FIB-SEM images of natural rock.

Super-Resolution Microscopy and FIB-SEM Imaging Reveal Parental Centriole-Derived, Hybrid Cilium in Mammalian Multiciliated Cells

Motile cilia are cellular beating machines that play a critical role in mucociliary clearance, cerebrospinal fluid movement, and fertility. In the airways, hundreds of motile cilia present on the surface of a multiciliated epithelia cell beat coordinately to protect the epithelium from bacteria, viruses, and harmful particulates. During multiciliated cell differentiation, motile cilia are templated from basal bodies, each extending a basal foot-an appendage linking motile cilia together to ensure coordinated beating. Here, we demonstrate that among the many motile cilia of a multiciliated cell, a hybrid cilium with structural features of both primary and motile cilia is harbored. The hybrid cilium is conserved in mammalian multiciliated cells, originates from parental centrioles, and its cellular position is biased and dependent on ciliary beating. Furthermore, we show that the hybrid cilium emerges independently of other motile cilia and functions in regulating basal body alignment.

3D Ultrastructural Study of Synapses in the Human Entorhinal Cortex

The entorhinal cortex (EC) is a brain region that has been shown to be essential for memory functions and spatial navigation. However, detailed three-dimensional (3D) synaptic morphology analysis and identification of postsynaptic targets at the ultrastructural level have not been performed before in the human EC. In the present study, we used Focused Ion Beam/Scanning Electron Microscopy to perform a 3D analysis of the synapses in the neuropil of medial EC in layers II and III from human brain autopsies. Specifically, we studied synaptic structural parameters of 3561 synapses, which were fully reconstructed in 3D. We analyzed the synaptic density, 3D spatial distribution, and type (excitatory and inhibitory), as well as the shape and size of each synaptic junction. Moreover, the postsynaptic targets of synapses could be clearly determined. The present work constitutes a detailed description of the synaptic organization of the human EC, which is a necessary step to better understand the functional organization of this region in both health and disease.

mSphere of Influence: the Dynamic Nature of the Nuclear Envelope during Mitosis of Malaria Parasites

Sabrina Absalon works in the field of cellular and molecular biology of Plasmodium falciparum, the most virulent parasite causing malaria in humans. In this mSphere of Influence article, she reflects on how the paper “3D nuclear architecture reveals coupled cell cycle dynamics of chromatin and nuclear pores in the malaria parasite Plasmodium falciparum” by Allon Weiner et al. (A. Weiner, N. Dahan-Pasternak, E. Shimoni, V. Shinder, et al., Cell Microbiol 13:967–977, 2011, https://doi.org/10.1111/j.1462-5822.2011.01592.x) triggered her aspiration to study the molecular mechanisms governing nuclear envelope assembly and integrity of P. falciparum throughout the intraerythrocytic development cycle.

Sabrina Absalon works in the field of cellular and molecular biology of Plasmodium falciparum, the most virulent parasite causing malaria in humans. In this mSphere of Influence article, she reflects on how the paper “3D nuclear architecture reveals coupled cell cycle dynamics of chromatin and nuclear pores in the malaria parasite Plasmodium falciparum” by Allon Weiner et al. (A. Weiner, N. Dahan-Pasternak, E. Shimoni, V. Shinder, et al., Cell Microbiol 13:967–977, 2011, https://doi.org/10.1111/j.1462-5822.2011.01592.x) triggered her aspiration to study the molecular mechanisms governing nuclear envelope assembly and integrity of P. falciparum throughout the intraerythrocytic development cycle.

An introduction to cryo-FIB-SEM cross-sectioning of frozen, hydrated Life Science samples

The introduction of cryo‐techniques to the focused ion‐beam scanning electron microscope (FIB‐SEM) has brought new opportunities to study frozen, hydrated samples from the field of Life Sciences. Cryo‐techniques have long been employed in electron microscopy. Thin electron transparent sections are produced by cryo‐ultramicrotomy for observation in a cryo‐transmission electron microscope (TEM). Cryo‐TEM is presently reaching the imaging of macromolecular structures. In parallel, cryo‐fractured surfaces from bulk materials have been investigated by cryo‐SEM.

Both cryo‐TEM and cryo‐SEM have provided a wealth of information, despite being 2D techniques. Cryo‐TEM tomography does provide 3D information, but the thickness of the volume has a maximum of 200–300 nm, which limits the 3D information within the context of specific structures. FIB‐milling enables imaging additional planes by creating cross‐sections (e.g. cross‐sectioning or site‐specific X‐sectioning) perpendicular to the cryo‐fracture surface, thus adding a third imaging dimension to the cryo‐SEM. This paper discusses how to produce suitable cryo‐FIB‐SEM cross‐section results from frozen, hydrated Life Science samples with emphasis on ‘common knowledge’ and reoccurring observations.

Lay Description

Life Sciences studies life down to the smallest details. Visualising the smallest details requires electron microscopy, which utilises high‐vacuum chambers. One method to maintain the integrity of Life Sciences samples under vacuum conditions is freezing. Frozen samples can remain in a suspended state. As a result, research can be carried out without having to change the chemistry or internal physical structure of the samples.

Two types of electron microscopes equipped with cryo‐sample handling facilities are used to investigate samples: The scanning electron microscope (SEM) which investigates surfaces and the transmission electron microscope (TEM) which investigates thin electron transparent sections (called lamellae). A third method of investigation combines a SEM with a focused ion beam (FIB) to form a cryo‐FIB‐SEM, which is the basis of this paper. The electron beam images the cryo‐sample surface while the ion beam mills into the surface to expose the interior of the sample. The latter is called cross‐sectioning and the result provides a way of investigating the 3rd dimension of the sample. This paper looks at the making of cross‐sections in this manner originating from knowledge and experience gained with this technique over many years. This information is meant for newcomers, and experienced researchers in cryo‐microscopy alike.

An optimized approach using cryofixation for high-resolution 3D analysis by FIB-SEM

Compared with conventional two-dimensional transmission electron microscopy (TEM), focused ion beam scanning electron microscopy (FIB-SEM) can provide more comprehensive 3D information on cell substructures at the nanometer scale. Biological samples prepared by cryofixation using high-pressure freezing demonstrate optimal preservation of the morphology of cellular structures, as these are arrested instantly in their near-native states. However, samples from cryofixation often show a weak back-scatter electron signal and bad image contrast in FIB-SEM imaging. In addition, it is impossible to do large amounts of heavy metal staining. This is commonly achieved via established osmium impregnation (OTO) en bloc staining protocols. Here, we compared the FIB-SEM image quality of brain tissues prepared using several common freeze-substitution media, and we developed an approach that overcomes these limitations through a combination of osmium tetroxide, uranyl acetate, tannic acid, and potassium permanganate at proper concentrations, respectively. Using this optimized sample preparation protocol for high-pressure freezing and freeze-substitution, perfect smooth membrane morphology, even of the lipid bilayers of the cell membrane, was readily obtained using FIB-SEM. In addition, our protocol is broadly applicable and we demonstrated successful application to brain tissues, plant tissues, Caenorhabditis elegans, Candida albicans, and chlorella. This approach combines the potential of cryofixation for 3D large volume analysis of subcellular structures with the high-resolution capabilities of FIB-SEM.

Deep learning for 3D imaging and image analysis in biomineralization research

Biomineralization research examines structure-function relations in all types of exo- and endo-skeletons and other hard tissues of living organisms, and it relies heavily on 3D imaging. Segmentation of 3D renderings of biomineralized structures has long been a bottleneck because of human limitations such as our available time, attention span, eye-hand coordination, cognitive biases, and attainable precision, amongst other limitations. Since recently, some of these routine limitations appear to be surmountable thanks to the development of deep-learning algorithms for biological imagery in general, and for 3D image segmentation in particular. Many components of deep learning often appear too abstract for a life scientist. Despite this, the basic principles underlying deep learning have many easy-to-grasp commonalities with human learning and universal logic. This primer presents these basic principles in what we feel is an intuitive manner, without relying on prerequisite knowledge of informatics and computer science, and with the aim of improving the reader's general literacy in artificial intelligence and deep learning. Here, biomineralization case studies are presented to illustrate the application of deep learning for solving segmentation and analysis problems of 3D images ridden by various artifacts, and/or which are plainly difficult to interpret. The presented portfolio of case studies includes three examples of imaging using micro-computed tomography (µCT), and three examples using focused-ion beam scanning electron microscopy (FIB-SEM), all on mineralized tissues. We believe this primer will expand the circle of users of deep learning amongst biomineralization researchers and other life scientists involved with 3D imaging, and will encourage incorporation of this powerful tool into their professional skillsets and to explore it further.

Novel Applications of FIB-SEM-Based ToF-SIMS in Atom Probe Tomography Workflows

Atom probe tomography (APT) is used to quantify atomic-scale elemental and isotopic compositional variations within a very small volume of material (typically <0.01 µm3). The small analytical volume ideally contains specific compositional or microstructural targets that can be placed within the context of the previously characterized surface in order to facilitate a correct interpretation of APT data. In this regard, careful targeting and preparation are paramount to ensure that the desired target, which is often smaller than 100 nm, is optimally located within the APT specimen. Needle-shaped specimens required for atom probe analysis are commonly prepared using a focused ion beam scanning electron microscope (FIB-SEM). Here, we utilize FIB-SEM-based time-of-flight secondary ion mass spectrometry (ToF-SIMS) to illustrate a novel approach to targeting <100 nm compositional and isotopic variations that can be used for targeting regions of interest for subsequent lift-out and APT analysis. We present a new method for high-spatial resolution targeting of small features that involves using FIB-SEM-based electron deposition of platinum “buttons” prior to standard lift-out and sharpening procedures for atom probe specimen manufacture. In combination, FIB-ToF-SIMS analysis and application of the “button” method ensure that even the smallest APT targets can be successfully captured in extracted needles.

Monosized Polymeric Microspheres Designed for Passive Lung Targeting: Biodistribution and Pharmacokinetics after Intravenous Administration

Local as well as systemic therapy is often used to treat bacterial lung infections. Delivery of antibiotics to the vascular side of infected lung tissue using lung-targeting microspheres (MS) is a good alternative to conventional administration routes, allowing for localized high levels of antibiotics. This delivery route can also complement inhaled antibiotic therapy, especially in the case of compromised lung function. We prepared and characterized monodisperse poly(lactic-co-glycolic acid) (PLGA) MS loaded with levofloxacin using a flow-focusing glass microfluidic chip. In vitro characterization showed that the encapsulated LVX displayed a biphasic controlled release during 5 days and preserved its antibacterial activity. The MS degradation was investigated in vitro by cross-sectioning the MS using a focused ion beam scanning electron microscope and in vivo by histological examination of lung tissue from mice intravenously administered with the MS. The MS showed changes in the surface morphology and internal matrix, whereas the degradation in vivo was 3 times faster than that in vitro. No effect on the viability of endothelial and lung epithelial cells or hemolytic activity was observed. To evaluate the pharmacokinetics and biodistribution of the MS, complete quantitative imaging of the ¹¹¹indium-labeled PLGA MS was performed in vivo with single-photon emission computed tomography imaging over 10 days. The PLGA MS distributed homogeneously in the lung capillaries. Overall, intravenous administration of 12 μm PLGA MS is suitable for passive lung targeting and pulmonary therapy.

Three-dimensional structural interrelations between cells, extracellular matrix, and mineral in normally mineralizing avian leg tendon

The spatial-temporal relationship between cells, extracellular matrices, and mineral deposits is fundamental for an improved understanding of mineralization mechanisms in vertebrate tissues. By utilizing focused ion beam-scanning electron microscopy with serial surface imaging, normally mineralizing avian tendons have been studied with nanometer resolution in three dimensions with volumes exceeding tens of micrometers in range. These parameters are necessary to yield sufficiently fine ultrastructural details while providing a comprehensive overview of the interrelationships between the tissue structural constituents. Investigation reveals a complex lacuno-canalicular network in highly mineralized tendon regions, where ∼100 nm diameter canaliculi emanating from cell (tenocyte) lacunae surround extracellular collagen fibril bundles. Canaliculi are linked to smaller channels of ∼40 nm diameter, occupying spaces between fibrils. Close to the tendon mineralization front, calcium-rich deposits appear between the fibrils and, with time, mineral propagates along and within them. These close associations between tenocytes, tenocyte lacunae, canaliculi, small channels, collagen, and mineral suggest a concept for the mineralization process, where ions and/or mineral precursors may be transported through spaces between fibrils before they crystallize along the surface of and within the fibrils.

Unique three-dimensional structure of a fish pharyngeal jaw subjected to unusually high mechanical loads

We examine the structure of the bone of the pharyngeal jaws of a large fish, the black drum (Pogonias cromis), that uses its tooth-jaw complex to crush hard-shelled bivalve mollusks. During mastication huge compressive forces are concentrated in a tiny zone at the tooth-bone interface. We report on the structure of this bone, with emphasis on its contact with the teeth, at different hierarchical levels and in 3D. Micro-CT shows that the molariform teeth do not have roots and are supported by a circular narrow bony rim that surrounds the periphery of the tooth base. The lower pharyngeal jaw is highly porous, as seen by reflected light microscopy and secondary electron microscopy (SE-SEM). Porosity decreases close to the bone-tooth interface and back-scattered electron (BSE-SEM) microscopy shows a slight elevation in mineral density. Focused ion beam - scanning electron microscopy (FIB-SEM) in the serial surface view (SSV) mode reveals a most surprising organization at the nanoscale level: parallel arrays of mineralized collagen fibrils surrounding channels of ~100 nm diameter, both with their long axes oriented along the load direction. The channels are filled with organic matter. These fibril-channel arrays are surrounded by a highly disordered mineralized material. This unusual structure clearly functions efficiently under compression, but the precise way by which this unique arrangement achieves this function is unknown.

Axonal debris accumulates in corneal epithelial cells after intraepithelial corneal nerves are damaged: A focused Ion Beam Scanning Electron Microscopy (FIB-SEM) study

The intraepithelial corneal nerves (ICNs) that innervate the corneal epithelium are maintained through interactions with corneal epithelial cells and the extracellular matrix they produce. One to several axons bundle together within the basal cell layer and extend parallel to the ocular surface or branch and extend apically. Here we use 3-dimentional (3D) ultrastructural reconstructions of control and trephine injured mouse corneal epithelium and stroma produced using Focused Ion Beam Scanning Electron Microscope (FIB-SEM) to determine whether corneal epithelial or immune cells resident in the epithelium remove axonal debris and degrade it in their lysosomes after trephine injury to the cornea. We demonstrate that axonal fragments are internalized in the corneal epithelium and accumulate within electron dense structures consistent with lysosomes 3 h after trephine injury in both epithelial and immune cells located among the basal cells of the trephine injured cornea. Confocal imaging showed fewer CD45⁺ immune cells within the corneal epithelium after trephine injury compared to controls. The resolution obtained using FIB-SEM also allowed us to show that the presence of sensory axons at the basal aspect of the epithelial basal cells close to the anterior aspect of the epithelial basement membrane (EBM) is associated with a focal reduction in EBM thickness. In addition, we show using FIB-SEM and confocal imaging that superficial trephine injuries that do not penetrate the stroma, damage the integrity of anterior stromal nerves. These studies are the first to look at the mouse cornea following nerve injury using FIB-SEM.

A workflow for visualizing human cancer biopsies using large-format electron microscopy

Recent developments in large format electron microscopy have enabled generation of images that provide detailed ultrastructural information on normal and diseased cells and tissues. Analyses of these images increase our understanding of cellular organization and interactions and disease-related changes therein. In this manuscript, we describe a workflow for two-dimensional (2D) and three-dimensional (3D) imaging, including both optical and scanning electron microscopy (SEM) methods, that allow pathologists and cancer biology researchers to identify areas of interest from human cancer biopsies. The protocols and mounting strategies described in this workflow are compatible with 2D large format EM mapping, 3D focused ion beam-SEM and serial block face-SEM. The flexibility to use diverse imaging technologies available at most academic institutions makes this workflow useful and applicable for most life science samples. Volumetric analysis of the biopsies studied here revealed morphological, organizational and ultrastructural aspects of the tumor cells and surrounding environment that cannot be revealed by conventional 2D EM imaging. Our results indicate that although 2D EM is still an important tool in many areas of diagnostic pathology, 3D images of ultrastructural relationships between both normal and cancerous cells, in combination with their extracellular matrix, enables cancer researchers and pathologists to better understand the progression of the disease and identify potential therapeutic targets.

Three-Dimensional Visualization of APEX2-Tagged Erg11 in Saccharomyces cerevisiae Using Focused Ion Beam Scanning Electron Microscopy

The determination of the exact location of a protein in the cell is essential to the understanding of biological processes. Here, we report for the first time the visualization of a protein of interest in Saccharomyces cerevisiae using focused ion beam scanning electron microscopy (FIB-SEM). As a proof of concept, the integral endoplasmic reticulum (ER) membrane protein Erg11 has been C-terminally tagged with APEX2, which is an engineered peroxidase that catalyzes an electron-dense deposition of 3,3'-diaminobenzidine (DAB), as such marking the location of the fused protein of interest in electron microscopic images. As DAB is unable to cross the yeast cell wall to react with APEX2, cell walls have been partly removed by the formation of spheroplasts. This has resulted in a clear electron-dense ER signal for the Erg11 protein using FIB-SEM. With this study, we have validated the use of the APEX2 tag for visualization of yeast proteins in electron microscopy. Furthermore, we have introduced a methodology that enables precise and three-dimensional (3D) localization studies in yeast, with nanometer resolution and without the need for antibody staining. Because of these properties, the described technique can offer valuable information on the molecular functions of studied proteins.IMPORTANCE With this study, we have validated the use of the APEX2 tag to define the localization of proteins in the model yeast S. cerevisiae As such, FIB-SEM can identify the exact 3D location of a protein of interest in the cell with nanometer-scale resolution. Such detailed imaging could provide essential information on the elucidation of various biological processes. APEX2, which adds electron density to a fused protein of interest upon addition of the substrate DAB, originally was used in mammalian studies. With this study, we expand its use to protein localization studies in one of the most important models in molecular biology.

Increased intracellular survival of Salmonella Typhimurium ST313 in HIV-1-infected primary human macrophages is not associated with Salmonella hijacking the HIV compartment

BACKGROUND

Non-typhoidal Salmonella (NTS) causes a severe invasive syndrome (iNTS disease) described in HIV-positive adults. The impact of HIV-1 on Salmonella pathogenesis and the molecular basis for the differences between these bacteria and classical diarrhoeal S. Typhimurium remains unclear.

RESULTS

Here, we show that iNTS-associated S. Typhimurium Sequence Type 313 (ST313) bacteria show greater intracellular survival in primary human macrophages, compared with a 'classical' diarrhoeal S. Typhimurium ST19 isolate. The increased intracellular survival phenotype of ST313 is more pronounced in HIV-infected macrophages. We explored the possibility that the bacteria take advantage of the HIV-associated viral-containing compartments created in human macrophages that have low pH. Confocal fluorescence microscopy and focussed ion beam-scanning electron microscopy tomography showed that Salmonella did not co-localise extensively with HIV-positive compartments.

CONCLUSION

The capacity of ST313 bacteria to survive better than ST19 bacteria within primary human macrophages is enhanced in cells pre-infected with HIV-1. Our results indicate that the ST313 bacteria do not directly benefit from the niche created by the virus in HIV-1-infected macrophages, and that they might take advantage from a more globally modified host cell.

SIGNIFICANCE

A better understanding of the interplay between HIV-1 and Salmonella is important not only for these bacteria but also for other opportunistic pathogens.