Insights on Platelet-Derived Growth Factor Receptor α-Positive Interstitial Cells in the Male Reproductive Tract

Male infertility is a significant factor in approximately half of all infertility cases and is marked by a decreased sperm count and motility. A decreased sperm count is caused by not only a decreased production of sperm but also decreased numbers successfully passing through the male reproductive tract. Smooth muscle movement may play an important role in sperm transport in the male reproductive tract; thus, understanding the mechanism of this movement is necessary to elucidate the cause of sperm transport disorder. Recent studies have highlighted the presence of platelet-derived growth factor receptor α (PDGFRα)-positive interstitial cells (PICs) in various smooth muscle organs. Although research is ongoing, PICs in the male reproductive tract may be involved in the regulation of smooth muscle movement, as they are in other smooth muscle organs. This review summarizes the findings to date on PICs in male reproductive organs. Further exploration of the structural, functional, and molecular characteristics of PICs could provide valuable insights into the pathogenesis of male infertility and potentially lead to new therapeutic approaches.

Novel Method for the Preparation of Lamellas From Porous and Brittle Materials for In Situ TEM Heating/Biasing

A novel method for the preparation of lamellas made from porous and brittle compressed green powder using a focused ion beam (FIB) is described. One of the main purposes for the development of this methodology is to use this type of samples in micro-electromechanical systems (MEMS) chips for in situ transmission electron microscopy heating/biasing experiments, concomitant with maintaining the mechanical integrity and the absence of contamination of samples. This is accomplished through a modification of the standard FIB procedure for the preparation of lamellas, the adaptation of conventional chips, as well as the specific transfer of the lamella onto the chips. This method is versatile enough to be implemented in most commercially available FIB systems and MEMS chips.

Focused ion beam-SEM 3D study of osteodentin in the teeth of the Atlantic wolfish Anarhichas lupus

The palette of mineralized tissues in fish is wide, and this is particularly apparent in fish dentin. While the teeth of all vertebrates except fish contain a single dentinal tissue type, called orthodentin, dentin in the teeth of fish can be one of several different tissue types. The most common dentin type in fish is orthodentin. Orthodentin is characterized by several key structural features that are fundamentally different from those of bone and from those of osteodentin. Osteodentin, the second-most common dentin type in fish (based on the tiny fraction of fish species out of ∼30,000 extant fish species in which tooth structure was so far studied), is found in most Selachians (sharks and rays) as well as in several teleost species, and is structurally different from orthodentin. Here we examine the hypothesis that osteodentin is similar to anosteocytic bone tissue in terms of its micro- and nano-structure. We use Focused Ion Beam-Scanning Electron Microscopy (FIB/SEM), as well as several other high-resolution imaging techniques, to characterize the 3D architecture of the three main components of osteodentin (denteons, inter-denteonal matrix, and the transition zone between them). We show that the matrix of osteodentin, although acellular, is extremely similar to mammalian osteonal bone matrix, both in general morphology and in the three-dimensional nano-arrangement of its mineralized collagen fibrils. We also document the presence of a complex network of nano-channels, similar to such networks recently described in bone. Finally, we document the presence of strings of hyper-mineralized small 'pearls' which surround the denteonal canals, and characterize their structure.

Robust Preparation of Sub-20-nm-Thin Lamellae for Aberration-Corrected Electron Microscopy

Aberration-corrected scanning transmission electron microscopy (STEM) has been advancing resolution, sensitivity, and microanalysis due to the intense demands of atomic-level microstructural investigations. Recent STEM technologies require preparing a thin lamella whose thickness is ideally below 20 nm. Although focused-ion-beam/scanning-electron-microscopy (FIB/SEM) is an established method to prepare a high-quality lamella, nanometer-level controllability of lamella thickness remains a fundamental problem. Here, the robust preparation of a sub-20-nm-thin lamella is demonstrated by FIB/SEM with real-time feedback from thickness quantification. The lamella thickness is quantified by back-scattered-electron SEM imaging in a thickness range between 0 and 100 nm without any reference to numerical simulation. Using real-time feedback from the thickness quantification, the FIB/SEM terminates thinning a lamella at a targeted thickness. The real-time feedback system eventually provides 1-nm-level controllability of the lamella thickness. As a proof-of-concept, a near-10-nm-thin lamella is prepared from a SrTiO3 crystal by our methodology. Moreover, the lamella thickness is controllable at a target heterointerface. Thus, a sub-20-nm-thin lamella is prepared from a LaAlO3 /SrTiO3 heterointerface. The methodology offers a robust and operator-independent platform to prepare a sub-20-nm-thin lamella from various materials. This platform will broadly impact aberration-corrected STEM studies in materials science and the semiconductor industry.

Structural segregation in GSR from mercuric primers. A preliminary study

Since the second half of the XX century, primer mixtures based on mercury fulminate have become a rare occurrence on small ammunition markets in Western Europe and North America. As a consequence, Hg-containing gunshot residue (GSR) particles have not been as deeply investigated as residues from lead-based primer mixtures. As a matter of fact, no mention of GSR particles from mercuric primers is made by the current ASTM standard procedure for gunshot residue analysis. However, those laboratories dealing with ammunition and firearms produced in Eastern Europe or Asia still have a forensic interest in Hg-containing GSR. In this paper, a brief description of chemical composition and inner morphology of GSR particles from three different mercuric primers is reported. Regarding composition, arguments are given to promote SbSnHg residues to Characteristic of GSR particles when mercuric primers are discharged. From a morphological point of view, presence of inner nodules and other inhomogeneities were shown in GSR particles milled in a FIB/SEM. Moreover, mercury vaporization under the electron beam was observed for a particle reduced to a lamella. Mercury evanescence in GSR was interpreted in terms of mercury segregation during particle formation and higher mobility of Hg atoms in presence of defects (vacancies) in a strained lattice.

The cranial apparatus glands of the canthariphilous Pyrochroa coccinea (Coleoptera: Pyrochroidae: Pyrochroinae), and their implications in sexual behaviour

Some Pyrochroidae species are known as "canthariphilous" for their attraction to cantharidin (CTD), a toxic terpene with anti-predatory effects, produced in nature by only two beetle families (Meloidae and Oedemeridae). It has been demonstrated that males of Neopyrochroa flabellata ingesting CTD are positively selected by females. Indeed, the compound is re-emitted from a glandular cranial apparatus as secretions that are licked up by females during courtship behaviour, inducing copulation. Herein, we provide the first description of the glands associated to the cranial apparatus of male Pyrochroinae using the European species Pyrochroa coccinea as a model. Morphological analyses show that the cranial apparatus consists of a concave pit lined with short setae retaining secretions emitted through numerous glandular pores. Ultrastructural investigations reveal the presence of two different class 3 glands (Gl.A and Gl.B), intermixed at the level of the pit but exhibiting distinct features. Gl.A are mainly characterised by short conducting canals, rounded nuclei and electrondense vesicles while Gl.B are characterised by long conducting canals, irregular nuclei, vesicles containing a particulate substance and a multifolded plasma membrane. Observations of sexual behaviour are also reported for P. coccinea and compared to N. flabellata, confirming the involvement of cranial apparatus secretions in courtship behaviour.

The enigmatic nucleus of the marine dinoflagellate Prorocentrum cordatum

The marine, bloom-forming dinoflagellate Prorocentrum cordatum CCMP 1329 (formerly P. minimum) has a genome atypical of eukaryotes, with a large size of ~4.15 Gbp, organized in plentiful, highly condensed chromosomes and packed in a dinoflagellate-specific nucleus (dinokaryon). Here, we apply microscopic and proteogenomic approaches to obtain new insights into this enigmatic nucleus of axenic P. cordatum. High-resolution focused ion beam/scanning electron microscopy analysis of the flattened nucleus revealed highest density of nuclear pores in the vicinity of the nucleolus, a total of 62 tightly packed chromosomes (~0.4-6.7 µm3), and interaction of several chromosomes with the nucleolus and other nuclear structures. A specific procedure for enriching intact nuclei was developed to enable proteomic analyses of soluble and membrane protein-enriched fractions. These were analyzed with geLC and shotgun approaches employing ion-trap and timsTOF (trapped-ion-mobility-spectrometry time-of-flight) mass spectrometers, respectively. This allowed identification of 4,052 proteins (39% of unknown function), out of which 418 were predicted to serve specific nuclear functions; additional 531 proteins of unknown function could be allocated to the nucleus. Compaction of DNA despite very low histone abundance could be accomplished by highly abundant major basic nuclear proteins (HCc2-like). Several nuclear processes including DNA replication/repair and RNA processing/splicing can be fairly well explained on the proteogenomic level. By contrast, transcription and composition of the nuclear pore complex remain largely elusive. One may speculate that the large group of potential nuclear proteins with currently unknown functions may serve yet to be explored functions in nuclear processes differing from those of typical eukaryotic cells. IMPORTANCE Dinoflagellates form a highly diverse group of unicellular microalgae. They provide keystone species for the marine ecosystem and stand out among others by their very large, unusually organized genomes embedded in the nuclei markedly different from other eukaryotic cells. Functional insights into nuclear and other cell biological structures and processes of dinoflagellates have long been hampered by the paucity of available genomic sequences. The here studied cosmopolitan P. cordatum belongs to the harmful algal bloom-forming, marine dinoflagellates and has a recently de novo assembled genome. We present a detailed 3D reconstruction of the P. cordatum nucleus together with comprehensive proteogenomic insights into the protein equipment mastering the broad spectrum of nuclear processes. This study significantly advances our understanding of mechanisms and evolution of the conspicuous dinoflagellate cell biology.

Design and implementation of suspended drop crystallization

In this work, a novel crystal growth method termed suspended drop crystallization has been developed. Unlike traditional methods, this technique involves mixing protein and precipitant directly on an electron microscopy grid without any additional support layers. The grid is then suspended within a crystallization chamber designed in-house, allowing for vapor diffusion to occur from both sides of the drop. A UV-transparent window above and below the grid enables the monitoring of crystal growth via light, UV or fluorescence microscopy. Once crystals have formed, the grid can be removed and utilized for X-ray crystallography or microcrystal electron diffraction (MicroED) directly without having to manipulate the crystals. To demonstrate the efficacy of this method, crystals of the enzyme proteinase K were grown and its structure was determined by MicroED following focused ion beam/scanning electron microscopy milling to render the sample thin enough for cryoEM. Suspended drop crystallization overcomes many of the challenges associated with sample preparation, providing an alternative workflow for crystals embedded in viscous media, sensitive to mechanical stress and/or subject to preferred orientation on electron microscopy grids.

The structure of the neurotoxin palytoxin determined by MicroED

Palytoxin (PTX) is a potent neurotoxin found in marine animals that can cause serious symptoms such as muscle contractions, haemolysis of red blood cells and potassium leakage. Despite years of research, very little is known about the mechanism of PTX. However, recent advances in the field of cryoEM, specifically the use of microcrystal electron diffraction (MicroED), have allowed us to determine the structure of PTX. It was discovered that PTX folds into a hairpin motif and is able to bind to the extracellular gate of Na,K-ATPase, which is responsible for maintaining the electrochemical gradient across the plasma membrane. These findings, along with molecular docking simulations, have provided important insights into the mechanism of PTX and can potentially aid in the development of molecular agents for treating cases of PTX exposure.

Three-dimensional ultrastructure analysis of organelles in injured motor neuron

Morphological analysis of organelles is one of the important clues for understanding the cellular conditions and mechanisms occurring in cells. In particular, nanoscale information within crowded intracellular organelles of tissues provide more direct implications when compared to analyses of cells in culture or isolation. However, there are some difficulties in detecting individual shape using light microscopy, including super-resolution microscopy. Transmission electron microscopy (TEM), wherein the ultrastructure can be imaged at the membrane level, cannot determine the whole structure, and analyze it quantitatively. Volume EM, such as focused ion beam/scanning electron microscopy (FIB/SEM), can be a powerful tool to explore the details of three-dimensional ultrastructures even within a certain volume, and to measure several parameters from them. In this review, the advantages of FIB/SEM analysis in organelle studies are highlighted along with the introduction of mitochondrial analysis in injured motor neurons. This would aid in understanding the morphological details of mitochondria, especially those distributed in the cell bodies as well as in the axon initial segment (AIS) in mouse tissues. These regions have not been explored thus far due to the difficulties encountered in accessing their images by conditional microscopies. Some mechanisms of nerve regeneration have also been discussed with reference to the obtained findings. Finally, future perspectives on FIB/SEM are introduced. The combination of biochemical and genetic understanding of organelle structures and a nanoscale understanding of their three-dimensional distribution and morphology will help to match achievements in genomics and structural biology.

Warp-Free TEM Sample Preparation Methods Using FIB/SEM Systems

Warping is a limiting factor when preparing transmission electron microscopy (TEM) samples using focused ion beam (FIB)/scanning electron microscope (SEM) systems. The conventional FIB sputtering process leaves at least one side of the lamella too thin to provide structural support to offset inherent stresses. As a result, warping can occur impacting imagining and reducing the potential size of lamellae. For example, capturing more than a few back-end metal layers in a 3 μm wide cross-section lamella can be difficult. Frequently, TEM analysts must perform multiple stage adjustments to analyze such a sample. In this paper, two methods are presented that enable FIB/SEM operators to prepare TEM samples where the thinned region of interest is surrounded by thick structures. As a result, these methods reduce warping and enable the fabrication of TEM lamellae not possible by conventional means. For example, these methods have been used to produce a 10 μm wide by 8 μm tall cross-section TEM sample that captured front-end transistors and 14 back-end metal layers. Furthermore, warping was so limited that only one alignment was needed by the TEM analyst to complete the imaging of the sample. The methods, called the horizontal bracing and window methods, make use of the deposition of low-Z amorphous films that are electron transparent in the TEM.

Mitochondrial dysfunction in mandibular hypoplasia, deafness and progeroid features with concomitant lipodystrophy (MDPL) patients

Mandibular hypoplasia, Deafness and Progeroid features with concomitant Lipodystrophy is a rare, genetic, premature aging disease named MDPL Syndrome, due to almost always a de novo variant in POLD1 gene, encoding the DNA polymerase δ. In previous in vitro studies, we have already described several hallmarks of aging, including genetic damage, telomere shortening, cell senescence and proliferation defects. Since a clear connection has been reported between telomere shortening and mitochondria malfunction to initiate the aging process, we explored the role that mitochondrial metabolism and activity play in pathogenesis of MDPL Syndrome, an aspect that has not been addressed yet. We thus evaluated mtDNA copy number, assessing a significant decrease in mutated cells.

The expression level of genes related to mitochondrial biogenesis and activity also revealed a significant reduction, highlighting a mitochondrial dysfunction in MDPL cells. Even the expression levels of mitochondrial marker SOD2, as assessed by immunofluorescence, were reduced. The decrease in this antioxidant enzyme correlated with increased production of mitochondrial ROS in MDPL cells, compared to WT. Consistent with these data, Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) analysis revealed in MDPL cells fewer mitochondria, which also displayed morphological abnormalities. Accordingly, we detected autophagic vacuoles containing partially digested mitochondria.

Overall, our results demonstrate a dramatic impairment of mitochondrial biogenesis and activity in MDPL Syndrome. Administration of Metformin, though unable to restore mitochondrial impairment, proved efficient in rescuing nuclear abnormalities, suggesting its use to specifically ameliorate the premature aging phenotype.

Three-Dimensional Analysis of Interstitial Cells in the Smooth Muscle Layer of Murine Vas Deferens Using Confocal Laser Scanning Microscopy and FIB/SEM

The smooth muscle contraction of the vas deferens has the important function of transporting sperm. Interstitial cells (ICs) play a critical role in the pacing and modulation of various smooth muscle organs by interactions with nerves and smooth muscle. Elucidating the three-dimensional (3D) architecture of ICs is important for understanding their spatial relationship on the mesoscale between ICs, smooth muscle cells (SMCs), and nerves. In this study, the 3D ultrastructure of ICs in the smooth muscle layer of murine vas deferens and the spatial relationships between ICs, nerves, and smooth muscles were observed using confocal laser scanning microscopy and focused ion beam/scanning electron microscopy. ICs have sheet-like structures as demonstrated by 3D observation using modern analytical techniques. Sheet-like ICs have two types of 3D structures, one flattened and the other curled. Multiple extracellular vesicle (EV)-like structures were frequently observed in ICs. Various spatial relations were observed in areas between ICs, nerves, and SMCs, which formed a complex 3D network with each other. These results suggest that ICs in the smooth muscle layer of murine vas deferens may have two subtypes with different sheet-like structures and may be involved in neuromuscular signal transmission via physical interaction and EVs.

Neuron Class and Target Variability in the Three-Dimensional Localization of SK2 Channels in Hippocampal Neurons as Detected by Immunogold FIB-SEM

Small-conductance calcium-activated potassium (SK) channels are crucial for learning and memory. However, many aspects of their spatial organization in neurons are still unknown. In this study, we have taken a novel approach to answering these questions combining a pre-embedding immunogold labeling with an automated dual-beam electron microscope that integrates focused ion beam milling and scanning electron microscopy (FIB/SEM) to gather 3D map ultrastructural and biomolecular information simultaneously. Using this new approach, we evaluated the number and variability in the density of extrasynaptic SK2 channels in 3D reconstructions from six dendritic segments of excitatory neurons and six inhibitory neurons present in the stratum radiatum of the CA1 region of the mouse. SK2 immunoparticles were observed throughout the surface of hippocampal neurons, either scattered or clustered, as well as at intracellular sites. Quantitative volumetric evaluations revealed that the extrasynaptic SK2 channel density in spines was seven times higher than in dendritic shafts and thirty-five times higher than in interneurons. Spines showed a heterogeneous population of SK2 expression, some spines having a high SK2 content, others having a low content and others lacking SK2 channels. SK2 immunonegative spines were significantly smaller than those immunopositive. These results show that SK2 channel density differs between excitatory and inhibitory neurons and demonstrates a large variability in the density of SK2 channels in spines. Furthermore, we demonstrated that SK2 expression was associated with excitatory synapses, but not with inhibitory synapses in CA1 pyramidal cells. Consequently, regulation of excitability and synaptic plasticity by SK2 channels is expected to be neuron class- and target-specific. These data show that immunogold FIB/SEM represent a new powerful EM tool to correlate structure and function of ion channels with nanoscale resolution.

Axonal injury alters the extracellular glial environment of the axon initial segment and allows substantial mitochondrial influx into axon initial segment

The axon initial segment (AIS) is structurally and functionally distinct from other regions of the axon, yet alterations in the milieu of the AIS after brain injury have not been well characterized. In this study, we have examined extracellular and intracellular changes in the AIS after hypoglossal nerve injury. Microglial adhesions to the AIS were rarely observed in healthy controls, whereas microglial adhesions to the AIS became apparent in the axonal injury model. Regarding intra-AIS morphology, we focused on mitochondria because mitochondrial flow into the injured axon appears critical for axonal regeneration. To visualize mitochondria specifically in injured axons, we used Atf3:BAC transgenic mice whose mitochondria were labeled with GFP in response to nerve injury. These mice clearly showed mitochondrial localization in the AIS after nerve injury. To precisely confirm the light microscopic observations, we performed three-dimensional ultrastructural analysis using focused ion beam/scanning electron microscopy (FIB/SEM). Although the healthy AIS was not surrounded by microglia, tight microglial adhesions with thick processes adhering to the AIS were observed after injury. FIB/SEM simultaneously allowed the observation of mitochondrial localization in the AIS. In the AIS of non-injured neurons, few mitochondria were observed, whereas mitochondria were abundantly localized in the cell body, axon hillock, and axon. Intriguingly, in the injured AIS, numerous mitochondria were observed throughout the AIS. Taken together, axonal injury changes the extracellular glial environment surrounding the AIS and intracellular mitochondrial localization in the AIS. These changes would be crucial responses, perhaps for injured neurons to regenerate after axonal injury.

3D Analysis of the Synaptic Organization in the Entorhinal Cortex in Alzheimer's Disease

The entorhinal cortex (EC) is especially vulnerable in the early stages of Alzheimer's disease (AD). In particular, cognitive deficits have been linked to alterations in the upper layers of EC. In the present report, we examined Layers II and III from eight human brain autopsies (four subjects with no recorded neurologic alterations and four AD cases). We used stereological methods to assess cortical atrophy of the EC and possible changes in the volume occupied by different cortical elements (neuronal and glial cell bodies; blood vessels; and neuropil). We performed 3D ultrastructural analyses of synapses using focused ion beam/scanning electron microscopy (FIB/SEM) to examine possible alterations related to AD. At the light microscope level, we found a significantly lower volume fraction occupied by neuronal bodies in Layer III and a higher volume fraction occupied by glial cell bodies in Layer II in AD cases. At the ultrastructural level, we observed that (1) there was a significantly lower synaptic density in both layers in AD cases; (2) synapses were larger and more complex in Layer II in AD cases; and (3) there was a greater proportion of small and simple synapses in Layer III in AD cases than in control individuals. These structural differences may play a role in the anatomic basis for the impairment of cognitive functions in AD.

3D Synaptic Organization of the Rat CA1 and Alterations Induced by Cocaine Self-Administration

The hippocampus plays a key role in contextual conditioning and has been proposed as an important component of the cocaine addiction brain circuit. To gain knowledge about cocaine-induced alterations in this circuit, we used focused ion beam milling/scanning electron microscopy to reveal and quantify the three-dimensional synaptic organization of the neuropil of the stratum radiatum of the rat CA1, under normal circumstances and after cocaine-self administration (SA). Most synapses are asymmetric (excitatory), macular-shaped, and in contact with dendritic spine heads. After cocaine-SA, the size and the complexity of the shape of both asymmetric and symmetric (inhibitory) synapses increased but no changes were observed in the synaptic density. This work constitutes the first detailed report on the 3D synaptic organization in the stratum radiatum of the CA1 field of cocaine-SA rats. Our data contribute to the elucidation of the normal and altered synaptic organization of the hippocampus, which is crucial for better understanding the neurobiological mechanisms underlying cocaine addiction.

Three-dimensional analysis of synaptic organization in the hippocampal CA1 field in Alzheimer's disease

Alzheimer's disease is the most common form of dementia, characterized by a persistent and progressive impairment of cognitive functions. Alzheimer's disease is typically associated with extracellular deposits of amyloid-β peptide and accumulation of abnormally phosphorylated tau protein inside neurons (amyloid-β and neurofibrillary pathologies). It has been proposed that these pathologies cause neuronal degeneration and synaptic alterations, which are thought to constitute the major neurobiological basis of cognitive dysfunction in Alzheimer's disease. The hippocampal formation is especially vulnerable in the early stages of Alzheimer's disease. However, the vast majority of electron microscopy studies have been performed in animal models. In the present study, we performed an extensive 3D study of the neuropil to investigate the synaptic organization in the stratum pyramidale and radiatum in the CA1 field of Alzheimer's disease cases with different stages of the disease, using focused ion beam/scanning electron microscopy (FIB/SEM). In cases with early stages of Alzheimer's disease, the synapse morphology looks normal and we observed no significant differences between control and Alzheimer's disease cases regarding the synaptic density, the ratio of excitatory and inhibitory synapses, or the spatial distribution of synapses. However, differences in the distribution of postsynaptic targets and synaptic shapes were found. Furthermore, a lower proportion of larger excitatory synapses in both strata were found in Alzheimer's disease cases. Individuals in late stages of the disease suffered the most severe synaptic alterations, including a decrease in synaptic density and morphological alterations of the remaining synapses. Since Alzheimer's disease cases show cortical atrophy, our data indicate a reduction in the total number (but not the density) of synapses at early stages of the disease, with this reduction being much more accentuated in subjects with late stages of Alzheimer's disease. The observed synaptic alterations may represent a structural basis for the progressive learning and memory dysfunctions seen in Alzheimer's disease cases.

Cryo-correlative light and electron microscopy workflow for cryo-focused ion beam milled adherent cells

In situ cryo-electron tomography of cryo-focused ion beam (cryo-FIB) milled cells enables the study of cellular organelles in unperturbed conditions and close to the molecular resolution. However, due to the crowdedness of the cellular environment, the identification of individual macromolecular complexes either on organelles or inside the cytosol in cryo-electron tomograms is challenging. Cryo-correlative light and electron microscopy (cryo-CLEM) employs a fluorescently labeled feature of interest imaged by cryo-light microscopy that is correlated to cryo-electron microscopy maps of cryo-FIB milled lamellae using correlation markers discernable by both imaging methods. Here, we provide a protocol for a post-correlation on-lamella cryo-CLEM approach for localization of fluorescently labeled organelles of interest in cryo-lamellae after cryo-FIB milling and tomography of adherent plunge frozen cells.

MicroED structure of lipid-embedded mammalian mitochondrial voltage-dependent anion channel

A structure of the murine voltage-dependent anion channel (VDAC) was determined by microcrystal electron diffraction (MicroED). Microcrystals of an essential mutant of VDAC grew in a viscous bicelle suspension, making it unsuitable for conventional X-ray crystallography. Thin, plate-like crystals were identified using scanning-electron microscopy (SEM). Crystals were milled into thin lamellae using a focused-ion beam (FIB). MicroED data were collected from three crystal lamellae and merged for completeness. The refined structure revealed unmodeled densities between protein monomers, indicative of lipids that likely mediate contacts between the proteins in the crystal. This body of work demonstrates the effectiveness of milling membrane protein microcrystals grown in viscous media using a focused ion beam for subsequent structure determination by MicroED. This approach is well suited for samples that are intractable by X-ray crystallography. To our knowledge, the presented structure is a previously undescribed mutant of the membrane protein VDAC, crystallized in a lipid bicelle matrix and solved by MicroED.

Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software

In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissues. These tasks remain challenging and are often rate-limiting to most users. Here we provide a step-by-step guide to image processing and manual correlation using ImageJ and Amira software of a confocal microscopy stack and a focused ion beam/scanning electron microscopy (FIB/SEM) tomogram acquired using a correlative pipeline. These previously published datasets capture a highly transient invasion event by the bacterium Shigella flexneri infecting an epithelial cell grown in culture, and are made available here in their pre-processed form for readers who wish to gain hands-on experience in image processing and correlation using existing data. In this guide we describe a simple protocol for correlation based on internal sample features clearly visible by both fluorescence and electron microscopy, which is normally sufficient when correlating standard fluorescence microscopy stacks with FIB/SEM data. While the guide describes the treatment of specific datasets, it is applicable to a wide variety of samples and different microscopy approaches that require basic correlation and visualization of two or more datasets in a single integrated framework.

The male reproductive accessory glands of the blister beetle Meloe proscarabaeus Linnaeus, 1758 (Coleoptera: Meloidae): Anatomy and ultrastructure of the cantharidin-storing organs

Blister beetles owe their name to their ability to release cantharidin, a blistering terpene, the highest concentration of which is retained in male accessory glands. The anatomy and ultrastructure of the three pairs of male reproductive accessory glands and the glandular region of the two vasa deferentia of Meloe proscarabaeus were investigated using light, electron and ion beam microscopy. All of the mesodermal glands here analysed share a common structural organization with an outer muscular layer and an inner glandular epithelium facing a broad lumen in which the secretory products are released. Developed rough endoplasmic reticulum, Golgi systems, abundant mitochondria, numerous secretory vesicles and a microvillated apical membrane are commonly found in the cells of different glandular epithelia, suggesting that all accessory gland pairs as well as the vasa deferentia are involved in an active synthesis. Nevertheless, each pair of glands appears specialized in the production of a specific set of substances, as suggested by the peculiarities in cellular ultrastructure and by the different aspect of the secretions stored in their glandular lumen. The above cited features of male accessory glands of M. proscarabaeus are compared with those of other beetles and some hints on their potential role in producing and/or concentrating cantharidin are provided.

Geometry and the Organizational Principle of Spine Synapses along a Dendrite

Precise information on synapse organization in a dendrite is crucial to understanding the mechanisms underlying voltage integration and the variability in the strength of synaptic inputs across dendrites of different complex morphologies. Here, we used focused ion beam/scanning electron microscope (FIB/SEM) to image the dendritic spines of mice in the hippocampal CA1 region, CA3 region, somatosensory cortex, striatum, and cerebellum (CB). Our results show that the spine geometry and dimensions differ across neuronal cell types. Despite this difference, dendritic spines were organized in an orchestrated manner such that the postsynaptic density (PSD) area per unit length of dendrite scaled positively with the dendritic diameter in CA1 proximal stratum radiatum (PSR), cortex, and CB. The ratio of the PSD area to neck length was kept relatively uniform across dendrites of different diameters in CA1 PSR. Computer simulation suggests that a similar level of synaptic strength across different dendrites in CA1 PSR enables the effective transfer of synaptic inputs from the dendrites toward soma. Excitatory postsynaptic potentials (EPSPs), evoked at single spines by glutamate uncaging and recorded at the soma, show that the neck length is more influential than head width in regulating the EPSP magnitude at the soma. Our study describes thorough morphologic features and the organizational principles of dendritic spines in different brain regions.

Cellular network across cementum and periodontal ligament elucidated by FIB/SEM tomography

Cementocytes in cementum form a lacuna-canalicular network. However, the 3D ultrastructure and range of the cementocyte network are unclear. Here, the 3D ultrastructure of the cementocyte network at the interface between cementum and periodontal ligament (PDL) was investigated on the mesoscale using FIB/SEM tomography. The results revealed a cellular network of cementocytes and PDL cells. A previous histomorphological study revealed the osteocyte-osteoblast-PDL cellular network. We extended this knowledge and revealed the cementum-PDL-bone cellular network, which may orchestrate the remodeling and modification of periodontal tissue, using a suitable method for imaging of complex tissue.

Evolution of SLA-Based Al2O3 Microstructure During Additive Manufacturing Process

Evolution of additively manufactured (AM) ceramics' microstructure between manufacturing stages is a hardly explored topic. These data are of high demand for advanced numerical modeling. In this work, 3D microstructural models of Al₂O₃ greenbody, brownbody and sintered material are presented and analyzed, for ceramic samples manufactured with SLA-based AM workflow, using a commercially available ceramic paste and 3D printer. The novel data, acquired at the micro- and mesoscale, using Computed Tomography (CT), Scanning Electron Microscopy (SEM) and Focused Ion-Beam SEM (FIB/SEM) techniques, allowed a deep insight into additive ceramics characteristics. We demonstrated the spatial 3D distribution of ceramic particles, an organic binder and pores at every stage of AM workflow. The porosity of greenbody samples (1.6%), brownbody samples (37.3%) and sintered material (4.9%) are analyzed. Pore distribution and possible originating mechanisms are discussed. The location and shape of pores and ceramic particles are indicative of specific physical processes driving the ceramics manufacturing. We will use the presented microstructural 3D models as input and verification data for advanced numerical simulations developed in the project.

Developmental Changes in Dendritic Spine Morphology in the Striatum and Their Alteration in an A53T α-Synuclein Transgenic Mouse Model of Parkinson's Disease

The aging process is accompanied by various neurophysiological changes, and the severity of neurodegenerative disorders such as Parkinson’s disease (PD) increases with aging. However, the precise neuroanatomical changes that accompany the aging process in both normal and pathologic conditions remain unknown. This is in part because there is a lack of high-resolution imaging tool that has the capacity to image a desired volume of neurons in a high-throughput and automated manner. In the present study, focused ion beam/scanning electron microscopy (FIB/SEM) was used to image striatal neuropil in both wild-type (WT) mice and an A53T bacterial artificial chromosome (BAC) human α-synuclein (A53T-BAC-SNCA) transgenic (Tg) mouse model of PD, at 1, 3, 6, and 22 months of age. We demonstrated that spine density gradually decreases, and average spine head volume gradually increases with age in WT mice, suggesting a homeostatic balance between spine head volume and spine density. However, this inverse relationship between spine head volume and spine density was not observed in A53T-BAC-SNCA Tg mice. Taken together, our data suggest that PD is accompanied by an abnormality in the mechanisms that control synapse growth and maturity.

Macular pucker formation after macular hole surgery with inverted internal limiting membrane flap technique and silicone oil tamponade

Purpose

The inverted internal limiting membrane (ILM) technique was recently introduced for refractory macular hole. Here, we evaluate a case of macular pucker formation after macular hole surgery using the inverted ILM flap technique and silicone oil tamponade. After undergoing vitrectomy combined with ILM removal, the patient had a good visual prognosis.

Observations

A 49-year-old male with macular hole affecting both of his eyes underwent vitrectomies. Three months after the first surgery in his right eye, macular pucker formation was observed in the macula, which was associated with the ILM flap used to cover the macular hole. After peeling the ILM, the macula returned to a normal contour and visual acuity improved. Examination of the removed ILM revealed macrophage-like cells containing silicone oil particles that were responsible for the ILM contraction.

Conclusions and Importance

When using the inverted ILM flap technique and silicone oil, macular pucker may occur after macular hole surgery. Peeling of the ILM flap restored the macular shape and did not reopen the macular hole, thereby improving visual acuity. Thus, silicone oil should be used with caution when performing macular hole surgery with the ILM flap technique.

Unique synaptic topography of crest-type synapses in the interpeduncular nucleus

Neurons in the central nervous system display a great diversity of synaptic architecture. While much of our knowledge on the excitatory synapse morphology derives from the prototypical asymmetric synapses, little has been studied about the atypical crest-type synapse that exists in the restricted brain regions. Here, we used focused ion beam scanning electron microscopy (FIB/SEM) to image a neuropil volume of interpeduncular nucleus (IPN) and manually reconstructed several dendrites to obtain an insight about the topography and quantitative features of crest synapses. Three-dimensional reconstruction showed numerous U-shaped structures protruding from the IPN dendrites. On either faces of the U-shaped structure, a pair of crest synapses are aligned in parallel such that there exists a positive correlation between the postsynaptic density (PSD) area of synapses that participate in pair formation. Interestingly, mitochondria are excluded from the site of crest synapses. Several presynaptic axons run through the hollow, cylindrical space of the U-shape grooves such that the plasma membrane of the axon and the dendrite are organized in a tight opposition without any intervening glial membrane. Unlike the peculiar dendritic morphology, IPN neurons possess typical somatic morphology with an oval, centrally located nucleus. In conclusion, our data reveals a hitherto unknown unique topographical feature of crest synapses in the IPN.

Ultrastructural Observation of Glutamatergic Synapses by Focused Ion Beam Scanning Electron Microscopy (FIB/SEM)

A thorough understanding of the synaptic ultrastructure is necessary to bridge our current knowledge gap about the relationship between neuronal structure and function. Recent development of focused ion beam scanning electron microscopy (FIB/SEM) has made it possible to image neuronal structures with high speed and efficiency. Here, we present our routine protocol for correlative two-photon microscopy and FIB/SEM imaging of glutamatergic synapses. Femtosecond-pulsed near-infrared laser was used to create fiducial marks around the dendrite of interest in aldehyde-fixed tissues. Thereafter, samples were subjected to en bloc staining with rOTO (reduced osmium tetroxide-thiocarbohydrazide-osmium tetroxide), followed by lead aspartate and uranyl acetate to enhance tissue contrast. Reliable detection of postsynaptic density (PSD) and plasma membrane contours by the sample preparation protocol optimized for FIB/SEM allows us to precisely evaluate morphological features that shape glutamatergic synaptic transmission.

3D Electron Microscopy Study of Synaptic Organization of the Normal Human Transentorhinal Cortex and Its Possible Alterations in Alzheimer's Disease

The transentorhinal cortex (TEC) is an obliquely oriented cortex located in the medial temporal lobe and, together with the entorhinal cortex, is one of the first affected areas in Alzheimer’s disease (AD). One of the most widely accepted hypotheses is that synaptopathy (synaptic alterations and loss) represents the major structural correlate of the cognitive decline observed in AD. However, very few electron microscope (EM) studies are available; the most common method to estimate synaptic density indirectly is by counting, at the light microscopic level, immunoreactive puncta using synaptic markers. To investigate synaptic morphology and possible alterations related to AD, a detailed three-dimensional (3D) ultrastructural analysis using focused ion beam/scanning EM (FIB/SEM) was performed in the neuropil of Layer II of the TEC in human brain samples from non-demented subjects and AD patients. Evaluation of the proportion and shape of asymmetric synapses (AS) and symmetric synapses (SS) targeting spines or dendritic shafts was performed using 3D reconstructions of every synapse. The 3D analysis of 4722 synapses revealed that the preferable targets were spine heads for AS and dendritic shafts for SS, both in control and AD cases. However, in AD patients, we observed a reduction in the percentage of synapses targeting spine heads. Regarding the shape of synapses, in both control cases and AD samples, the vast majority of synapses had a macular shape, followed by perforated or horseshoe-shaped synapses, with fragmented synapses being the least frequent type. Moreover, comparisons showed an increased number of fragmented AS in AD patients.

The ant nest "bomber": Explosive defensive system of the flanged bombardier beetle Paussus favieri (Coleoptera, Carabidae)

Bombardier beetles are famous for their unique ability to explosively discharge hot quinones from their pygidial glands when threatened. Here we provide the first detailed description of the ultrastructure of the defensive gland system of the genus Paussus, the most speciose genus in the ground beetle subfamily Paussinae. Paussine beetles are commonly known as "flanged bombardier beetles" due to the presence of a flange on their elytra that assists in directing their defensive chemicals toward the front of their bodies. In this paper, we use optical, fluorescence and focused ion beam (FIB/SEM) microscopy to analyse and illustrate anatomy and ultrastructure of the explosive defensive system of Paussus favieri, a charismatic myrmecophilous species. The defensive system of this species consists of two independent, symmetrical glands each composed of secretory lobes, a long collecting duct, a bilobed reservoir chamber, a cuticular valve, a sclerotized reaction chamber, and an accessory chamber, associated with the reaction chamber, that is surrounded by several isolated glandular cells. Differences between the pygidial defensive systems of Paussus favieri and those of Brachininae are discussed.

Morpho-functional analysis of the explosive defensive system of basal bombardier beetles (Carabidae: Paussinae: Metriini)

Bombardier beetles, belonging to the carabid subfamilies Paussinae and Brachininae, are famous for their unique ability to explosively discharge a hot spray of quinones from their pygidial glands when threatened. The paussine tribe Metriini is broadly acknowledged as the most basal group of bombardiers. In order to complement the available information on the chemical substances and the primitive discharging mechanism of Metriini, we provide a detailed morpho-functional analysis of the explosive defensive system of Metrius contractus Eschscholtz, 1829 and Sinometrius turnai Wrase and J. Schmidt, 2006, representatives of the two genera in this tribe. We use dissections, histology, scanning electron microscopy (SEM), and focused ion beam microscopy (FIB/SEM) to describe and illustrate various levels of anatomical complexity. FIB/SEM microscopy is used to analyse ultrastructural features of the cellular regions, replacing the classical transmission electron microscopy (TEM). Compared to other Paussinae tribes, Metriini lacks the typical flange of Coanda, the elytral fold used to direct the defensive secretions forward, but has a similar arrangement of internal components. We find that the internal components of the explosive defensive system, including the secretory lobes, collecting duct, reservoir chamber, valve, reaction chamber, accessory chamber and accessory glands, are only slightly different between Metrius Eschscholtz, 1829 and Sinometrius Wrase and J. Schmidt, 2006. The accessory chamber to the reaction chamber is a unique, derived character state common to all Paussinae examined and therefore represents a clear apomorphy of the Paussinae. We use the same microscopy techniques as used in a recent publication on the Brachininae, to compare the defensive systems of Metriini and Brachininae. We find a lack of morphological similarity at the ultrastructural level, suggesting that the bombarding mechanism may have evolved independently in the Paussinae and the Brachininae, perhaps in response to different ecological pressures.

Assessment of in vitro particle dosimetry models at the single cell and particle level by scanning electron microscopy

Background

Particokinetic models are important to predict the effective cellular dose, which is key to understanding the interactions of particles with biological systems. For the reliable establishment of dose–response curves in, e.g., the field of pharmacology and toxicology, mostly the In vitro Sedimentation, Diffusion and Dosimetry (ISDD) and Distorted Grid (DG) models have been employed. Here, we used high resolution scanning electron microscopy to quantify deposited numbers of particles on cellular and intercellular surfaces and compare experimental findings with results predicted by the ISDD and DG models.

Results

Exposure of human lung epithelial A549 cells to various concentrations of differently sized silica particles (100, 200 and 500 nm) revealed a remarkably higher dose deposited on intercellular regions compared to cellular surfaces. The ISDD and DG models correctly predicted the areal densities of particles in the intercellular space when a high adsorption (“stickiness”) to the surface was emulated. In contrast, the lower dose on cells was accurately inferred by the DG model in the case of “non-sticky” boundary conditions. Finally, the presence of cells seemed to enhance particle deposition, as aerial densities on cell-free substrates were clearly reduced.

Conclusions

Our results further validate the use of particokinetic models but also demonstrate their limitations, specifically, with respect to the spatial distribution of particles on heterogeneous surfaces. Consideration of surface properties with respect to adhesion and desorption should advance modelling approaches to ultimately predict the cellular dose with higher precision.

Electronic supplementary material

The online version of this article (10.1186/s12951-018-0426-2) contains supplementary material, which is available to authorized users.

Senescence-associated ultrastructural features of long-term cultures of induced pluripotent stem cells (iPSCs)

Induced pluripotent stem cells (iPSCs) hold great promise for developing personalized regenerative medicine, however characterization of their biological features is still incomplete. Moreover, changes occurring in long-term cultured iPSCs have been reported, suggesting these as a model of cellular aging. For this reason, we addressed the ultrastructural characterization of iPSCs, with a focus on possible time-dependent changes, involving specific cell compartments. To this aim, we comparatively analysed cultures at different timepoints, by an innovative electron microscopic technology (FIB/SEM). We observed progressive loss of cell-to-cell contacts, associated with increased occurrence of exosomes. Mitochondria gradually increased, while acquiring an elongated shape, with well-developed cristae. Such mitochondrial maturation was accompanied by their turnover, as assessed by the presence of autophagomes (undetectable in young iPSCs), some containing recognizable mitochondria. This finding was especially frequent in middle-aged iPSCs, while being occasional in aged cells, suggesting early autophagic activation followed by a decreased efficiency of the process with culturing time. Accordingly, confocal microscopy showed age-dependent alterations to the expression and distribution of autophagic markers. Interestingly, responsivity to rapamycin, highest in young iPSCs, was almost lost in aged cells. Overall, our results strongly support long-term cultured iPSCs as a model for studying relevant aspects of cellular senescence, involving intercellular communication, energy metabolism, and autophagy.

Precise and economic FIB/SEM for CLEM: with 2 nm voxels through mitosis

A portfolio is presented documenting economic, high-resolution correlative focused ion beam scanning electron microscopy (FIB/SEM) in routine, comprising: (i) the use of custom-labeled slides and coverslips, (ii) embedding of cells in thin, or ultra-thin resin layers for correlative light and electron microscopy (CLEM) and (iii) the claim to reach the highest resolution possible with FIB/SEM in xyz. Regions of interest (ROIs) defined in light microscope (LM), can be relocated quickly and precisely in SEM. As proof of principle, HeLa cells were investigated in 3D context at all stages of the cell cycle, documenting ultrastructural changes during mitosis: nuclear envelope breakdown and reassembly, Golgi degradation and reconstitution and the formation of the midzone and midbody.

Three-dimensional analysis of synapses in the transentorhinal cortex of Alzheimer's disease patients

Synaptic dysfunction or loss in early stages of Alzheimer’s disease (AD) is thought to be a major structural correlate of cognitive dysfunction. Early loss of episodic memory, which occurs at the early stage of AD, is closely associated with the progressive degeneration of medial temporal lobe (MTL) structures of which the transentorhinal cortex (TEC) is the first affected area. However, no ultrastructural studies have been performed in this region in human brain samples from AD patients.

In the present study, we have performed a detailed three-dimensional (3D) ultrastructural analysis using focused ion beam/scanning electron microscopy (FIB/SEM) to investigate possible synaptic alterations in the TEC of patients with AD. Surprisingly, the analysis of the density, morphological features and spatial distribution of synapses in the neuropil showed no significant differences between AD and control samples. However, light microscopy studies showed that cortical thickness of the TEC was severely reduced in AD samples, but there were no changes in the volume occupied by neuronal and glial cell bodies, blood vessels, and neuropil. Thus, the present results indicate that there is a dramatic loss of absolute number of synapses, while the morphology of synaptic junctions and synaptic spatial distribution are maintained. How these changes affect cognitive impairment in AD remains to be elucidated.

Reelin Regulates the Maturation of Dendritic Spines, Synaptogenesis and Glial Ensheathment of Newborn Granule Cells

Significance Statement

The extracellular protein Reelin has an important role in neurological diseases, including epilepsy, Alzheimer's disease and psychiatric diseases, targeting hippocampal circuits. Here we address the role of Reelin in the development of synaptic contacts in adult-generated granule cells (GCs), a neuronal population that is crucial for learning and memory and implicated in neurological and psychiatric diseases. We found that the Reelin pathway controls the shapes, sizes, and types of dendritic spines, the complexity of multisynaptic innervations and the degree of the perisynaptic astroglial ensheathment that controls synaptic homeostasis. These findings show a pivotal role of Reelin in GC synaptogenesis and provide a foundation for structural circuit alterations caused by Reelin deregulation that may occur in neurological and psychiatric disorders.

Removal of choroidal neovascular membrane in a case of macular hole after anti-VEGF therapy for age-related macular degeneration

Purpose

The formation of macular hole after receiving anti-vascular endothelial growth factor (anti-VEGF) therapy is rare. We report a case of macular hole that occurred after intravitreal injection of an anti-VEGF agent for age-related macular degeneration (AMD) in a patient, who underwent vitrectomy combined with choroidal neovascularization (CNV) removal.

Observations

A 64-year-old female with AMD affecting her right eye received an intravitreal injection of an anti-VEGF agent. After treatment, we identified a full thickness macular hole (MH) that was associated with the rapid resolution of the macular edema and contraction of the CNV. After performing vitrectomy combined with CNV removal, the MH closed and her visual acuity improved. Examination of the removed CNV revealed a network of microvessels devoid of pericytes.

Conclusions and importance

The present findings suggest that rapid resolution of macular edema and contraction of the CNV and/or mild increase in the vitreous traction after anti-VEGF therapy could potentially cause MH. CNV removal via the MH may be an acceptable procedure, if the MH remains open, the CNV is of the classic type, and it spares a central portion of the fovea.

Volume electron microscopy of the distribution of synapses in the neuropil of the juvenile rat somatosensory cortex

Knowing the proportions of asymmetric (excitatory) and symmetric (inhibitory) synapses in the neuropil is critical for understanding the design of cortical circuits. We used focused ion beam milling and scanning electron microscopy (FIB/SEM) to obtain stacks of serial sections from the six layers of the juvenile rat (postnatal day 14) somatosensory cortex (hindlimb representation). We segmented in three-dimensions 6184 synaptic junctions and determined whether they were established on dendritic spines or dendritic shafts. Of all these synapses, 87–94% were asymmetric and 6–13% were symmetric. Asymmetric synapses were preferentially located on dendritic spines in all layers (80–91%) while symmetric synapses were mainly located on dendritic shafts (62–86%). Furthermore, we found that less than 6% of the dendritic spines establish more than one synapse. The vast majority of axospinous synapses were established on the spine head. Synapses on the spine neck were scarce, although they were more common when the dendritic spine established multiple synapses. This study provides a new large quantitative dataset that may contribute not only to the knowledge of the ultrastructure of the cortex, but also towards defining the connectivity patterns through all cortical layers.

A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans

Based on serial sectioning, focused ion beam scanning electron microscopy (FIB/SEM), and electron tomography, we depict in detail the highly unusual anatomy of the marine hyperthermophilic crenarchaeon, Ignicoccus hospitalis. Our data support a complex and dynamic endomembrane system consisting of cytoplasmic protrusions, and with secretory function. Moreover, we reveal that the cytoplasm of the putative archaeal ectoparasite Nanoarchaeum equitans can get in direct contact with this endomembrane system, complementing and explaining recent proteomic, transcriptomic and metabolomic data on this inter-archaeal relationship. In addition, we identified a matrix of filamentous structures and/or tethers in the voluminous inter-membrane compartment (IMC) of I. hospitalis, which might be responsible for membrane dynamics. Overall, this unusual cellular compartmentalization, ultrastructure and dynamics in an archaeon that belongs to the recently proposed TACK superphylum prompts speculation that the eukaryotic endomembrane system might originate from Archaea.

Corrigendum: FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

[This corrects the article on p. 60 in vol. 9, PMID: 26052271.].

HID-1 is required for homotypic fusion of immature secretory granules during maturation

Secretory granules, also known as dense core vesicles, are generated at the trans-Golgi network and undergo several maturation steps, including homotypic fusion of immature secretory granules (ISGs) and processing of prehormones to yield active peptides. The molecular mechanisms governing secretory granule maturation are largely unknown. Here, we investigate a highly conserved protein named HID-1 in a mouse model. A conditional knockout of HID-1 in pancreatic β cells leads to glucose intolerance and a remarkable increase in the serum proinsulin/insulin ratio caused by defective proinsulin processing. Large volume three-dimensional electron microscopy and immunofluorescence imaging reveal that ISGs are much more abundant in the absence of HID-1. We further demonstrate that HID-1 deficiency prevented secretory granule maturation by blocking homotypic fusion of immature secretory granules. Our data identify a novel player during the early maturation of immature secretory granules.

Functional anatomy of the explosive defensive system of bombardier beetles (Coleoptera, Carabidae, Brachininae)

This paper provides the first comparative anatomical study of the explosive pygidial defensive system of bombardier beetles in species classified in three brachinine subtribes: Brachinus (Brachinina), Pheropsophus (Pheropsophina) and Aptinus (Aptinina). We investigated the morphology and ultrastructure of this system using optical, fluorescence, and focused ion beam (FIB/SEM) microscopy. In doing so, we characterized and comparatively discussed: (1) the ultrastructure of the gland tissues producing hydroquinones and hydrogen peroxide (secretory lobes), and those producing catalases and peroxidases (accessory glands); (2) the complex anatomy of the collecting duct; (3) the arrangement of the muscular bundles and the folding of the cuticle of the reservoir, suggesting a functional division of this chamber (dynamic part and storage part); (4) the great structural diversity of sculpticles inside the reaction chamber, where we could recognize six main types of microsculpture located in specific districts of the chamber. Additionally, using fluorescence microscopy, we highlighted the presence of resilin in two structures strongly subjected to mechanical stress during the discharge, the valve and the turrets of the reaction chamber. The results of this paper give a solid anatomic overview of the most popular beetle defensive system, contributing to the debate on its evolution within the Carabidae.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3–4 and 8–9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner.

3D and 2D structural characterization of 1D Al/Al2 O3 biphasic nanostructures

1D Al/Al2 O3 nanostructures have been synthesized by chemical vapour deposition (CVD) of the molecular precursor [(t) BuOAlH2 ]2 . The deposited nanostructures grow chaotically on the substrate forming a layer with a high porosity (80%). Depending on the deposition time, diverse nanostructured surfaces with different distribution densities were achieved. A three-dimensional (3D) reconstruction has been evaluated for every nanostructure density using the Focus Ion Beam (FIB) tomography technique and reconstruction software tools. Several structural parameters such as porosity, Euler number, geometrical tortuosity and aspect ratio have been quantified through the analysis with specified software of the reconstructions. Additionally roughness of the prepared surfaces has been characterized at micro- and nanoscale using profilometry and AFM techniques, respectively. While high aspects ratio around 20-30 indicates a strong anisotropy in the structure, high porosity values (around 80%) is observed as a consequence of highly tangled geometry of such 1D nanostructures.

Three-dimensional reconstruction of the human skeletal muscle mitochondrial network as a tool to assess mitochondrial content and structural organization

AIM

Mitochondria undergo continuous changes in shape as result of complex fusion and fission processes. The physiological relevance of mitochondrial dynamics is still unclear. In the field of mitochondria bioenergetics, there is a need of tools to assess cell mitochondrial content. To develop a method to visualize mitochondrial networks in high resolution and assess mitochondrial volume.

METHODS

Confocal fluorescence microscopy imaging of mitochondrial network stains in human vastus lateralis single muscle fibres and focused ion beam/ scanning electron microscopy (FIB/SEM) imaging, combined with 3D reconstruction was used as a tool to analyse mitochondrial morphology and measure mitochondrial fractional volume.

RESULTS

Most type I and type II muscle fibres have tubular highly interconnected profusion mitochondria, which are thicker and more structured in type I muscle fibres (Fig. 1). In some muscle fibres, profission-isolated ellipsoid-shaped mitochondria were observed. Mitochondrial volume was significantly higher in type I muscle fibres and showed no correlation with any of the investigated molecular and biochemical mitochondrial measurements (Fig. 2). Three-dimensional reconstruction of FIB/SEM data sets shows that some subsarcolemmal mitochondria are physically interconnected with some intermyofibrillar mitochondria (Fig. 3).

CONCLUSION

Two microscopy methods to visualize skeletal muscle mitochondrial networks in 3D are described and can be used as tools to investigate mitochondrial dynamics in response to life-style interventions and/or in certain pathologies. Our results question the classification of mitochondria into subsarcolemmal and intermyofibrillar pools, as they are physically interconnected.

Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis

The biggest problem when analyzing the brain is that its synaptic connections are extremely complex. Generally, the billions of neurons making up the brain exchange information through two types of highly specialized structures: chemical synapses (the vast majority) and so-called gap junctions (a substrate of one class of electrical synapse). Here we are interested in exploring the three-dimensional spatial distribution of chemical synapses in the cerebral cortex. Recent research has showed that the three-dimensional spatial distribution of synapses in layer III of the neocortex can be modeled by a random sequential adsorption (RSA) point process, i.e., synapses are distributed in space almost randomly, with the only constraint that they cannot overlap. In this study we hypothesize that RSA processes can also explain the distribution of synapses in all cortical layers. We also investigate whether there are differences in both the synaptic density and spatial distribution of synapses between layers. Using combined focused ion beam milling and scanning electron microscopy (FIB/SEM), we obtained three-dimensional samples from the six layers of the rat somatosensory cortex and identified and reconstructed the synaptic junctions. A total volume of tissue of approximately 4500μm(3) and around 4000 synapses from three different animals were analyzed. Different samples, layers and/or animals were aggregated and compared using RSA replicated spatial point processes. The results showed no significant differences in the synaptic distribution across the different rats used in the study. We found that RSA processes described the spatial distribution of synapses in all samples of each layer. We also found that the synaptic distribution in layers II to VI conforms to a common underlying RSA process with different densities per layer. Interestingly, the results showed that synapses in layer I had a slightly different spatial distribution from the other layers.