Genetically encoded barcodes for correlative volume electron microscopy.

While genetically encoded reporters are common for fluorescence microscopy, equivalent multiplexable gene reporters for electron microscopy (EM) are still scarce. Here, by installing a variable number of fixation-stable metal-interacting moieties in the lumen of encapsulin nanocompartments of different sizes, we developed a suite of spherically symmetric and concentric barcodes (EMcapsulins) that are readable by standard EM techniques. Six classes of EMcapsulins could be automatically segmented and differentiated. The coding capacity was further increased by arranging several EMcapsulins into distinct patterns via a set of rigid spacers of variable length. Fluorescent EMcapsulins were expressed to monitor subcellular structures in light and EM. Neuronal expression in Drosophila and mouse brains enabled the automatic identification of genetically defined cells in EM. EMcapsulins are compatible with transmission EM, scanning EM and focused ion beam scanning EM. The expandable palette of genetically controlled EM-readable barcodes can augment anatomical EM images with multiplexed gene expression maps.

Retinal horizontal cells use different synaptic sites for global feedforward and local feedback signaling.

In the outer plexiform layer (OPL) of the mammalian retina, cone photoreceptors (cones) provide input to more than a dozen types of cone bipolar cells (CBCs). In the mouse, this transmission is modulated by a single horizontal cell (HC) type. HCs perform global signaling within their laterally coupled network but also provide local, cone-specific feedback. However, it is unknown how HCs provide local feedback to cones at the same time as global forward signaling to CBCs and where the underlying synapses are located. To assess how HCs simultaneously perform different modes of signaling, we reconstructed the dendritic trees of five HCs as well as cone axon terminals and CBC dendrites in a serial block-face electron microscopy volume and analyzed their connectivity. In addition to the fine HC dendritic tips invaginating cone axon terminals, we also identified "bulbs," short segments of increased dendritic diameter on the primary dendrites of HCs. These bulbs are in an OPL stratum well below the cone axon terminal base and make contacts with other HCs and CBCs. Our results from immunolabeling, electron microscopy, and glutamate imaging suggest that HC bulbs represent GABAergic synapses that do not receive any direct photoreceptor input. Together, our data suggest the existence of two synaptic strata in the mouse OPL, spatially separating cone-specific feedback and feedforward signaling to CBCs. A biophysical model of a HC dendritic branch and voltage imaging support the hypothesis that this spatial arrangement of synaptic contacts allows for simultaneous local feedback and global feedforward signaling by HCs.

Double Cones and the Diverse Connectivity of Photoreceptors and Bipolar Cells in an Avian Retina.

Double cones are the most common photoreceptor cell type in most avian retinas, but their precise functions remain a mystery. Among their suggested functions are luminance detection, polarized light detection, and light-dependent, radical pair-based magnetoreception. To better understand the function of double cones, it will be crucial to know how they are connected to the neural network in the avian retina. Here we use serial sectioning, multibeam scanning electron microscopy to investigate double-cone anatomy and connectivity with a particular focus on their contacts to other photoreceptor and bipolar cells in the chicken retina. We found that double cones are highly connected to neighboring double cones and with other photoreceptor cells through telodendria-to-terminal and telodendria-to-telodendria contacts. We also identified 15 bipolar cell types based on their axonal stratifications, photoreceptor contact pattern, soma position, and dendritic and axonal field mosaics. Thirteen of these 15 bipolar cell types contacted at least one or both members of the double cone. All bipolar cells were bistratified or multistratified. We also identified surprising contacts between other cone types and between rods and cones. Our data indicate a much more complex connectivity network in the outer plexiform layer of the avian retina than originally expected.SIGNIFICANCE STATEMENT Like in humans, vision is one of the most important senses for birds. Here, we present the first serial section multibeam scanning electron microscopy dataset from any bird retina. We identified many previously undescribed rod-to-cone and cone-to-cone connections. Surprisingly, of the 15 bipolar cell types we identified, 11 received input from rods and 13 of 15 received at least part of their input from double cones. Therefore, double cones seem to play many different and important roles in avian retinal processing, and the neural network and thus information processing in the outer retina are much more complex than previously expected. These fundamental findings will be very important for several fields of science, including vertebrate vision, avian magnetoreception, and comparative neuroanatomy.

FRET-based Tau seeding assay does not represent prion-like templated assembly of Tau filaments.

Tau aggregation into amyloid fibers based on the cross-beta structure is a hallmark of several Tauopathies, including Alzheimer Disease (AD). Trans-cellular propagation of Tau with pathological conformation has been suggested as a key disease mechanism. This is thought to cause the spreading of Tau pathology in AD by templated conversion of naive Tau in recipient cells into a pathological state, followed by assembly of pathological Tau fibers, similar to the mechanism of nucleated polymerization proposed for prion pathogenesis. In cell cultures, the process is often monitored by a FRET assay where the recipient cell expresses the Tau repeat domain (TauRD) with a pro-aggregant mutation, fused to GFP-based FRET pairs. Since the size of the reporter GFP (barrel of ~ 3 nm × 4 nm) is ~ 7 times larger than the ß-strand distance (0.47 nm), this points to a potential steric clash. Hence, we investigated the influence of the GFP tag on TauFL or TauRD aggregation. Using biophysical methods (light scattering, atomic force microscopy (AFM), and scanning-transmission electron microscopy (STEM)), we found that the assembly of TauRD-GFP was severely inhibited and incompatible with that of Alzheimer filaments. These observations argue against the hypothesis that the propagation of Tau pathology in AD is caused by the prion-like templated aggregation of Tau protein, transmitted via cell-to-cell spreading of Tau. Thus, even though the observed local increase of FRET in recipient cells may be a valid hallmark of a pathological reaction, our data argue that it is caused by a process distinct from assembly of TauRD filaments.

Extracellular Vesicle Isolation and Characterization from Periprosthetic Joint Synovial Fluid in Revision Total Joint Arthroplasty.

Extracellular vesicles (EVs) comprise an as yet insufficiently investigated intercellular communication pathway in the field of revision total joint arthroplasty (RTJA). This study examined whether periprosthetic joint synovial fluid contains EVs, developed a protocol for their isolation and characterized them with respect to quantity, size, surface markers as well as documented their differences between aseptic implant failure (AIF) and periprosthetic joint infection (PJI). EV isolation was accomplished using ultracentrifugation, electron microscopy (EM) and nanoparticle tracking analysis evaluated EV presence as well as particle size and quantity. EV surface markers were studied by a bead-based multiplex analysis. Using our protocol, EM confirmed the presence of EVs in periprosthetic joint synovial fluid. Higher EV particle concentrations and decreased particle sizes were apparent for PJI. Multiplex analysis confirmed EV-typical surface epitopes and revealed upregulated CD44 and HLA-DR/DP/DQ for AIF, as well as increased CD40 and CD105. Our protocol achieved isolation of EVs from periprosthetic joint synovial fluid, confirmed by EM and multiplex analysis. Characterization was documented with respect to size, concentration and epitope surface signature. Our results indicate various differences between PJI and AIF EVs. This pilot study enables new research approaches and rising diagnostic opportunities in the field of RTJA.

Supramolecular aptamer nano-constructs for receptor-mediated targeting and light-triggered release of chemotherapeutics into cancer cells.

Platforms for targeted drug-delivery must simultaneously exhibit serum stability, efficient directed cell internalization, and triggered drug release. Here, using lipid-mediated self-assembly of aptamers, we combine multiple structural motifs into a single nanoconstruct that targets hepatocyte growth factor receptor (cMet). The nanocarrier consists of lipidated versions of a cMet-binding aptamer and a separate lipidated GC-rich DNA hairpin motif loaded with intercalated doxorubicin. Multiple 2',6'-dimethylazobenzene moieties are incorporated into the doxorubicin-binding motif to trigger the release of the chemotherapeutics by photoisomerization. The lipidated DNA scaffolds self-assemble into spherical hybrid-nanoconstructs that specifically bind cMet. The combined features of the nanocarriers increase serum nuclease resistance, favor their import into cells presumably mediated by endocytosis, and allow selective photo-release of the chemotherapeutic into the targeted cells. cMet-expressing H1838 tumor cells specifically internalize drug-loaded nanoconstructs, and subsequent UV exposure enhances cell mortality. This modular approach thus paves the way for novel classes of powerful aptamer-based therapeutics.

The SWI/SNF subunit Bcl7a contributes to motor coordination and Purkinje cell function.

Chromatin remodelers have emerged as prominent regulators of epigenetic processes and potential drivers of various human pathologies. The multi-subunit chromatin-remodeling SWI/SNF complex determines gene expression programs and, consequently, contributes to the differentiation, maturation and plasticity of neurons. Here, we investigate the elusive biological function of Bcl7a and Bcl7b, two newly identified subunits of the SWI/SNF complex that are highly expressed throughout the brain. We generated ubiquitous and neuron-specific Bcl7a and Bcl7b single and double knockout mice. We provide evidence that Bcl7b is dispensable for animal survival as well as behavioral plasticity. Conversely, ubiquitous Bcl7a knockout results in perinatal lethality, while genetic deletion of Bcl7a in postmitotic neurons elicits motor abnormalities and affects dendritic branching of Purkinje cells, with no obvious synergistic relationship with Bcl7b. Collectively, our findings reveal novel insights into the cellular processes linked to BCL7-containing SWI/SNF complexes and their unrecognized roles in the brain.

Near-field study on the transition from localized to propagating plasmons on 2D nano-triangles.

In this manuscript we report on a near field study of two-dimensional plasmonic gold nano-triangles using electron energy loss spectroscopy in combination with scanning transmission electron microscopy, as well as discontinuous Galerkin time-domain computations. With increasing nano-triangle size, we observe a transition from localized surface plasmons on small nano-triangles to non-resonant propagating surface plasmon polaritons on large nano-triangles. Furthermore we demonstrate that nano-triangles with a groove cut can support localized as well as propagating plasmons in the same energy range.

The release and trans-synaptic transmission of Tau via exosomes.

BACKGROUND: Tau pathology in AD spreads in a hierarchical pattern, whereby it first appears in the entorhinal cortex, then spreads to the hippocampus and later to the surrounding areas. Based on this sequential appearance, AD can be classified into six stages ("Braak stages"). The mechanisms and agents underlying the progression of Tau pathology are a matter of debate. Emerging evidence indicates that the propagation of Tau pathology may be due to the transmission of Tau protein, but the underlying pathways and Tau species are not well understood. In this study we investigated the question of Tau spreading via small extracellular vesicles called exosomes. METHODS: Exosomes from different sources were analyzed by biochemical methods and electron microscopy (EM) and cryo-EM. Microfluidic devices that allow the culture of cell populations in different compartments were used to investigate the spreading of Tau. RESULTS: We show that Tau protein is released by cultured primary neurons or by N2a cells overexpressing different Tau constructs via exosomes. Neuron-derived exosomal Tau is hypo-phosphorylated, compared with cytosolic Tau. Depolarization of neurons promotes release of Tau-containing exosomes, highlighting the importance of neuronal activity. Using microfluidic devices we show that exosomes mediate trans-neuronal transfer of Tau depending on synaptic connectivity. Tau spreading is achieved by direct transmission of exosomes between neurons. In organotypic hippocampal slices, Tau-containing exosomes in conditioned medium are taken up by neurons and microglia, not astrocytes. In N2a cells, Tau assemblies are released via exosomes. They can induce inclusions of other Tau molecules in N2a cells expressing mutant human Tau. We also studied exosomes from cerebrospinal fluid in AD and control subjects containing monomeric and oligomeric Tau. Split-luciferase complementation reveals that exosomes from CSF can promote Tau aggregation in cultured cells. CONCLUSION: Our study demonstrates that exosomes contribute to trans-synaptic Tau transmission, and thus offer new approches to control the spreading of pathology in AD and other tauopathies.

Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics.

The visual pigment rhodopsin belongs to the family of G protein-coupled receptors that can form higher oligomers. It is controversial whether rhodopsin forms oligomers and whether oligomers are functionally relevant. Here, we study rhodopsin organization in cryosections of dark-adapted mouse rod photoreceptors by cryoelectron tomography. We identify four hierarchical levels of organization. Rhodopsin forms dimers; at least ten dimers form a row. Rows form pairs (tracks) that are aligned parallel to the disk incisures. Particle-based simulation shows that the combination of tracks with fast precomplex formation, i.e. rapid association and dissociation between inactive rhodopsin and the G protein transducin, leads to kinetic trapping: rhodopsin first activates transducin from its own track, whereas recruitment of transducin from other tracks proceeds more slowly. The trap mechanism could produce uniform single-photon responses independent of rhodopsin lifetime. In general, tracks might provide a platform that coordinates the spatiotemporal interaction of signaling molecules.

CRIS-a novel cAMP-binding protein controlling spermiogenesis and the development of flagellar bending.

The second messengers cAMP and cGMP activate their target proteins by binding to a conserved cyclic nucleotide-binding domain (CNBD). Here, we identify and characterize an entirely novel CNBD-containing protein called CRIS (cyclic nucleotide receptor involved in sperm function) that is unrelated to any of the other members of this protein family. CRIS is exclusively expressed in sperm precursor cells. Cris-deficient male mice are either infertile due to a lack of sperm resulting from spermatogenic arrest, or subfertile due to impaired sperm motility. The motility defect is caused by altered Ca(2+) regulation of flagellar beat asymmetry, leading to a beating pattern that is reminiscent of sperm hyperactivation. Our results suggest that CRIS interacts during spermiogenesis with Ca(2+)-regulated proteins that--in mature sperm--are involved in flagellar bending.

From isolated metaatoms to photonic metamaterials: evolution of the plasmonic near-field.

Metamaterials are artificial media which can provide optical properties not available from natural materials. These properties often result from the resonant excitation of plasmonic modes in the metallic building blocks ("metaatoms") of the metamaterial. Electromagnetic interactions between the metaatoms significantly modify the resonances of the individual metaatoms and influence the optical properties of the whole metamaterial. To better understand these interactions, we study in this Letter the evolution of the plasmonic near-field in the course of the transition from an isolated metaatom, in our case a split-ring resonator (SRR), to a photonic metamaterial via electron energy-loss spectroscopy. For small SRR ensembles, we observe the formation of discrete optical bright and dark modes due to coupling of the metaatoms. Large SRR arrays reveal a quasi-continuum of modes in the interior and distinct edge modes at the boundaries of the array. Our experimental results are in excellent agreement with numerical calculations.

Fabrication of Fresnel zone plates by ion-beam lithography and application as objective lenses in extreme ultraviolet microscopy at 13 nm wavelength.

Fresnel zone plates are used for imaging at extreme ultraviolet and soft x-ray wavelengths. Fabricating these zone plates is challenging due to small structure sizes (<150 nm) and complex nanostructuring processes. Fabrication techniques such as electron-beam lithography followed by etching and electroplating processes have been developed over the years. We are reporting on the development of a technique incorporating focused gallium ion-beam lithography to fabricate Fresnel zone plates with 120 nm outermost structure size in a process that combines pattern exposure and structure transfer in one single step. The fabricated zone plates were successfully applied in a microscopic setup at λ=13 nm wavelength.

Atomic vapor deposition approach to In2O3 thin films.

In2O3 thin films were grown by atomic vapor deposition (AVD) on Si(100) and glass substrates from a tris-guanidinate complex of indium [In(N(i)Pr2guanid)3] under an oxygen atmosphere. The effects of the growth temperature on the structure, morphology and composition of In2O3 films were investigated. X-ray diffraction (XRD) measurements revealed that In2O3 films deposited in the temperature range 450-700 degreesC crystallised in the cubic phase. The film morphology, studied by scanning electron microscopy (SEM) and atomic force microscopy (AFM), was strongly dependent on the substrate temperature. Stoichiometric In2O3 films were formed under optimised processing conditions as was confirmed by X-ray photoelectron and X-ray excited Auger electron spectroscopies (XPS, XE-AES), as well as by Rutherford backscattering spectrometry (RBS). Finally, optical properties were investigated by photoluminescence (PL) measurements, spectroscopic ellipsometry (SE) and optical absorption. In2O3 films grown on glass exhibited excellent transparency (approximately 90%) in the Visible (Vis) spectral region.

Interdigitating biocalcite dendrites form a 3-D jigsaw structure in brachiopod shells.

We report a newly discovered dense microstructure of dendrite-like biocalcite that is formed by marine organisms. High spatial resolution electron backscatter diffraction (EBSD) was carried out under specific analytical conditions (15 and 10 kV) on the primary layer of the modern brachiopod Gryphus vitreus. The primary layer of modern brachiopods, previously termed nanocrystalline, is formed by an array of concave/convex calcite grains with interdigitated recesses and protrusions of abutting crystals without any cavities in or between the dendrites. The interface topology of this structure ranges from a few tens of nanometres to tens of micrometres, giving a nanoscale structure to the material fabric. The dendritic grains show a spread of crystallographic orientation of several degrees and can thus be referred to as mesocrystals. Individual dendritic mesocrystals reach sizes in one dimension larger than 20 µm. The preferred crystallographic orientation is similar in the primary and adjacent fibrous shell layers, even though these two layers show completely different crystal morphologies and grain boundary topologies. This observation indicates that two separate control mechanisms are active when the primary and the fibrous shell layers are formed. We propose a growth model for the interdigitated dendritic calcite grain structure based on a precursor of vesicles filled with amorphous calcium carbonate (ACC).

Malonate complexes of dysprosium: synthesis, characterization and application for LI-MOCVD of dysprosium containing thin films.

A series of malonate complexes of dysprosium were synthesized as potential metalorganic precursors for Dy containing oxide thin films using chemical vapor deposition (CVD) related techniques. The steric bulkiness of the dialkylmalonato ligand employed was systematically varied and its influence on the resulting structural and physico-chemical properties that is relevant for MOCVD was studied. Single crystal X-ray diffraction analysis revealed that the five homoleptic tris-malonato Dy complexes (1-5) are dimers with distorted square-face bicapped trigonal-prismatic geometry and a coordination number of eight. In an attempt to decrease the nuclearity and increase the solubility of the complexes in various solvents, the focus was to react these dimeric complexes with Lewis bases such as 2,2'-biypridyl and pyridine (6-9). This resulted in monomeric tris-malonato mono Lewis base adduct complexes with improved thermal properties. Finally considering the ease of synthesis, the monomeric nature and promising thermal characteristics, the silymalonate adduct complex [Dy(dsml)(3)bipy] (8) was selected as single source precursor for growing DySi(x)O(y) thin films by liquid injection metalorganic chemical vapor deposition (LI-MOCVD) process. The as-deposited films were analyzed for their morphology and composition by scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analysis, Rutherford backscattering (RBS) analysis and X-ray photoelectron spectroscopy.

Measurement of submicrometre diameters of tapered optical fibres using harmonic generation.

Applications of subwavelength-diameter optical fibres in nonlinear optics require precise knowledge of the submicrometre fibre waist diameter. We demonstrate a new technique for optical measurement of the diameter based on second- and third-harmonic generation with an accuracy of better than 2%. To generate the harmonic light, inter-modal phase matching must be achieved. We find that the phase-matching condition allows us to unambiguously deduce the fibre diameter from the wavelength of the harmonic light. High-resolution scanning electron microscope imaging is used to verify the results.

Using human neural crest-derived progenitor cells to investigate osteogenesis: an in vitro study.

Human tooth contains a distinct population of neural crest-derived progenitor cells (dNC-PCs) which are known to give rise to specialized daughter cells of an osteogenic lineage. We hypothesised that dNC-PCs could develop into neural crest-derived bone in a self-propagating and extracorporal culture system. Thus, we examined the three-dimensional structure obtained from osteogenic-stimulated dNC-PCs by morphological, biochemical and spectroscopic methods. After the onset of stimulation, cells formed a multilayer with outer cells covering the surface and inner cells secreting a hyaline matrix. With prolonged culture, multilayers contracted and formed a three-dimensional construct which subsequently converted to a calcified mass. Differentiation of progenitor cells was associated with apoptosis. Cell types which survived were smooth muscle actin-positive cells and bone-like cells. The expression of osteoblastic markers and the secretion of a collagenous matrix indicate that the bone cells had acquired their functional phenotype. Furthermore, these cells produced and secreted membrane-bound vesicles into the newly forming matrix. Consequently, an early biomineralized extracellular matrix was found with calcium phosphate deposits being associated with the newly formed collagen matrix framework. The molar calcium-phosphorus-ratio of the mineralized collagen indicated that amorphous calcium phosphate was present within this matrix. The data suggest that stimulated cultures of dNC-PCs are able to recapitulate some processes of the early phase of osteogenesis.

The morphology of anisotropic 3D-printed hydroxyapatite scaffolds.

Three-dimensional (3D) scaffolds with tailored pores ranging from the nanometer to millimeter scale can support the reconstruction of centimeter-sized osseous defects. Three-dimensional-printing processes permit the voxel-wise fabrication of scaffolds. The present study rests upon 3D-printing with nano-porous hydroxyapatite granulates. The cylindrical design refers to a hollow bone with higher density at the periphery. The millimeter-wide central channel follows the symmetry axis and connects the perpendicularly arranged micro-pores. Synchrotron radiation-based micro computed tomography has served for the non-destructive characterization of the scaffolds. The 3D data treatment is essential, since, for example, the two-dimensional distance maps overestimate the mean distances to the material by 33-50% with respect to the 3D analysis. The scaffolds contain 70% micrometer-wide pores that are interconnected. Using virtual spheres, which might be related to the cells migrating along the pores, the central channel remains accessible through the micro-pores for spheres with a diameter of up to (350+/-35)mum. Registering the tomograms with their 3D-printing matrices has yielded the almost isotropic shrinking of (27+/-2)% owing to the sintering process. This registration also allows comparing the design and tomographic data in a quantitative manner to extract the quality of the fabricated scaffolds. Histological analysis of the scaffolds seeded with osteogenic-stimulated progenitor cells has confirmed the suitability of the 3D-printed scaffolds for potential clinical applications.

Synthesis of flexible, ultrathin gold nanowires in organic media.

Gold nanoparticles are very interesting because of their potential applications in microelectronics, optical devices, analytical detection schemes, and biomedicine. Though shape control has been achieved in several polar solvents, the capability to prepare organosols containing elongated gold nanoparticles has been very limited. In this work we report a novel, simplified method to produce long, thin gold nanowires in an organic solvent (oleylamine), which can be readily redispersed into nonpolar organic solvents. These wires have a characteristic flexible, hairy morphology arising from a small thickness (<2 nm) and an enormous length (up to several micrometers), with the possibility of adjusting the dimensions through modification of the growth conditions, in particular, the gold salt concentration. Despite their extreme aspect ratio, the wires are stable in solution for long periods of time but easily break when irradiated with high-energy electron beams during transmission electron microscopy.