Fluorescently Labelled Silica Coated Gold Nanoparticles as Fiducial Markers for Correlative Light and Electron Microscopy

Antibacterial potentials of carbon dots immobilized on chitosan and glass surfaces

Due to their antibacterial activity, chitosan‑carbon dot composites possess great potential for pharmaceuticals, medicine, and food preservation. Conducting a comprehensive study of the interactions between chitosan, carbon dots, and bacteria is crucial to understanding the processes behind applying these composites. This study aimed to immobilize carbon dots (C-dots) synthesized from Elaeagnus angustifolia fruits on chitosan and glass microbeads' surfaces, to characterize the test materials obtained after synthesis and immobilization, and to investigate their antibacterial potentials. C-dot synthesis was carried out from water extract in an acidic medium with the help of microwave irradiation, and their structural and optical properties were characterized by TEM, XRD, FT-IR, UV-vis, Zeta potential, and fluorescence methods. The surface of the glass microbeads was first activated and functionalized with surface amine groups with a silaning agent. C-dots were immobilized on both glass and chitosan microbeads using a crosslinking agent. Antibacterial potentials of nine different test materials, obtained before or after immobilization, were evaluated both qualitatively (MIC and MBC) and quantitatively (GI50) on E. coli, S. typhimurium, B. subtilis, and S. aureus, with the standard broth microdilution method. FT-IR and SEM-EDX analyses showed that C-dots were immobilized on chitosan (˂1 mm) and glass (˂100 μm) microbead surfaces. C-dots reduced the cell viability by ~25 % on S. typhimurium and B. subtilis (MIC = 25 mg/mL). It was also found that the highest antibacterial effect was recorded for C-dots-glass microbeads, which had a toxic effect of 43 % on S. aureus. In addition, binding C-dots to glass microbeads increased the antibacterial effect selectively in Gram-positive bacteria, while binding to chitosan microbeads was effective in all bacteria. The study showed that the antibacterial potential of C-dots-chitosan microbeads is more effective than C-dots-glass microbeads. C-dots could be used as carbon-based nanomaterials in antibacterial surface preparation once immobilized.

Focused ion beam-scanning electron microscopy provides novel insights of drug delivery phenomena

Scanning electron microscopy (SEM) has long been a standard tool for morphological analyses, providing sub micrometer resolution of pharmaceutical formulations. However, analysis of internal morphologies of such formulations can often be biased due to the introduction of artifacts that originate from sample preparation. A recent advancement in SEM, is the focused ion beam scanning electron microscopy (FIB-SEM). This technique uses a focused ion beam (FIB) to remove material with nanometer precision, to provide virtually sample-independent access to sub-surface structures. The FIB can be combined with SEM imaging capabilities within the same instrumentation. As a powerful analytical tool, electron microscopy and FIB-milling are performed sequentially to produce high-resolution 3D models of structural peculiarities of diverse drug delivery systems or their behavior in a biological environment, i.e. intracellular or -tissue distribution. This review paper briefly describes the technical background of the method, outlines a wide array of potential uses within the drug delivery field, and focuses on intracellular transport where high-resolution images are an essential tool for mechanistical insights.

Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy

Fluorescent biosensors are valuable tools to monitor protein activities and the functional state of organelles in live cells. However, the information provided by fluorescent microscopy (FM) is mostly limited in resolution and lacks ultrastructural context information. Protein activities are confined to organelle zones with a distinct membrane morphology, which can only be seen by electron microscopy (EM). EM, however, intrinsically lacks information on protein activities. The lack of methods to integrate these two imaging modalities has hampered understanding the functional organization of cellular organelles. Here we introduce "functional correlative microscopy" (functional CLEM) to directly infer functional information from live cells to EM with nanometer resolution. We label and visualize live cells with fluorescent biosensors after which they are processed for EM and imaged using a volume electron microscopy technique. Within a single dataset we correlate hundreds of fluorescent spots enabling quantitative analysis of the functional-ultrastructural data. We employ our method to monitor essential functional parameters of late endo-lysosomal compartments, i.e., pH, calcium, enzyme activities and cholesterol content. Our data reveal a steep functional difference in enzyme activity between late endosomes and lysosomes and unexpectedly high calcium levels in late endosomes. The presented CLEM workflow is compatible with a large repertoire of probes and paves the way for large scale functional studies of all types of cellular structures.

In situ single particle characterization of the themoresponsive and co-nonsolvent behavior of PNIPAM microgels and silica@PNIPAM core-shell colloids

Poly(N-isopropylacrylamide) (PNIPAM) microgels and PNIPAM colloidal shells attract continuous strong interest due to their thermoresponsive behavior, as their size and properties can be tuned by temperature. The direct single particle observation and characterization of pure, unlabeled PNIPAM microgels in their native aqueous environment relies on imaging techniques that operate either at interfaces or in cryogenic conditions, thus limiting the observation of their dynamic nature. Liquid Cell (Scanning) Transmission Electron Microscopy (LC-(S) TEM) imaging allows the characterization of materials and dynamic processes such as nanoparticle growth, etching, and diffusion, at nanometric resolution in liquids. Here we show that via a facile post-synthetic in situ polymer labelling step with high-contrast marker core-shell Au@SiO₂ nanoparticles (NPs) it is possible to determine the full volume of PNIPAM microgels in water. The labelling allowed for the successful characterization of the thermoresponsive behavior of PNIPAM microgels and core shell silica@PNIPAM hybrid microgels, as well as the co-nonsolvency of PNIPAM in aqueous alcoholic solutions. The interplay between electron beam irradiation and PNIPAM systems in water resulted in irreversible shrinkage due to beam induced water radiolysis products, which in turn also affected the thermoresponsive behavior of PNIPAM. The addition of 2-propanol as radical scavenger improved PNIPAM stability in water under electron beam irradiation.

Quercetin Loaded Silica and Gold - Coated Silica Nanoparticles: Characterization, Evaluation and Comparison of Their in vitro Characteristics

Herein, silica nanoparticles (NPs) and gold-silica NPs were loaded with the anti-cancer agent quercetin (QC) to produce silica NPs-QC and gold coated silica NPs-QC, respectively. The nanosystems were characterized using transmission electron microscopy (TEM), dynamic light scattering (DLS) and Fourier transform infrared (FTIR). Drug encapsulation efficiency (EE), loading capacity (LC) and release rate were measured using UV spectrophotometer. The drug was encapsulated in silica NPs in a high percentage (71%) and reduced by about 16% after gold coating. The mean particle size increased after coating and QC loading with a polydispersity index (PDI) between (∼ 0.2 - 0.6) and negative zeta potential (-13 to - 15 mV). The intensity of FTIR peaks of silica NPs has been significantly decreased upon gold coating indicating a successful attachment of the gold thin layer. The drug release was slightly faster from coated compared to uncoated NPs but both slower than free QC. The percentages of their cell toxicity were almost the same but lower than free QC and generally were higher against HeLa cells compared to fibroblast cells. Both nanosystems could be considered as promising nanocarriers with reasonable EE, slower release rate and lower toxicity compared to the free drug.

Novel metal enhanced dual-mode fluorometric and SERS aptasensor incorporating a heterostructure nanoassembly for ultrasensitive T-2 toxin detection

Fluorescent gold (Au) nanostructures have emerged as burgeoning materials to fabricate nanomaterial assemblies which play a vital role in improving the detection sensitivity and specificity for various biomolecules. In this work, a fluorescence labelled (Rhodamine-B-Isothiocyanate) silica shell with Au metal core (AuNPs@PVP@RITC@SiO₂) and a graphene-Au nanostar nanocomposite (rGO-AuNS) are presented as a metal enhanced fluorescence (MEF) material and Raman signal enhancer, respectively. Their composite (AuNPs@PVP@RITC@SiO₂NPs/rGO-AuNS) was employed as a dual-mode fluorescence (FL) and surface-enhanced Raman scattering (SERS) nanoprobe for selective and sensitive detection of T-2 toxin. To comprehend the dual-modality, a core-shell nanostructure, AuNPs@PVP@RITC@SiO₂, was functionalized with an aptamer (donor) and adsorbed on the surface of rGO-AuNS through electrostatic forces and π-π stacking which act as a FL quencher and SERS signal enhancer. When exposed to T-2 toxin, the apt-AuNPs@PVP@RITC@SiO₂NPs move away from the surface of rGO-AuNS, resulting in the restoration of FL and reduction of the SERS signal. There was distinct linearity between the T-2 toxin concentration and the dual FL and SERS signals with lower limits of detection (LOD) of 85 pM and 12 pM, as compared to the previous methods, respectively. The developed FL and SERS aptasensor presented excellent recovery ratio and RSD in wheat and maize, respectively, as compared with the standard ELISA method. The complementary performances of the developed stratagem revealed a high correlation between the FL and SERS sensing modes with exquisite detection properties.

An optimized protocol for immuno-electron microscopy of endogenous LC3

MAP1LC3/LC3 (microtubule associated protein 1 light chain 3) is widely used as marker of autophagic compartments at different stages of maturation. Electron microscopy (EM) combined with immunolabeling is the only technique that can reveal the ultrastructural identity of LC3-labeled compartments. However, immuno-EM of endogenous LC3 proteins has proven difficult. Here, we test a panel of commercially available antibodies and apply different labeling conditions to present an optimized procedure for LC3 immuno-EM. Using ultrathin cryosections and protein A-colloidal gold or gold enhancement labeling, we localize endogenous LC3 in starved cells or tissues in the presence or absence of the proton pump inhibitor bafilomycin A₁. We localize LC3 to early and late stage autophagic compartments that can be classified by their morphology. By on-section correlative light-electron microscopy (CLEM) we show that comparable fluorescent LC3-positive puncta can represent different autophagic intermediates. We also show that our approach is sufficiently robust to label endogenous LC3 simultaneously with other lysosomal and autophagy markers, LAMP1 or SQSTM1/p62, and can be used for quantitative approaches. Thus, we demonstrate that bafilomycin A₁ treatment from 2.5 up to 24 h does not inhibit fusion between autophagosomes and lysosomes, but leads to the accumulation of LC3-positive material inside autolysosomes. Together, this is the first study presenting an extensive overview of endogenous LC3 localization at ultrastructural resolution without the need for cell permeabilization and using a commercially available antibody. This provides researchers with a tool to study canonical and non-canonical roles of LC3 in native conditions.Abbreviations: BafA1: bafilomycin A₁; BSA: bovine serum albumin; BSA-c: acetylated BSA; BSA⁵: BSA conjugated to 5-nm gold particles; CLEM: correlative light-electron microscopy; EGFP: enhanced green fluorescent protein; EM: electron microscopy; FBS: fetal bovine serum; FSG: fish skin gelatin; GA: glutaraldehyde; IF: immunofluorescence; LAMP1: lysosomal associated membrane protein 1; LC3s: LC3 proteins; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; ON: overnight; PAG: protein A-conjugated gold particles; PAG1-3: PAG5, PAG10, PAG15, protein A conjugated to 1-3-, 5-, 10-, or 15-nm gold particles; PB: Sorensen's phosphate buffer; PBS: phosphate-buffered saline; PFA: paraformaldehyde; RT: room temperature.

Fluorescence CLEM in biology: historic developments and current super-resolution applications

Correlative light and electron microscopy (CLEM) is a powerful imaging approach that allows the direct correlation of information obtained on a light and an electron microscope. There is a growing interest in the application of CLEM in biology, mainly attributable to technical advances in field of fluorescence microscopy in the past two decades. In this review, we summarize the important developments in CLEM for biological applications, focusing on the combination of fluorescence microscopy and electron microscopy. We first provide a brief overview of the early days of fluorescence CLEM usage starting with the initial rise in the late 1970s and the subsequent optimization of CLEM workflows during the following two decades. Next, we describe how the engineering of fluorescent proteins and the development of super-resolution fluorescence microscopy have significantly renewed the interest in CLEM resulting in the present application of fluorescence CLEM in many different areas of cellular and molecular biology. Lastly, we present the promises and challenges for the future of fluorescence CLEM discussing novel workflows, probe development and quantification possibilities.

Bimodal endocytic probe for three-dimensional correlative light and electron microscopy

We present a bimodal endocytic tracer, fluorescent BSA-gold (fBSA-Au), as a fiducial marker for 2D and 3D correlative light and electron microscopy (CLEM) applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent BSA. The conjugate is efficiently endocytosed and distributed throughout the 3D endolysosomal network of cells and has an excellent visibility in both fluorescence microscopy (FM) and electron microscopy (EM). We demonstrate that fBSA-Au facilitates rapid registration in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryoelectron microscopy (cryo-EM). Endocytosed fBSA-Au benefits from a homogeneous 3D distribution throughout the endosomal system within the cell, does not obscure any cellular ultrastructure, and enables accurate (50-150 nm) correlation of fluorescence to EM data. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo)CLEM applications.

Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes

Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.

Recent Developments in Correlative Super-Resolution Fluorescence Microscopy and Electron Microscopy

The recently developed correlative super-resolution fluorescence microscopy (SRM) and electron microscopy (EM) is a hybrid technique that simultaneously obtains the spatial locations of specific molecules with SRM and the context of the cellular ultrastructure by EM. Although the combination of SRM and EM remains challenging owing to the incompatibility of samples prepared for these techniques, the increasing research attention on these methods has led to drastic improvements in their performances and resulted in wide applications. Here, we review the development of correlative SRM and EM (sCLEM) with a focus on the correlation of EM with different SRM techniques. We discuss the limitations of the integration of these two microscopy techniques and how these challenges can be addressed to improve the quality of correlative images. Finally, we address possible future improvements and advances in the continued development and wide application of sCLEM approaches.

Organic building blocks at inorganic nanomaterial interfaces

This tutorial review presents our perspective on designing organic molecules for the functionalization of inorganic nanomaterial surfaces, through the model of an "anchor-functionality" paradigm. This "anchor-functionality" paradigm is a streamlined design strategy developed from a comprehensive range of materials (e.g., lead halide perovskites, II-VI semiconductors, III-V semiconductors, metal oxides, diamonds, carbon dots, silicon, etc.) and applications (e.g., light-emitting diodes, photovoltaics, lasers, photonic cavities, photocatalysis, fluorescence imaging, photo dynamic therapy, drug delivery, etc.). The structure of this organic interface modifier comprises two key components: anchor groups binding to inorganic surfaces and functional groups that optimize their performance in specific applications. To help readers better understand and utilize this approach, the roles of different anchor groups and different functional groups are discussed and explained through their interactions with inorganic materials and external environments.

Diatom Mediated Production of Fluorescent Flower Shaped Silver-Silica Nanohybrid

Fabrication of flower-like nanostructures are gaining attention because of their high surface/volume ratio and extensive adsorption capacity. In the present investigation, flower-shaped, autofluorescent silver-silica (Ag-SiO₂) hybrid nanoparticles have been fabricated exploiting diatoms as a source of nanosilica. Two different species of Gedaniella including G. flavovirens and G. mutabilis showed their efficacy in synthesizing fluorescent Ag-SiO₂ nanoflowers (NFs) and nanospheres (NSs) against 9 mM silver nitrate solution, respectively. The biogenic nanoconjugate (Ag-SiO₂) was characterized by Uv-vis spectroscopy, energy dispersive X-ray spectroscopy (EDS), scanning (SEM) and transmission (TEM) electron microscopy. Production of Ag-SiO₂ hybrid nanoparticle was confirmed by observing both Ag and Si signals from a single nanoparticle in an EDS study. The broad and single absorption band at ~420 nm in Uv-vis spectroscopy confirmed proper miscibility and production of hybrid nanoparticles. The Ag-SiO₂ nanohybrids revealed autofluorescent property under the blue light region (excitation ~450–490 nm). SEM images of particles synthesized by G. flavovirens revealed the production of microscopic flower shaped Ag-SiO₂ particles with several layers of petals. A TEM study confirmed that the synthesized Ag-SiO₂ NFs are variable in size with 100–500 nm in diameter. Decolorization of methylene blue after exposure to Ag-SiO₂ particles confirmed catalytic activity of synthesized nanostructures. This eco-friendly method provides a new dimension in nanobiotechnology for biogenesis of such hierarchical nanostructure in a cost-effective way.

Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures

3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).

Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy

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The use of a negative bias potential was empirically optimized for tissue imaging with SEM.

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Optimized bias potential leads to a factor 20 increase in imaging speeds as well as an order of magnitude improvement to SNR.

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SNR increase results from a combination of BSE acceleration and detector response.

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Similar increases to SNR can be obtained when a magnetic immersion field is combined with a negative bias potential.

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Stage bias can be applied within an integrated fluorescence and electron microscope allowing for fast correlative imaging of tissue sections.

Large-scale electron microscopy (EM) allows analysis of both tissues and macromolecules in a semi-automated manner, but acquisition rate forms a bottleneck. We reasoned that a negative bias potential may be used to enhance signal collection, allowing shorter dwell times and thus increasing imaging speed. Negative bias potential has previously been used to tune penetration depth in block-face imaging. However, optimization of negative bias potential for application in thin section imaging will be needed prior to routine use and application in large-scale EM. Here, we present negative bias potential optimized through a combination of simulations and empirical measurements. We find that the use of a negative bias potential generally results in improvement of image quality and signal-to-noise ratio (SNR). The extent of these improvements depends on the presence and strength of a magnetic immersion field. Maintaining other imaging conditions and aiming for the same image quality and SNR, the use of a negative stage bias can allow for a 20-fold decrease in dwell time, thus reducing the time for a week long acquisition to less than 8 h. We further show that negative bias potential can be applied in an integrated correlative light electron microscopy (CLEM) application, allowing fast acquisition of a high precision overlaid LM-EM dataset. Application of negative stage bias potential will thus help to solve the current bottleneck of image acquisition of large fields of view at high resolution in large-scale microscopy.

CorRelator: Interactive software for real-time high precision cryo-correlative light and electron microscopy

Cryo-correlative light and electron microscopy (CLEM) is a technique that uses the spatiotemporal cues from fluorescence light microscopy (FLM) to investigate the high-resolution ultrastructure of biological samples by cryo-electron microscopy (cryo-EM). Cryo-CLEM provides advantages for identifying and distinguishing fluorescently labeled proteins, macromolecular complexes, and organelles from the cellular environment. Challenges remain on how correlation workflows and software tools are implemented on different microscope platforms to support automated cryo-EM data acquisition. Here, we present CorRelator: an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection. CorRelator implements a pixel-coordinate-to-stage-position transformation for flexible, high accuracy on-the-fly and post-acquisition correlation. CorRelator can be integrated into cryo-CLEM workflows and easily adapted to standard fluorescence and transmission electron microscope (TEM) system configurations. CorRelator was benchmarked under live-cell and cryogenic conditions using several FLM and TEM instruments, demonstrating that CorRelator reliably supports real-time, automated correlative cryo-EM/ET acquisition, through a combination of software-aided and interactive alignment. CorRelator is a cross-platform software package featuring an intuitive Graphical User Interface (GUI) that guides the user through the correlation process. CorRelator source code is available at: https://github.com/wright-cemrc-projects/corr.

Endocytosed nanogold fiducials for improved in-situ cryo-electron tomography tilt-series alignment

Cryo-electron tomography (CET) on cryo-focused ion beam (FIB)-milled lamellae is becoming a powerful technique for determining the structure of macromolecular complexes in their native cellular environment. Prior to tomogram reconstruction, CET tilt-series recorded on FIB lamellae need to be aligned. Traditionally, CET tilt-series alignment is performed with 5-20 nm gold fiducials, but it has thus far proven difficult to apply this to FIB lamellae of eukaryotic cells. In here, we describe a simple method to allow uptake of bovine serum albumin (BSA)-gold fiducials into mammalian cells via endocytosis, which can subsequently be used as fiducials for tilt-series alignment of cryo-FIB lamellae. We compare the alignment of tilt-series with BSA-gold fiducials to fiducial-less patch-tracking, and find better alignment results with BSA-gold. This technique can contribute to understand cells at a structural and ultrastructural level with both cryo- and room-temperature electron tomography. Furthermore, fluorescently labeled BSA-gold has the potential to be used as fiducials for correlative light and electron microscopy studies.

Photonic-chip assisted correlative light and electron microscopy

Correlative light and electron microscopy (CLEM) unifies the versatility of light microscopy (LM) with the high resolution of electron microscopy (EM), allowing one to zoom into the complex organization of cells. Here, we introduce photonic chip assisted CLEM, enabling multi-modal total internal reflection fluorescence (TIRF) microscopy over large field of view and high precision localization of the target area of interest within EM. The photonic chips are used as a substrate to hold, to illuminate and to provide landmarking of the sample through specially designed grid-like numbering systems. Using this approach, we demonstrate its applicability for tracking the area of interest, imaging the three-dimensional (3D) structural organization of nano-sized morphological features on liver sinusoidal endothelial cells such as fenestrations (trans-cytoplasmic nanopores), and correlating specific endo-lysosomal compartments with its cargo protein upon endocytosis.

Tinguely et al. develop a photonic chip-based correlative light-electron microscopy system to generate co-registered multi-modal total internal reflection fluorescence microscopy (TIRF) and electron microscopy (EM) images of biological samples at nanometer scale.

On-section correlative light and electron microscopy of large cellular volumes using STEM tomography

The application of both fluorescence and electron microscopy results in a powerful combination of imaging modalities called "correlative light and electron microscopy" (CLEM). Whereas conventional transmission electron microscopy (TEM) tomography is only able to image sections up to a thickness of ~300nm, scanning transmission electron microscopy (STEM) tomography at 200kV allows the analysis of sections up to a thickness of 900nm in three dimensions. In the current study we have successfully integrated STEM tomography into CLEM as demonstrated for human retinal pigment epithelial 1 (RPE1) cells expressing various fluorescent fusion proteins which were high-pressure frozen and then embedded in Lowicryl HM20. Fluorescently labeled gold nanoparticles were applied onto resin sections and imaged by fluorescence and electron microscopy. STEM tomograms were recorded at regions of interest, and overlays were generated using the eC-CLEM software package. Through the nuclear staining of living cells, the use of fluorescently labeled gold fiducials for the generation of overlays, and the integration of STEM tomography we have markedly extended the application of the Kukulski protocol (Kukulski et al., 2011, 2012). Various fluorescently tagged proteins localizing to different cellular organelles could be assigned to their ultrastructural compartments. By combining STEM tomography with on-section CLEM, fluorescently tagged proteins can be localized in three-dimensional ultrastructural environments with a volume of at least 2.7×2.7×0.5μm.

Super-resolution correlative light-electron microscopy using a click-chemistry approach for studying intracellular trafficking

Correlative light and electron microscopy (CLEM) entails a group of multimodal imaging techniques that are combined to pinpoint to the location of fluorescently labeled molecules in the context of their ultrastructural cellular environment. Here we describe a detailed workflow for STORM-CLEM, in which STochastic Optical Reconstruction Microscopy (STORM), an optical super-resolution technique, is correlated with transmission electron microscopy (TEM). This protocol has the advantage that both imaging modalities have resolution at the nanoscale, bringing higher synergies on the information obtained. The sample is prepared according to the Tokuyasu method followed by click-chemistry labeling and STORM imaging. Then, after heavy metal staining, electron microscopy imaging is performed followed by correlation of the two images. The case study presented here is on intracellular pathogens, but the protocol is versatile and could potentially be applied to many types of samples.

An accelerated procedure for approaching and imaging of optically branded region of interest in tissue

Many areas of biology have benefited from advances in light microscopy (LM). However, one limitation of the LM approach is that numerous critically important aspects of subcellular machineries are well beyond the resolution of conventional LM. For studying these, electron microscopy (EM) remains the technique of choice to visualize and identify macromolecules at the ultrastructural level. The most powerful approach is combining both techniques, LM and EM (i.e., to apply correlative light/electron microscopy, CLEM) to image exactly the same region of interest. This combination allows, for example, to immuno-localize proteins by LM and then to visualize the ultrastructural context of the same region of the sample. However, the identification and correlation of the regions of interest (ROIs) at the levels of LM and EM remains a major challenge, mostly due to the difficulties with correlation along the Z-axis for both modalities. In this chapter, we address this difficulty and describe an approach for performing CLEM in tissue samples using marks from near-infrared branding as indicators of a ROI, and then using serial block face-scanning electron microscopy (SBF-SEM) to identify and approach this ROI. Once a ROI has been approached, serial sections are collected on grids for high-resolution imaging by transmission EM, and subsequent correlation with LM images showing labeled proteins.

An Alternative Perfusion Approach for the Intensification of Virus-Like Particle Production in HEK293 Cultures

Virus-like particles (VLPs) have gained interest over the last years as recombinant vaccine formats, as they generate a strong immune response and present storage and distribution advantages compared to conventional vaccines. Therefore, VLPs are being regarded as potential vaccine candidates for several diseases. One requirement for their further clinical testing is the development of scalable processes and production platforms for cell-based viral particles. In this work, the extended gene expression (EGE) method, which consists in consecutive media replacements combined with cell retransfections, was successfully optimized and transferred to a bioreactor operating in perfusion. A process optimization using design of experiments (DoE) was carried out to obtain optimal values for the time of retransfection, the cell specific perfusion rate (CSPR) and transfected DNA concentration, improving 86.7% the previously reported EGE protocol in HEK293. Moreover, it was successfully implemented at 1.5L bioreactor using an ATF as cell retention system achieving concentrations of 6.8·10¹⁰ VLP/mL. VLP interaction with the ATF hollow fibers was studied via confocal microscopy, field emission scanning electron microscopy, and nanoparticle tracking analysis to design a bioprocess capable of separating unassembled Gag monomers and concentrate VLPs in one step.

Integrated super resolution fluorescence microscopy and transmission electron microscopy

In correlative light and electron microscopy (CLEM), the capabilities of fluorescence microscopy (FM) and electron microscopy (EM) are united. FM combines a large field of view with high sensitivity for detecting fluorescence, which makes it an excellent tool for identifying regions of interest. EM has a much smaller field of view but offers superb resolution that allows studying cellular ultrastructure. In CLEM, the potentials of both techniques are combined but a limiting factor is the large difference in resolution between the two imaging modalities. Adding super resolution FM to CLEM reduces the resolution gap between FM and EM; it offers the possibility of identifying multiple targets within the diffraction limit and can increase correlation accuracy. CLEM is usually carried out in two separate setups, which requires transfer of the sample. This may result in distortion and damage of the specimen, which can complicate finding back regions of interest. By integrating the two imaging modalities, such problems can be avoided. Here, an integrated super resolution correlative microscopy approach is presented based on a wide-field super resolution FM integrated in a Transmission Electron Microscope (TEM). Switching imaging modalities is accomplished by rotation of the TEM sample holder. First imaging experiments are presented on sections of Lowicryl embedded Human Umbilical Vein Endothelial Cells labeled for Caveolin both with Protein A-Gold, and Alexa Fluor®647. TEM and FM images were overlaid using fiducial markers visible in both imaging modalities with an overlay accuracy of 28 ± 11 nm. This is close to the optical resolution of ~50 nm.

Polydopamine Coating as a Scaffold for Ring-Opening Chemistry To Functionalize Gold Nanoparticles

Gold nanoparticles (GNPs) are promising nanomaterials for various biomedical applications owing to their remarkable optical properties and biocompatibility. However, their interfacial properties require modification for practical use in such applications. Herein, a simple method for modifying the surface of GNPs with polydopamine (PDA) to serve as a scaffold for the subsequent polymerization of hyperbranched polyglycerol (HPG) is reported. GNPs were first coated with PDA (GNP-PDA), and then ring-opening chemistry was used at this interface to modify GNP-PDA with HPG (GNP-PDA-HPG). The produced GNP-PDA-HPG shows not only excellent dispersibility in a salt-containing solution but also strong resistance to aggregation in high- and low-pH solutions, even after 10 days. Moreover, we demonstrate a one-pot method for functionalizing GNP-PDA with HPG and either COOH or trimethylammonium. Finally, we conjugated the trimethylammonium-functionalized GNP-PDA-HPG with fluorescent nanodiamonds to investigate the photothermal ability of the functional GNPs.

Development & Characterization of Fluorescently Tagged Nanocellulose for Nanotoxicological Studies

The rapid adoption of nanocellulose-based engineered nanomaterials (CNM) by many industries generates environmental health and safety (EHS) concerns. This work presents the development of fluorescently tagged CNM which can be used to study their interactions with biological systems. Specifically, cellulose nano-fibrils and cellulose nano-crystals with covalently attached fluorescein isothiocyanate (FITC) molecules on their surface were synthesized. The fluorescence of the FITC-tagged materials was assessed along with potential FITC detachment under pH conditions encountered in the human gastrointestinal tract, in intracellular compartments, and in cell culture media. Finally, the potential cytotoxicity due to the presence of FITC molecules on the surface of CNM was assessed using a cellular gut epithelium model. The results showed that neither FITC-CNF nor FITC-CNC were cytotoxic and that they have a comparable bioactivity to their untagged counterparts, rendering them suitable for biological studies.

Bridging the gap: 3D real-space characterization of colloidal assemblies via FIB-SEM tomography

Insight in the structure of nanoparticle assemblies up to a single particle level is key to understand the collective properties of these assemblies, which critically depend on the individual particle positions and orientations. However, the characterization of large, micron sized assemblies containing small, 10-500 nanometer, sized colloids is highly challenging and cannot easily be done with the conventional light, electron or X-ray microscopy techniques. Here, we demonstrate that focused ion beam-scanning electron microscopy (FIB-SEM) tomography in combination with image processing enables quantitative real-space studies of ordered and disordered particle assemblies too large for conventional transmission electron tomography, containing particles too small for confocal microscopy. First, we demonstrate the high resolution structural analysis of spherical nanoparticle assemblies, containing small anisotropic gold nanoparticles. Herein, FIB-SEM tomography allows the characterization of assembly dimensions which are inaccessible to conventional transmission electron microscopy. Next, we show that FIB-SEM tomography is capable of characterizing much larger ordered and disordered assemblies containing silica colloids with a diameter close to the resolution limit of confocal microscopes. We determined both the position and the orientation of each individual (nano)particle in the assemblies by using recently developed particle tracking routines. Such high precision structural information is essential in the understanding and design of the collective properties of new nanoparticle based materials and processes.