Fluorescence Photobleaching as an Intrinsic Tool to Quantify the 3D Expansion Factor of Biological Samples in Expansion Microscopy

Four years after its first report, expansion microscopy (ExM) is now being routinely applied in laboratories worldwide to achieve super-resolution imaging on conventional fluorescence microscopes. By chemically anchoring all molecules of interest to the polymer meshwork of an expandable hydrogel, their physical distance is increased by a factor of ∼4-5× upon dialysis in water, resulting in an imprint of the original sample with a lateral resolution up to 50-70 nm. To ensure a correct representation of the original spatial distribution of the molecules, it is crucial to confirm that the expansion is isotropic, preferentially in all three dimensions. To address this, we present an approach to evaluate the local expansion factor within a biological sample and in all three dimensions. We use photobleaching to introduce well-defined three-dimensional (3D) features in the cell and, by comparing the size and shape pre- and postexpansion, these features can be used as an intrinsic ruler. In addition, our method is capable of pointing out sample distortions and can be used as a quality control tool for expansion microscopy experiments in biological samples.

Thermal unequilibrium of strained black CsPbI3 thin films

The high-temperature, all-inorganic CsPbI3 perovskite black phase is metastable relative to its yellow, nonperovskite phase at room temperature. Because only the black phase is optically active, this represents an impediment for the use of CsPbI3 in optoelectronic devices. We report the use of substrate clamping and biaxial strain to render black-phase CsPbI3 thin films stable at room temperature. We used synchrotron-based, grazing incidence, wide-angle x-ray scattering to track the introduction of crystal distortions and strain-driven texture formation within black CsPbI3 thin films when they were cooled after annealing at 330°C. The thermal stability of black CsPbI3 thin films is vastly improved by the strained interface, a response verified by ab initio thermodynamic modeling.

The 2018 correlative microscopy techniques roadmap

Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.

Imaging Heterogeneously Distributed Photo-Active Traps in Perovskite Single Crystals

Organic-inorganic halide perovskites (OIHPs) have demonstrated outstanding energy conversion efficiency in solar cells and light-emitting devices. In spite of intensive developments in both materials and devices, electronic traps and defects that significantly affect their device properties remain under-investigated. Particularly, it remains challenging to identify and to resolve traps individually at the nanoscopic scale. Here, photo-active traps (PATs) are mapped over OIHP nanocrystal morphology of different crystallinity by means of correlative optical differential super-resolution localization microscopy (Δ-SRLM) and electron microscopy. Stochastic and monolithic photoluminescence intermittency due to individual PATs is observed on monocrystalline and polycrystalline OIHP nanocrystals. Δ-SRLM reveals a heterogeneous PAT distribution across nanocrystals and determines the PAT density to be 1.3 × 10¹⁴ and 8 × 10¹³ cm^-3 for polycrystalline and for monocrystalline nanocrystals, respectively. The higher PAT density in polycrystalline nanocrystals is likely related to an increased defect density. Moreover, monocrystalline nanocrystals that are prepared in an oxygen- and moisture-free environment show a similar PAT density as that prepared at ambient conditions, excluding oxygen or moisture as chief causes of PATs. Hence, it is concluded that the PATs come from inherent structural defects in the material, which suggests that the PAT density can be reduced by improving crystalline quality of the material.

Highly controllable direct femtosecond laser writing of gold nanostructures on titanium dioxide surfaces

A highly reproducible and controllable deposition procedure for gold nanostructures on a titanium dioxide (TiO₂) surface using femtosecond laser light has been demonstrated. This is realized by precisely focusing onto the TiO₂ surface in the presence of a pure gold ion solution. The deposition is demonstrated both in dot arrays and line structures. Thanks to the multi-photon excitation, we observe that the deposition area of the nanostructures can be confined to a degree far greater than the diffraction limited focal spot. Finally, we demonstrate that catalytic activity with visible light irradiation is enhanced, proving the applicability of our new deposition technique to the catalytic field.

Rationalizing Acid Zeolite Performance on the Nanoscale by Correlative Fluorescence and Electron Microscopy

The performance of zeolites as solid acid catalysts is strongly influenced by the accessibility of active sites. However, synthetic zeolites typically grow as complex aggregates of small nanocrystallites rather than perfect single crystals. The structural complexity must therefore play a decisive role in zeolite catalyst applicability. Traditional tools for the characterization of heterogeneous catalysts are unable to directly relate nanometer-scale structural properties to the corresponding catalytic performance. In this work, an innovative correlative super-resolution fluorescence and scanning electron microscope is applied, and the appropriate analysis procedures are developed to investigate the effect of small-port H-mordenite (H-MOR) morphology on the catalytic performance, along with the effects of extensive acid leaching. These correlative measurements revealed catalytic activity at the interface between intergrown H-MOR crystallites that was assumed inaccessible, without compromising the shape selective properties. Furthermore, it was found that extensive acid leaching led to an etching of the originally accessible microporous structure, rather than the formation of an extended mesoporous structure. The associated transition of small-port to large-port H-MOR therefore did not render the full catalyst particle functional for catalysis. The applied characterization technique allows a straightforward investigation of the zeolite structure-activity relationship beyond the single-particle level. We conclude that such information will ultimately lead to an accurate understanding of the relationship between the bulk scale catalyst behavior and the nanoscale structural features, enabling a rationalization of catalyst design.

Methyltransferase-Directed Labeling of Biomolecules and its Applications

Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.

Facet-Dependent Photoreduction on Single ZnO Crystals

Photocatalytic reactions occur at the crystal-solution interface, and hence specific crystal facet expression and surface defects can play an important role. Here we investigate the structure-related photoreduction at zinc oxide (ZnO) microparticles via integrated light and electron microscopy in combination with silver metal photodeposition. This enables a direct visualization of the photoreduction activity at specific crystallographic features. It is found that silver nanoparticle photodeposition on dumbbell-shaped crystals mainly takes place at the edges of O-terminated (0001̅) polar facets. In contrast, on ZnO microrods photodeposition is more homogeneously distributed with an increased activity at {101̅1̅} facets. Additional time-resolved measurements reveal a direct spatial link between the enhanced photoactivity and increased charge carrier lifetimes. These findings contradict previous observations based on indirect, bulk-scale experiments, assigning the highest photocatalytic activity to polar facets. The presented research demonstrates the need for advanced microscopy techniques to directly probe the location of photocatalytic activity.

Resolving Interparticle Heterogeneities in Composition and Hydrogenation Performance between Individual Supported Silver on Silica Catalysts

Supported metal nanoparticle catalysts are commonly obtained through deposition of metal precursors onto the support using incipient wetness impregnation. Typically, empirical relations between metal nanoparticle structure and catalytic performance are inferred from ensemble averaged data in combination with high-resolution electron microscopy. This approach clearly underestimates the importance of heterogeneities present in a supported metal catalyst batch. Here we show for the first time how incipient wetness impregnation leads to 10-fold variations in silver loading between individual submillimeter-sized silica support granules. This heterogeneity has a profound impact on the catalytic performance, with 100-fold variations in hydrogenation performance at the same level. In a straightforward fashion, optical microscopy interlinks single support particle level catalytic measurements to structural and compositional information. These detailed correlations reveal the optimal silver loading. A thorough consideration of catalyst heterogeneity and the impact thereof on the catalytic performance is indispensable in the development of catalysts.

Noninvasive Nanoscopy Uncovers the Impact of the Hierarchical Porous Structure on the Catalytic Activity of Single Dealuminated Mordenite Crystals

Spatial restrictions around catalytic sites, provided by molecular-sized micropores, are beneficial to reaction selectivity but also inherently limit diffusion. The molecular transport can be enhanced by introducing meso- and macropores. However, the impact of this extraframework porosity on the local nanoscale reactivity is relatively unexplored. Herein we show that the area of enhanced reactivity in hierarchical zeolite, examined with super-resolution fluorescence microscopy, is spatially restricted to narrow zones around meso- and macropores, as observed with focused ion-beam-assisted scanning electron microscopy. This comparison indicates that reagent molecules efficiently reach catalytic active sites only in the micropores surrounding extraframework porosity and that extensive macroporosity does not warrant optimal reactivity distribution throughout a hierarchical porous zeolite.

Reshaping anisotropic gold nanoparticles through oxidative etching: the role of the surfactant and nanoparticle surface curvature

We study reshaping of gold nanorods, bipyramids and triangles to reveal roles of the surfactant in the oxidative etching process.

Emerging technologies for hybridization based single nucleotide polymorphism detection

Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.

Nucleic acids for ultra-sensitive protein detection

Major advancements in molecular biology and clinical diagnostics cannot be brought about strictly through the use of genomics based methods. Improved methods for protein detection and proteomic screening are an absolute necessity to complement to wealth of information offered by novel, high-throughput sequencing technologies. Only then will it be possible to advance insights into clinical processes and to characterize the importance of specific protein biomarkers for disease detection or the realization of "personalized medicine". Currently however, large-scale proteomic information is still not as easily obtained as its genomic counterpart, mainly because traditional antibody-based technologies struggle to meet the stringent sensitivity and throughput requirements that are required whereas mass-spectrometry based methods might be burdened by significant costs involved. However, recent years have seen the development of new biodetection strategies linking nucleic acids with existing antibody technology or replacing antibodies with oligonucleotide recognition elements altogether. These advancements have unlocked many new strategies to lower detection limits and dramatically increase throughput of protein detection assays. In this review, an overview of these new strategies will be given.

Multiplexed protein detection using an affinity aptamer amplification assay

Affinity probe capillary electrophoresis (APCE) is potentially one of the most versatile technologies for protein diagnostics, offering an excellent balance between robustness, analysis speed and sensitivity. Combining the immunosensing and separating strength of capillary electrophoresis with the signal enhancement power of nucleic acid amplification, aptamers can further push the analytical limits of APCE to offer ultrasensitive, multiplexed detection of protein biomarkers, even when differences in electrophoretic mobility between the different aptamer-target complexes are limited. It is demonstrated how, through careful selection of experimental parameters, simultaneous detection of picomolar levels of three target proteins can be achieved even with aptamers that were initially selected under very different conditions and further taking into account that the aptamers need to be modified to allow successful PCR amplification. Aptamer-enhanced APCE offers limits of detection that are orders of magnitude lower than those that can be achieved through traditional capillary electrophoresis-based immunosensing. With recent developments in aptamer selection that for the first time realise the promise of aptamers as easily accessible, high affinity recognition molecules, it can therefore be envisioned that aptamer-enhanced APCE on parallel microfluidic platforms can be the basis for a truly high-throughput multiplexed proteomics platform, rivalling genetic screening for the first time.

Enabling fiber optic serotyping of pathogenic bacteria through improved anti-fouling functional surfaces

Significant research efforts are continually being directed towards the development of sensitive and accurate surface plasmon resonance biosensors for sequence specific DNA detection. These sensors hold great potential for applications in healthcare and diagnostics. However, the performance of these sensors in practical usage scenarios is often limited due to interference from the sample matrix. This work shows how the co-immobilization of glycol(PEG) diluents or 'back filling' of the DNA sensing layer can successfully address these problems. A novel SPR based melting assay is used for the analysis of a synthetic oligomer target as well as PCR amplified genomic DNA extracted from Legionella pneumophila. The benefits of sensing layer back filling on the assay performance are first demonstrated through melting analysis of the oligomer target and it is shown how back filling enables accurate discrimination of Legionella pneumophila serogroups directly from the PCR reaction product with complete suppression of sensor fouling.

Nanocrystalline diamond impedimetric aptasensor for the label-free detection of human IgE

Like antibodies, aptamers are highly valuable as bioreceptor molecules for protein biomarkers because of their excellent selectivity, specificity and stability. The integration of aptamers with semiconducting materials offers great potential for the development of reliable aptasensors. In this paper we present an aptamer-based impedimetric biosensor using a nanocrystalline diamond (NCD) film as a working electrode for the direct and label-free detection of human immunoglobulin E (IgE). Amino (NH(2))-terminated IgE aptamers were covalently attached to carboxyl (COOH)-modified NCD surfaces using carbodiimide chemistry. Electrochemical impedance spectroscopy (EIS) was applied to measure the changes in interfacial electrical properties that arise when the aptamer-functionalized diamond surface was exposed to IgE solutions. During incubation, the formation of aptamer-IgE complexes caused a significant change in the capacitance of the double-layer, in good correspondence with the IgE concentration. The linear dynamic range of IgE detection was from 0.03 μg/mL to 42.8 μg/mL. The detection limit of the aptasensor reached physiologically relevant concentrations (0.03 μg/mL). The NCD-based aptasensor was demonstrated to be highly selective even in the presence of a large excess of IgG. In addition, the aptasensor provided reproducible signals during six regeneration cycles. The impedimetric aptasensor was successfully tested on human serum samples, which opens up the potential of using EIS for direct and label-free detection of IgE levels in blood serum.

Fiber optic SPR biosensing of DNA hybridization and DNA-protein interactions

In this paper we present a fiber optic surface plasmon resonance (SPR) sensor as a reusable, cost-effective and label free biosensor for measuring DNA hybridization and DNA-protein interactions. This is the first paper that combines the concept of a fiber-based SPR system with DNA aptamer bioreceptors. The fibers were sputtered with a 50nm gold layer which was then covered with a protein repulsive self-assembled monolayer of mixed polyethylene glycol (PEG). Streptavidin was attached to the PEG's carboxyl groups to serve as a versatile binding element for biotinylated ssDNA. The ssDNA coated SPR fibers were first evaluated as a nucleic acid biosensor through a DNA-DNA hybridization assay for a random 37-mer ssDNA. This single stranded DNA showed a 15 nucleotides overlap with the receptor ssDNA on the SPR fiber. A linear calibration curve was observed in 0.5-5 microM range. A negative control test did not reveal any significant non-specific binding, and the biosensor was easily regenerated. In a second assay the fiber optic SPR biosensor was functionalized with ssDNA aptamers against human immunoglobulin E. Limits of detection (2nM) and quantification (6nM) in the low nanomolar range were observed. The presented biosensor was not only useful for DNA and protein quantification purposes, but also to reveal the binding kinetics occurring at the sensor surface. The dissociation constant between aptamer and hIgE was equal to 30.9+/-2.9nM. The observed kinetics fully comply with most data from the literature and were also confirmed by own control measurements.

Novel Transition-Metal-Free Heterogeneous Epoxidation Catalysts Discovered by Means of High-Throughput Experimentation

Various transition-metal-free oxides have been studied as catalysts for the epoxidation of cyclooctene with hydrogen peroxide by means of high-throughput experimentation. Different boron, aluminium, and gallium oxides were prepared according to various synthesis methods. A number of pure aluminium and gallium oxides showed very good catalytic performances, while the results obtained with boron oxides or mixed oxides were less positive. The best results were obtained with a gallium oxide catalyst, which gave an epoxide yield of 71 % and a selectivity of 99 % after reaction for 4 h at 80 degrees C. Gallium oxides had not been reported previously as active epoxidation catalysts. The use of high-throughput experimentation proved useful both for discovering new active catalysts and for identifying a number of relationships between the synthesis conditions and the catalytic properties of the transition-metal-free oxides.