Reliable and Scalable SARS-CoV-2 qPCR Testing at a High Sample Throughput: Lessons Learned from the Belgian Initiative.

We present our approach to rapidly establishing a standardized, multi-site, nation-wide COVID-19 screening program in Belgium. Under auspices of a federal government Task Force responsible for upscaling the country's testing capacity, we were able to set up a national testing initiative with readily available resources, putting in place a robust, validated, high-throughput, and decentralized qPCR molecular testing platform with embedded proficiency testing. We demonstrate how during an acute scarcity of equipment, kits, reagents, personnel, protective equipment, and sterile plastic supplies, we introduced an approach to rapidly build a reliable, validated, high-volume, high-confidence workflow based on heterogeneous instrumentation and diverse assays, assay components, and protocols. The workflow was set up with continuous quality control monitoring, tied together through a clinical-grade information management platform for automated data analysis, real-time result reporting across different participating sites, qc monitoring, and making result data available to the requesting physician and the patient. In this overview, we address challenges in optimizing high-throughput cross-laboratory workflows with minimal manual intervention through software, instrument and assay validation and standardization, and a process for harmonized result reporting and nation-level infection statistics monitoring across the disparate testing methodologies and workflows, necessitated by a rapid scale-up as a response to the pandemic.

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.

Identifying microbial species by single-molecule DNA optical mapping and resampling statistics.

Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.

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.

A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA.

The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.

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.

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.

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.

Parts per Million Detection of Alcohol Vapors via Metal Organic Framework Functionalized Surface Plasmon Resonance Sensors.

The development of novel molecular sieves opens opportunities in the development of more sensitive analytical devices. In this paper, metal organic frameworks (MOFs), specifically ZIF-8 and ZIF-93, are grown on fiber optic based surface plasmon resonance (FO-SPR) sensors. FO-SPR has enabled sensitive sensing capabilities in biomedical settings and the addition of an MOF coating opens the way for the sensing of volatile organic compounds (VOCs) in gaseous media. FO-SPR probes were homogeneously functionalized with ZIF-8 and ZIF-93 in each case using two different precursor solutions to obtain a sequential nucleation and growth phase. The difference in MOF nucleation and growth kinetics of the two solutions was directly monitored by the FO-SPR system. The two established MOF-FO-SPR sensors were then subjected to sensing experiments with several alcohol vapors to establish their sensing capabilities. Vapors with mPa partial pressures, ppm concentrations, could successfully be detected, e.g., an LOD of 2.5 ppm for methanol detection was acquired. The difference in recognition behavior of the hydrophobic ZIF-8 and more hydrophilic ZIF-93 recognition layers can be exploited to yield qualitative information regarding the vapor composition.

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.

Photoluminescence Blinking of Single-Crystal Methylammonium Lead Iodide Perovskite Nanorods Induced by Surface Traps.

Photoluminescence (PL) of organometal halide perovskite materials reflects the charge dynamics inside of the material and thus contains important information for understanding the electro-optical properties of the material. Interpretation of PL blinking of methylammonium lead iodide (MAPbI3) nanostructures observed on polycrystalline samples remains puzzling owing to their intrinsic disordered nature. Here, we report a novel method for the synthesis of high-quality single-crystal MAPbI3 nanorods and demonstrate a single-crystal study on MAPbI3 PL blinking. At low excitation power densities, two-state blinking was found on individual nanorods with dimensions of several hundred nanometers. A super-resolution localization study on the blinking of individual nanorods showed that single crystals of several hundred nanometers emit and blink as a whole, without showing changes in the localization center over the crystal. Moreover, both the blinking ON and OFF times showed power-law distributions, indicating trapping-detrapping processes. This is further supported by the PL decay times of the individual nanorods, which were found to correlate with the ON/OFF states. Furthermore, a strong environmental dependence of the nanorod PL blinking was revealed by comparing the measurements in vacuum, nitrogen, and air, implying that traps locate close to crystal surfaces. We explain our observations by proposing surface charge traps that are likely related to under-coordinated lead ions and methylammonium vacancies to result in the PL blinking observed here.

Degradation of Methylammonium Lead Iodide Perovskite Structures through Light and Electron Beam Driven Ion Migration.

Organometal halide perovskites show promising features for cost-effective application in photovoltaics. The material instability remains a major obstacle to broad application because of the poorly understood degradation pathways. Here, we apply simultaneous luminescence and electron microscopy on perovskites for the first time, allowing us to monitor in situ morphology evolution and optical properties upon perovskite degradation. Interestingly, morphology, photoluminescence (PL), and cathodoluminescence of perovskite samples evolve differently upon degradation driven by electron beam (e-beam) or by light. A transversal electric current generated by a scanning electron beam leads to dramatic changes in PL and tunes the energy band gaps continuously alongside film thinning. In contrast, light-induced degradation results in material decomposition to scattered particles and shows little PL spectral shifts. The differences in degradation can be ascribed to different electric currents that drive ion migration. Moreover, solution-processed perovskite cuboids show heterogeneity in stability which is likely related to crystallinity and morphology. Our results reveal the essential role of ion migration in perovskite degradation and provide potential avenues to rationally enhance the stability of perovskite materials by reducing ion migration while improving morphology and crystallinity. It is worth noting that even moderate e-beam currents (86 pA) and acceleration voltages (10 kV) readily induce significant perovskite degradation and alter their optical properties. Therefore, attention has to be paid while characterizing such materials using scanning electron microscopy or transmission electron microscopy techniques.

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.

Single molecule methods for the study of catalysis: from enzymes to heterogeneous catalysts.

Structural and temporal inhomogeneities can have a marked influence on the performance of inorganic and biocatalytic systems alike. While these subtle variations are hardly ever accessible through bulk or ensemble averaged activity screening, insights into the molecular mechanisms underlying these diverse phenomena are absolutely critical for the development of optimized or novel catalytic systems and processes. Fortunately, state-of-the-art fluorescence microscopy methods have allowed experimental access to this intriguing world at the nanoscale. In this tutorial review we will first provide a broad overview of key concepts and developments in the application of single molecule fluorescence spectroscopy to (bio)catalysis research. In the second part topics specific to both bio and heterogeneous catalysis will be reviewed in more detail.

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.

Affinity comparison of p3 and p8 peptide displaying bacteriophages using surface plasmon resonance.

Ever increasing demands in sensitivity and specificity of biosensors have recently established a trend toward the use of multivalent bioreceptors. This trend has also been introduced in the field of bacteriophage affinity peptides, where the entire phage is used as a receptor rather than the individual peptides. Although this approach is gaining in popularity due to the numerous advantages, binding kinetics of complete phage particles have never been studied in detail, notwithstanding being essential for the efficient design of such applications. In this paper we used an in house developed fiber-optic surface plasmon resonance (FO-SPR) biosensor to study the affinity and binding kinetics of phages, displaying peptide libraries. By using either peptide expression on the p3 or on the p8 coat proteins, a corresponding density of 5 up to more than 2000 peptides on a single virus particle was obtained. Binding parameters of 26 different filamentous phages, displaying peptides selective for enhanced Green Fluorescent Protein (eGFP), were characterized. This study revealed a broad affinity range of phages for the target eGFP, indicating their potential to be used for applications with different requirements in binding kinetics. Moreover, detailed analysis of koff and kon values of several selected p3 and p8 phages, using the FO-SPR biosensor, clearly showed the correlation between the binding parameters and the density at which eGFP-peptides are being expressed. Consequently, although p3 and p8-based phages both revealed exceptionally high affinities for eGFP, two p8 phages were found to have the highest affinity with dissociation constants (Kd) in the femtomolar range.

Spherical nucleic acid enhanced FO-SPR DNA melting for detection of mutations in Legionella pneumophila.

A home-built fiber optic surface plasmon resonance platform (FO-SPR) was applied to directly screen PCR amplified DNA for mutations. The FO-SPR sensor was used for real-time monitoring of DNA duplex melting during high resolution temperature cycling. The signal of the DNA melting was enhanced by means of gold nanoparticle labels. This FO-SPR genetic assay allowed for detection of single-point mutations (SNP) in less than 20 min. The concept was demonstrated for the analysis of 9 different serogroups of the bacterium Legionella pneumophila, a common human pathogen responsible for atypical pneumonia. FO-SPR allowed us to detect genetic mutations inhibiting PCR, which could lead to amplification bias when molecular diagnostics are applied for L. pneumophila detection. All serogroups were found to display unique melting temperatures, indicating that mutations have accumulated in the target sequence. In a next step, clinical samples of L. pneumophila were analyzed using the FO-SPR sensor. This technology was proven to be reliable for the detection of mutations for those samples that previously displayed ambiguous qPCR quantification results. When these results were benchmarked, FO-SPR results were found to be consistent with Sanger sequencing but not with fluorescence based DNA melting. The presented results convincingly advocate the advantages of FO-SPR as a high resolution and fast genetic screening tool that can compete with the current standard techniques for SNP detection.

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.