Superresolving the kidney-a practical comparison of fluorescence nanoscopy of the glomerular filtration barrier.

Immunofluorescence microscopy is routinely used in the diagnosis of and research on renal impairments. However, this highly specific technique is restricted in its maximum resolution to about 250 nm in the lateral and 700 nm in the axial directions and thus not sufficient to investigate the fine subcellular structure of the kidney's glomerular filtration barrier. In contrast, electron microscopy offers high resolution, but this comes at the cost of poor preservation of immunogenic epitopes and antibody penetration alongside a low throughput. Many of these drawbacks were overcome with the advent of super-resolution microscopy methods. So far, four different super-resolution approaches have been used to study the kidney: single-molecule localization microscopy (SMLM), stimulated emission depletion (STED) microscopy, structured illumination microscopy (SIM), and expansion microscopy (ExM), however, using different preservation methods and widely varying labelling strategies. In this work, all four methods were applied and critically compared on kidney slices obtained from samples treated with the most commonly used preservation technique: fixation by formalin and embedding in paraffin (FFPE). Strengths and weaknesses, as well as the practicalities of each method, are discussed to enable users of super-resolution microscopy in renal research make an informed decision on the best choice of technique. The methods discussed enable the efficient investigation of biopsies stored in kidney banks around the world. Graphical abstract

Sustainable Synthesis of N-Alkyl-Pyrrolecarboxylic and Pyrrolepyrazinones Derivatives from Biosourced 3-Hydroxy-2-pyrones and Amines

Pyrroles are important compounds present in biological systems, used for drug synthesis and in material chemistry. A typical strategy for the pyrrolic ring formation is centered on the Paal−Knorr reaction, where 1,4-dicarbonyl compounds react with amines giving N-substituted pyrrole derivatives. Often, the main problem of this approach is the availability of the appropriate carbonyl compounds. Here, we report a sustainable synthesis of N-substituted pyrrole carboxylic acid derivatives by the reaction of primary amines and 3-hydroxy-2-pyrones. These last compounds can easily be prepared using renewable sources and show the property to be masked 1,4-dicarbonyl compounds that are able to react efficiently with amines to form substituted pyrrolic rings. The reactions can be performed under sustainable conditions without solvents at 50−75 °C or in basic water−methanol solutions at room temperature, obtaining symmetric and asymmetric pyrroles from good to high yields. Moreover, dihydropyrrolepyrazinone derivatives can easily be prepared in high yields by the reaction of 3-hydroxy-2-pyrones and ethylenediamine

A fluorescent reporter system enables spatiotemporal analysis of host cell modification during herpes simplex virus-1 replication.

Herpesviruses are large and complex viruses that have a long history of coevolution with their host species. One important factor in the virus-host interaction is the alteration of intracellular morphology during viral replication with critical implications for viral assembly. However, the details of this remodeling event are not well understood, in part because insufficient tools are available to deconstruct this highly heterogeneous process. To provide an accurate and reliable method of investigating the spatiotemporal dynamics of virus-induced changes to cellular architecture, we constructed a dual-fluorescent reporter virus that enabled us to classify four distinct stages in the infection cycle of herpes simplex virus-1 at the single cell level. This timestamping method can accurately track the infection cycle across a wide range of multiplicities of infection. We used high-resolution fluorescence microscopy analysis of cellular structures in live and fixed cells in concert with our reporter virus to generate a detailed and chronological overview of the spatial and temporal reorganization during viral replication. The highly orchestrated and striking relocation of many organelles around the compartments of secondary envelopment during transition from early to late gene expression suggests that the reshaping of these compartments is essential for virus assembly. We furthermore find that accumulation of HSV-1 capsids in the cytoplasm is accompanied by fragmentation of the Golgi apparatus with potential impact on the late steps of viral assembly. We anticipate that in the future similar tools can be systematically applied for the systems-level analysis of intracellular morphology during replication of other viruses

Light-Triggered Trafficking to the Cell Nucleus of a Cationic Polyamidoamine Functionalized with Ruthenium Complexes

Strategies for endosomal escape and access to the cell nucleus are highly sought for nanocarriers to deliver their load efficiently following endocytosis. In this work, we have studied the uptake and intracellular trafficking of a polycationic polyamidoamine endowed with a luminescent Ru complex, Ru-PhenAN, that shows unique trafficking to the cell nucleus. Live cell imaging confirmed the capacity of this polymer to access the nucleus, excluding artefacts due to cell fixation, and clarified that the mechanism of escape is light-triggered and relies on the presence of the Ru complexes and their capacity to absorb light and act as photosensitizers for singlet oxygen production. These results open up the possibility to use polyamidoamineruthenium complexes for targeted light-triggered delivery of genetic material or drugs to the cytosol and nucleus

Super-resolved volumetric optical imaging of virus-infected cells

Viruses are infectious agents that replicate within the cells of the organisms they infect. Most viruses are smaller than 200 nanometres, which makes them hard to visualise using diffraction-limited light microscopes. Yet, ‘seeing viruses’ is essential to unravel their infection mechanism within the organisms they highjack, which is key to understanding how such small entities can spark disruptive pandemics. This thesis shows how expansion microscopy is an excellent tool to achieve super-resolution when imaging virus-infected samples using optical microscopy. Expansion microscopy is a recently conceived sample preparation technique that physically expands fixed specimens after embedding them in water-absorbing polymers. By expanding virus-infected samples and imaging them on a light sheet microscope, it was possible to acquire super-resolved 3D images of virus-infected cells rapidly and in up to four colours simultaneously. The combination of expansion and light sheet microscopy was employed for studying the infection cycle of the emerging virus SARS-CoV-2 and for comparing the infection mechanism of two live attenuated influenza vaccine (LAIV) viruses characterised by differing vaccine effectiveness. In both cases, the increased resolution in three dimensions delivered details about the infection mechanism of these viruses that were not previously known. Imaging SARS-CoV-2 infected Vero cells revealed that the nucleocapsid protein of SARS-CoV-2 accumulates at the membrane of the viral replication organelles, strongly suggesting that this is where the encapsidation of the viral genome by the nucleocapsid protein occurs. Imaging the assembly of the viral genome of an optimal and suboptimal LAIV virus in A549 cells highlighted genome assembly faults for the suboptimal virus at the cytoplasmic level, which could be the main reason behind the reduced fitness of this LAIV strain.AstraZenec

Dataset for colocalization analysis

Zip folder containing set of images (.tif files) analysed in the paper: “The SARS-CoV-2 nucleocapsid protein associates with the replication organelles before viral assembly at the Golgi/ERGIC and lysosome-mediated egress”, doi: 10.1101/2021.06.15.448497. Fixed Vero cells were imaged with confocal microscope (pixel size is 70.6 nm). Zip folder contains images stained for different viral proteins: Spike (S), Envelope (E), Membrane (M), Nucleocapsid (N), lysosomes, ERGIC complex and Golgi apparatus. Images are already automatically cropped around each single cell (see associated article methods for automatic cropping details). Description of colors in each subset is present in txt files which are included in all subsets. These images were analysed for Manders and Spearman coefficients with ColocAnalyzer v.4 https://doi.org/10.17863/CAM.77726 For more details see associated manuscript

Tuning Polyamidoamine Design to Increase Uptake and Efficacy of Ruthenium Complexes for Photodynamic Therapy

In this work, we report the synthesis of [Ru(phen)3 2+]-based complexes and their use as photosensitizers for photodynamic therapy (PDT), a treatment of pathological conditions based on the photoactivation of bioactive compounds, which are not harmful in the absence of light irradiation. Of these complexes, Ru-PhenISA and Ru-PhenAN are polymer conjugates containing less than 5%, (on a molar basis), photoactive units. Their performance is compared with that of a small [Ru(phen)3 2+] compound, [Ru(phen)2BAP](OTf)2 (BAP = 4-(4′-aminobutyl)-1,10-phenanthroline, OTf = triflate anion), used as a model of the photoactive units. The polymer ligands, PhenISA and PhenAN, are polyamidoamines with different acid-base properties. At physiological pH, the former is zwitterionic, the latter moderately cationic, and both intrinsically cytocompatible. The photophysical characterizations show that the complexation to macromolecules does not hamper the Ru(phen)3 2+ ability to generate toxic singlet oxygen upon irradiation, and phosphorescence lifetimes and quantum yields are similar in all cases. All three compounds are internalized by HeLa cells and can induce cell death upon visible light irradiation. However, their relative PDT efficiency is different: the zwitterionic PhenISA endowed with the Ru-complex lowers the PDT efficiency of the free complex, while conversely, the cationic PhenAN boosts it. Flow cytometry demonstrates that the uptake efficiency of the three agents reflects the observed differences in PDT efficacy. Additionally, intracellular localization studies show that while [Ru(phen)2BAP](OTf)2 remains confined in vesicular structures, Ru-PhenISA localization is hard to determine due to the very low uptake efficiency. Very interestingly, instead, the cationic Ru-PhenAN accumulates inside the nucleus in all treated cells. Overall, the results indicate that the complexation of [Ru(phen)2BAP](OTf)2 with a cationic polyamidoamine to give the Ru-PhenAN complex is an excellent strategy to increase the Ru-complex cell uptake and, additionally, to achieve accumulation at the nuclear level. These unique features together make this compound an excellent photosensitizer with very high PDT efficiency

Combining sample expansion and light sheet microscopy for the volumetric imaging of virus-infected cells with super-resolution.

Expansion microscopy is a sample preparation technique that enables the optical imaging of biological specimens at super-resolution owing to their physical magnification, which is achieved through water-absorbing polymers. The technique uses readily available chemicals and does not require sophisticated equipment, thus offering super-resolution to laboratories that are not microscopy-specialised. Here we present a protocol combining sample expansion with light sheet microscopy to generate high-contrast, high-resolution 3D reconstructions of whole virus-infected cells. The results are superior to those achievable with comparable imaging modalities and reveal details of the infection cycle that are not discernible before expansion. An image resolution of approximately 95 nm could be achieved in samples labelled in 3 colours. We resolve that the viral nucleoprotein is accumulated at the membrane of vesicular structures within the cell cytoplasm and how these vesicles are positioned relative to cellular structures. We provide detailed guidance and a video protocol for the optimal application of the method and demonstrate its potential to study virus-host cell interactions

Fast, multicolour optical sectioning over extended fields of view with patterned illumination and machine learning

Structured illumination can reject out-of-focus signal from a sample, enabling high-speed and high-contrast imaging over large areas with widefield detection optics. However, this optical-sectioning technique is currently limited by image reconstruction artifacts and poor performance at low signal-to-noise ratios. We combine multicolour interferometric pattern generation with machine learning to achieve high-contrast, real-time reconstruction of image data that is robust to background noise and sample motion. We validate the method in silico and demonstrate imaging of diverse specimens, from fixed and live biological samples to synthetic biosystems, reconstructing data live at 11 Hz across a 44 X 44 μm^2 field of view, and demonstrate image acquisition speeds exceeding 154 H