The Fast mode for ZEISS LSM 880 with Airyscan: high-speed confocal imaging with super-resolution and improved signal-to-noise ratio

Cross-modality supervised image restoration enables nanoscale tracking of synaptic plasticity in living mice

Learning is thought to involve changes in glutamate receptors at synapses, submicron structures that mediate communication between neurons in the central nervous system. Due to their small size and high density, synapses are difficult to resolve in vivo, limiting our ability to directly relate receptor dynamics to animal behavior. Here we developed a combination of computational and biological methods to overcome these challenges. First, we trained a deep-learning image-restoration algorithm that combines the advantages of ex vivo super-resolution and in vivo imaging modalities to overcome limitations specific to each optical system. When applied to in vivo images from transgenic mice expressing fluorescently labeled glutamate receptors, this restoration algorithm super-resolved synapses, enabling the tracking of behavior-associated synaptic plasticity with high spatial resolution. This method demonstrates the capabilities of image enhancement to learn from ex vivo data and imaging techniques to improve in vivo imaging resolution.

Expansion microscopy of the chick embryo neural tube to overcome molecular crowding at the centrosomes-cilia

We describe an optimized protocol for application of expansion microscopy (ExM) on chick neural tube (NT) which enables different oriented nanoscale resolution imaging of the centrosomes/cilia. We explain embryo NT transversal sections and open-book preparations, immunohistochemistry for labeling, and sample preparation for 5-fold tissue expansion. Further, we detail sample orientation and Fast Airyscan confocal acquisition and show that NT-ExM retains fluorescence signals and overcomes biomolecules crowding in structural features that to date were only imaged with electron microscopy on tissues.

Active APPL1 sequestration by Plasmodium favors liver-stage development

Intracellular pathogens manipulate host cells to survive and thrive. Cellular sensing and signaling pathways are among the key host machineries deregulated to favor infection. In this study, we show that liver-stage Plasmodium parasites compete with the host to sequester a host endosomal-adaptor protein (APPL1) known to regulate signaling in response to endocytosis. The enrichment of APPL1 at the parasitophorous vacuole membrane (PVM) involves an atypical Plasmodium Rab5 isoform (Rab5b). Depletion of host APPL1 alters neither the infection nor parasite development; however, upon overexpression of a GTPase-deficient host Rab5 mutant (hRab5_Q79L), the parasites are smaller and their PVM is stripped of APPL1. Infection with the GTPase-deficient Plasmodium berghei Rab5b mutant (PbRab5b_Q91L) in this case rescues the PVM APPL1 signal and parasite size. In summary, we observe a robust correlation between the level of APPL1 retention at the PVM and parasite size during exoerythrocytic development.

Confocal Real-Time Analysis of Cutaneous Platelet Recruitment during Immune-Complex-Mediated Inflammation

Platelets preserve vascular integrity during immune complex (IC)-mediated skin inflammation by preventing neutrophil-provoked hemorrhage. However, the single cell dynamics of this hemostatic process have never been studied in real-time. To monitor the on-set of thrombocytopenia-associated hemorrhages and analyze platelet recruitment, we developed a confocal microscopy-based video-imaging platform for the dorsal skinfold chamber in living mice. For ultrastructural analysis of recruited platelets, we correlated our imaging approach with serial block-face scanning electron microscopy. We found that bleeding events were transient and occurred preferentially at vascular sites, which were repeatedly penetrated by extravasating neutrophils. Hemorrhage only resumed when previously affected sites were again breached by yet another neutrophil. In non-thrombocytopenic mice, we observed that neutrophil extravasation provoked recruitment of single platelets to the vessel wall, which required platelet ITAM-receptors GPVI and CLEC-2. Recruited platelets were found to spread across the endothelial barrier and some even across the basement membrane, while retaining their granules. Thus, by visualizing the spatiotemporal dynamics of thrombocytopenia-associated bleeding and platelet recruitment on a single cell level and in real-time, we provide further insights into how platelets preserve vascular integrity during IC-mediated skin inflammation.

Quantifying the Organization and Dynamics of the Plant Plasma Membrane Across Scales Using Light Microscopy

The plant cell surface continuum is composed of the cell wall, plasma membrane, and cytoskeleton. Plasmodesmata are specialized channels in the cell wall allowing intercellular communication and resource distribution. Proteins within these organelles play fundamental roles in development, perception of the external environment, and resource acquisition. Therefore, an understanding of protein dynamics and organization within the membrane and plasmodesmata is of fundamental importance to understanding both how plants develop as well as perceive the myriad of external stimuli they experience and initiate appropriate downstream responses. In this chapter, I will describe protocols for quantifying the dynamics and organization of the plasma membrane and plasmodesmata proteins across scales. The protocols described below allow researchers to determine bulk protein mobility within the membrane using fluorescence recovery after photobleaching (FRAP), imaging, and quantification of nanodomain size (with Airyscan confocal microscopy) and determining the dynamics of these nanodomains at the single particle level using total internal reflection (TIRF) single particle imaging.

The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder

Peroxisomal biogenesis disorders (PBDs) are genetic disorders of peroxisome biogenesis and metabolism that are characterized by profound developmental and neurological phenotypes. The most severe class of PBDs-Zellweger spectrum disorder (ZSD)-is caused by mutations in peroxin genes that result in both non-functional peroxisomes and mitochondrial dysfunction. It is unclear, however, how defective peroxisomes contribute to mitochondrial impairment. In order to understand the molecular basis of this inter-organellar relationship, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that peroxins were still expressed and a subset of them accumulated on the mitochondrial membrane, which resulted in gross mitochondrial abnormalities and impaired mitochondrial metabolic function. We showed that overexpression of ATAD1, a mitochondrial quality control factor, was sufficient to rescue several aspects of mitochondrial function in human ZSD fibroblasts. Together, these data suggest that aberrant peroxisomal protein localization is necessary and sufficient for the devastating mitochondrial morphological and metabolic phenotypes in ZSDs.

Toughening and polymerization stress control in composites using thiourethane-treated fillers

Filler particle functionalization with thiourethane oligomers has been shown to increase fracture toughness and decrease polymerization stress in dental composites, though the mechanism is poorly understood. The aim of this study was to systematically characterize the effect of the type of filler surface functionalization on the physicochemical properties of experimental resin composites containing fillers of different size and volume fraction. Barium glass fillers (1, 3 and 10 µm) were functionalized with 2 wt% thiourethane-silane (TU-Sil) synthesized de novo and characterized by thermogravimetric analysis. Fillers treated with 3-(Trimethoxysilyl)propyl methacrylate (MA-Sil) and with no surface treatment (No-Sil) served as controls. Fillers (50, 60 and 70 wt%) were incorporated into BisGMA-UDMA-TEGDMA (5:3:2) containing camphorquinone/ethyl-4-dimethylaminobenzoate (0.2/0.8 wt%) and 0.2 wt% di-tert-butyl hydroxytoluene. The functionalized particles were characterized by thermogravimetric analysis and a representative group was tagged with methacrylated rhodamine B and analyzed by confocal laser scanning microscopy. Polymerization kinetics were assessed by near-IR spectroscopy. Polymerization stress was tested in a cantilever system, and fracture toughness was assessed with single edge-notched beams. Fracture surfaces were characterized by SEM. Data were analyzed with ANOVA/Tukey's test (α = 0.05). The grafting of thiourethane oligomer onto the surface of the filler particles led to reductions in polymerization stress ranging between 41 and 54%, without affecting the viscosity of the composite. Fracture toughness increased on average by 35% for composites with the experimental fillers compared with the traditional methacrylate-silanized groups. SEM and confocal analyses demonstrate that the coverage of the filler surface was not homogeneous and varied with the size of the filler. The average silane layer for the 1 µm particle functionalized with the thiourethane was 206 nm, much thicker than reported for traditional silanes. In summary, this study systematically characterized the silane layer and established structure–property relationships for methacrylate and thiourethane silane-containing materials. The results demonstrate that significant stress reductions and fracture toughness increases are obtained by judiciously tailoring the organic–inorganic interface in dental composites.

ZEISS Airyscan: Optimizing Usage for Fast, Gentle, Super-Resolution Imaging

The Zeiss Airyscan microscope transforms a diffraction-limited, point-scanning confocal microscope into a super-resolution microscope using a specialized 32-channel Airyscan detector. By improving resolution twofold and signal-to-noise ratio eightfold relative to conventional confocal microscopes while retaining confocal functionality, the Airyscan microscope has become a very popular super-resolution imaging tool for cell biologists. In this chapter, we describe the fundamentals of Airyscan imaging, with the aim of helping the reader determine the proper acquisition settings for different types of experiments, optimize imaging conditions, and process the raw Airyscan images to obtain final images with the best quality. We also provide some tips, tricks, and best practices for Airyscan imaging. Of note, while our focus is on the Airyscan function of this microscope rather than its conventional confocal function, the Airyscan unit comes as an add-on to the conventional Zeiss laser scanning confocal microscope. This protocol is for the first generation Airyscan Zeiss 800 series microscope.

Overexpression of a Novel Arabidopsis Gene SUPA Leads to Various Morphological and Abiotic Stress Tolerance Alternations in Arabidopsis and Poplar

With the development of sequencing technology, the availability of genome data is rapidly increasing, while functional annotation of genes largely lags behind. In Arabidopsis, the functions of nearly half of the proteins are unknown and this remains one of the main challenges in current biological research. In an attempt to identify novel and rapid abiotic stress responsive genes, a number of salt-up (SUP) regulated genes were isolated by analyzing the public transcriptomic data, and one of them, SUPA, was characterized in this study. The expression of SUPA transcripts was rapidly up-regulated by various abiotic stress factors (<15 min), and SUPA protein is mainly localized in the peroxisome. Overexpression of SUPA in Arabidopsis leads to the elevated accumulation of reactive oxygen species (ROS), strong morphological changes and alternations in abiotic stress tolerance. The transcriptome analysis showed changes in expression of genes involved in stress response and plant development. Interestingly, ectopic overexpression of SUPA in poplar leads to a dwarf phenotype with severely curved leaves and changes in the plant tolerance of abiotic stresses. Our study reinforces the potential roles of SUPA in normal plant growth and the abiotic stress response.

Characterization of Retinol Stabilized in Phosphatidylcholine Vesicles with and without Antioxidants

Retinol stability has been reported to be improved by encapsulation in liposomes, both with and without cholesterol. However, this improvement is limited because of lipid peroxidation. In this study, we compare the stability of retinol in phosphatidylcholine liposomes under ultraviolet (UV) light or standard room air, with and without the addition of antioxidants. Both butylated hydroxytoluene (BHT) and a proprietary mix (StoppOx) improved the shelf stability from <10 to over 30 d. The addition of cholesterol had no effect. Fluorescence imaging showed a heterogeneous distribution of retinol within the vesicles, including within the aqueous layer. Fluorescence lifetimes were equally heterogeneous. Under UV irradiation, StoppOx protected retinol for significantly longer than BHT and via different mechanisms. This suggests that natural antioxidants work well to improve the retinol stability, but that further work to determine the optimal vesicle structure remains to be performed.

An image-based data-driven analysis of cellular architecture in a developing tissue

Quantitative microscopy is becoming increasingly crucial in efforts to disentangle the complexity of organogenesis, yet adoption of the potent new toolbox provided by modern data science has been slow, primarily because it is often not directly applicable to developmental imaging data. We tackle this issue with a newly developed algorithm that uses point cloud-based morphometry to unpack the rich information encoded in 3D image data into a straightforward numerical representation. This enabled us to employ data science tools, including machine learning, to analyze and integrate cell morphology, intracellular organization, gene expression and annotated contextual knowledge. We apply these techniques to construct and explore a quantitative atlas of cellular architecture for the zebrafish posterior lateral line primordium, an experimentally tractable model of complex self-organized organogenesis. In doing so, we are able to retrieve both previously established and novel biologically relevant patterns, demonstrating the potential of our data-driven approach.

Imaging of the immune system - towards a subcellular and molecular understanding

Immune responses involve many types of leukocytes that traffic to the site of injury, recognize the insult and respond appropriately. Imaging of the immune system involves a set of methods and analytical tools that are used to visualize immune responses at the cellular and molecular level as they occur in real time. We will review recent and emerging technological advances in optical imaging, and their application to understanding the molecular and cellular responses of neutrophils, macrophages and lymphocytes. Optical live-cell imaging provides deep mechanistic insights at the molecular, cellular, tissue and organism levels. Live-cell imaging can capture quantitative information in real time at subcellular resolution with minimal phototoxicity and repeatedly in the same living cells or in accessible tissues of the living organism. Advanced FRET probes allow tracking signaling events in live cells. Light-sheet microscopy allows for deeper tissue penetration in optically clear samples, enriching our understanding of the higher-level organization of the immune response. Super-resolution microscopy offers insights into compartmentalized signaling at a resolution beyond the diffraction limit, approaching single-molecule resolution. This Review provides a current perspective on live-cell imaging in vitro and in vivo with a focus on the assessment of the immune system.

Upon microbial challenge, human neutrophils undergo rapid changes in nuclear architecture and chromatin folding to orchestrate an immediate inflammatory gene program

Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neutrophils rapidly (<3 h) repositioned the ensemble of proinflammatory genes toward the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape, permitting an immediate transcriptional response upon bacterial exposure. We found that activated enhancers, marked by increased deposition of H3K27Ac, were highly enriched for cistromic elements associated with PU.1, CEBPB, TFE3, JUN, and FOSL2 occupancy. These data reveal how upon microbial challenge the cohesin machinery is recruited to an activated enhancer repertoire to instruct changes in chromatin folding, nuclear architecture, and to activate an inflammatory gene program.

Complementary Superresolution Visualization of Composite Plant Microtubule Organization and Dynamics

Microtubule bundling is an essential mechanism underlying the biased organization of interphase and mitotic microtubular systems of eukaryotes in ordered arrays. Microtubule bundle formation can be exemplified in plants, where the formation of parallel microtubule systems in the cell cortex or the spindle midzone is largely owing to the microtubule crosslinking activity of a family of microtubule associated proteins, designated as MAP65s. Among the nine members of this family in Arabidopsis thaliana, MAP65-1 and MAP65-2 are ubiquitous and functionally redundant. Crosslinked microtubules can form high-order arrays, which are difficult to track using widefield or confocal laser scanning microscopy approaches. Here, we followed spatiotemporal patterns of MAP65-2 localization in hypocotyl cells of Arabidopsis stably expressing fluorescent protein fusions of MAP65-2 and tubulin. To circumvent imaging difficulties arising from the density of cortical microtubule bundles, we use different superresolution approaches including Airyscan confocal laser scanning microscopy (ACLSM), structured illumination microscopy (SIM), total internal reflection SIM (TIRF-SIM), and photoactivation localization microscopy (PALM). We provide insights into spatiotemporal relations between microtubules and MAP65-2 crossbridges by combining SIM and ACLSM. We obtain further details on MAP65-2 distribution by single molecule localization microscopy (SMLM) imaging of either mEos3.2-MAP65-2 stochastic photoconversion, or eGFP-MAP65-2 stochastic emission fluctuations under specific illumination conditions. Time-dependent dynamics of MAP65-2 were tracked at variable time resolution using SIM, TIRF-SIM, and ACLSM and post-acquisition kymograph analysis. ACLSM imaging further allowed to track end-wise dynamics of microtubules labeled with TUA6-GFP and to correlate them with concomitant fluctuations of MAP65-2 tagged with tagRFP. All different microscopy modules examined herein are accompanied by restrictions in either the spatial resolution achieved, or in the frame rates of image acquisition. PALM imaging is compromised by speed of acquisition. This limitation was partially compensated by exploiting emission fluctuations of eGFP which allowed much higher photon counts at substantially smaller time series compared to mEos3.2. SIM, TIRF-SIM, and ACLSM were the methods of choice to follow the dynamics of MAP65-2 in bundles of different complexity. Conclusively, the combination of different superresolution methods allowed for inferences on the distribution and dynamics of MAP65-2 within microtubule bundles of living A. thaliana cells.