Correlative Super-Resolution Fluorescence Imaging and Atomic Force Microscopy for the Characterization of Biological Samples

Electromechanical Photophysics of GFP Packed Inside Viral Protein Cages Probed by Force-Fluorescence Hybrid Single-Molecule Microscopy

Packing biomolecules inside virus capsids has opened new avenues for the study of molecular function in confined environments. These systems not only mimic the highly crowded conditions in nature, but also allow their manipulation at the nanoscale for technological applications. Here, green fluorescent proteins are packed in virus-like particles derived from P22 bacteriophage procapsids. The authors explore individual virus cages to monitor their emission signal with total internal reflection fluorescence microscopy while simultaneously changing the microenvironment with the stylus of atomic force microscopy. The mechanical and electronic quenching can be decoupled by ≈10% each using insulator and conductive tips, respectively. While with conductive tips the fluorescence quenches and recovers regardless of the structural integrity of the capsid, with the insulator tips quenching only occurs if the green fluorescent proteins remain organized inside the capsid. The electronic quenching is associated with the coupling of the protein fluorescence emission with the tip surface plasmon resonance. In turn, the mechanical quenching is a consequence of the unfolding of the aggregated proteins during the mechanical disruption of the capsid.

Single Crystals Heterogeneity Impacts the Intrinsic and Extrinsic Properties of Metal-Organic Frameworks

At present, an enormous characterization gap exists between the study of the crystal structure of a material and its bulk properties. Individual particles falling within this gap cannot be fully characterized in a correlative manner by current methods. The authors address this problem by exploiting the noninvasive nature of optical microscopy and spectroscopy for the correlative analysis of metal-organic framework particles in situ. They probe the intrinsic as well as extrinsic properties in a correlated manner. The authors show that the crystal shape of MIL-88A strongly impacts its optical absorption. Furthermore, the question of how homogeneously water is distributed and adsorbed within one of the most promising materials for harvesting water from humid air, MOF-801, is addressed. The results demonstrate the considerable importance of the particle level and how it can affect the property of the material.

A feasible method for independently evaluating the mechanical properties of glial LC and RGC axons by combining atomic force microscopy measurement with image segmentation

PURPOSE

The deformation of lamina cribrosa (LC) under the elevated intraocular pressure (IOP) might squeeze the retinal ganglion cell (RGC) axons and impair the visual function. Mechanical behaviors of LC and RGC axons are supposed to be related to the optic nerve damage of glaucoma patients. However, they cannot be independently studied with the existing methods because the LC and RGC axons intertwine in the LC area. This study proposed a feasible method to evaluate the respective mechanical properties of glial LC and RGC axons of rats.

METHODS

The atomic force microscope (AFM) nano-indentation experiment was performed on unfixed cryosection samples acquired from the glial LC tissues of eight eyes from four rats. For each sample, three regions of interests (ROIs) with sizes of 20 × 20 μm² were selected from the ventral, central and dorsal regions of the sample, respectively, and the nano-indentation was performed on 128 × 128 points within each ROI to obtain a Young's modulus image. The glial LC and RGC axons were segmented on each modulus images using Otsu thresholding segmentation method, and their respective Young's modulus was further extracted for statistical analysis.

RESULTS

Young's modulus of glial LC and RGC axons are 297 ± 98 kPa and 76 ± 36 kPa in ventral regions, 342 ± 84 kPa and 84 ± 32 kPa in central regions, 280 ± 104 kPa and 75 ± 30 kPa in dorsal regions, respectively. No significant differences are found among the Young's modulus of different regions, both for glial LC and RGC axons.

CONCLUSIONS

This study takes the nature property of the LC area as a composite material into consideration, and proposes a feasible method to distinguish between the glial LC and RGC axons and measure their respective Young's modulus. These findings may provide useful information for establishing finite element models of the optic nerve head and promote the study on the deformation of the optic nerve under high intraocular pressure, and finally contribute to the early diagnosis of glaucoma.

A correlative super-resolution protocol to visualise structural underpinnings of fast second-messenger signalling in primary cell types

Nanometre-scale cellular information obtained through super-resolution microscopies are often unaccompanied by functional information, particularly transient and diffusible signals through which life is orchestrated in the nano-micrometre spatial scale. We describe a correlative imaging protocol which allows the ubiquitous intracellular second messenger, calcium (Ca2+), to be directly visualised against nanoscale patterns of the ryanodine receptor (RyR) Ca2+ channels which give rise to these Ca2+ signals in wildtype primary cells. This was achieved by combining total internal reflection fluorescence (TIRF) imaging of the elementary Ca2+ signals, with the subsequent DNA-PAINT imaging of the RyRs. We report a straightforward image analysis protocol of feature extraction and image alignment between correlative datasets and demonstrate how such data can be used to visually identify the ensembles of Ca2+ channels that are locally activated during the genesis of cytoplasmic Ca2+ signals.

Protein-, polymer-, and silica-based luminescent nanomaterial probes for super resolution microscopy: a review

Super resolution microscopy was developed to overcome the Abbe diffraction limit, which effects conventional optical microscopy, in order to study the smaller components of biological systems. In recent years nanomaterials have been explored as luminescent probes for super resolution microscopy, as many have advantages over traditional fluorescent dye molecules. This review will summarize several different types of nanomaterial probes, covering quantum dots, carbon dots, and dye doped nanoparticles. For the purposes of this review the term "nanoparticle" will be limited to polymer-based, protein-based, and silica-based nanoparticles, including core-shell structured nanoparticles. Luminescent nanomaterials have shown promise as super-resolution probes, and continued research in this area will yield new advances in both materials science and biochemical microscopy at the nanometer scale.

Combined AFM and super-resolution localisation microscopy: Investigating the structure and dynamics of podosomes

Podosomes are mechanosensitive attachment/invasion structures that form on the matrix-adhesion interface of cells and protrude into the extracellular matrix to probe and remodel. Despite their central role in many cellular processes, their exact molecular structure and function remain only partially understood. We review recent progress in molecular scale imaging of podosome architecture, including our newly developed localisation microscopy technique termed HAWK which enables artefact-free live-cell super-resolution microscopy of podosome ring proteins, and report new results on combining fluorescence localisation microscopy (STORM/PALM) and atomic force microscopy (AFM) on one setup, where localisation microscopy provides the location and dynamics of fluorescently labelled podosome components, while the spatial variation of stiffness is mapped with AFM. For two-colour localisation microscopy we combine iFluor-647, which has previously been shown to eliminate the need to change buffer between imaging modes, with the photoswitchable protein mEOS3.2, which also enables live cell imaging.

Direct Correlation of Single-Particle Motion to Amorphous Microstructural Components of Semicrystalline Poly(ethylene oxide) Electrolytic Films

Semicrystalline polymers constitute some of the most widely used materials in the world, and their functional properties are intimately connected to their structure on a range of length scales. Many of these properties depend on the micro- and nanoscale heterogeneous distribution of crystalline and amorphous phases, but this renders the interpretation of ensemble averaged measurements challenging. We use superlocalized widefield single-particle tracking in conjunction with AFM phase imaging to correlate the crystalline morphology of lithium-triflate-doped poly(ethylene oxide) thin films to the motion of individual fluorescent probes at the nanoscale. The results demonstrate that probe motion is intrinsically isotropic in amorphous regions and that, without altering this intrinsic diffusivity, closely spaced, often parallel, crystallite fibers anisotropically constrain probe motion along intercalating amorphous channels. This constraint is emphasized by the agreement between crystallite and anisotropic probe trajectory orientations. This constraint is also emphasized by the extent of the trajectory confinement correlated to the width of the measured gaps between adjacent crystallites. This study illustrates with direct nanoscale correlations how controlled and periodic arrangement of crystalline domains is a promising design principle for mass transport in semicrystalline polymer materials without compromising their mechanical stability.

STORM without enzymatic oxygen scavenging for correlative atomic force and fluorescence superresolution microscopy

Superresolution microscopy based on localisation is usually performed in a buffer containing enzymatic oxygen scavenger, which facilitates reversible photoswitching of the dye molecules. This makes correlative fluorescence localisation and atomic force microscopy (AFM) challenging, because enzymatic oxygen scavenging interferes with the AFM cantilevers. Here we report on the blinking kinetics of a new red cyanine dye, iFluor-647, which is similar to the Alexa-647 dye commonly used for superresolution microscopy, but with brightness and blinking properties which are superior to Alexa-647 in a buffer without enzymatic oxygen scavenger. We measure the blinking behaviour of iFluor-647 in buffers with and without enzymatic oxygen scavenger with different thiol concentrations. We then apply this dye for correlative localisation and atomic force microscopy in a buffer without enzymatic oxygen scavenger, which allows acquisition of AFM and superresolution images without buffer change.

Bridging the gap: Super-resolution microscopy of epithelial cell junctions

Cell junctions are critical for cell adhesion and communication in epithelial tissues. It is evident that the cellular distribution, size, and architecture of cell junctions play a vital role in regulating function. These details of junction architecture have been challenging to elucidate in part due to the complexity and size of cell junctions. A major challenge in understanding these features is attaining high resolution spatial information with molecular specificity. Fluorescence microscopy allows localization of specific proteins to junctions, but with a resolution on the same scale as junction size, rendering internal protein organization unobtainable. Super-resolution microscopy provides a bridge between fluorescence microscopy and nanoscale approaches, utilizing fluorescent tags to reveal protein organization below the resolution limit. Here we provide a brief introduction to super-resolution microscopy and discuss novel findings into the organization, structure and function of epithelial cell junctions.