Augmented 3D super-resolution of fluorescence-free nanoparticles using enhanced dark-field illumination based on wavelength-modulation and a least-cubic algorithm

Organelle Proximity Analysis for Enhanced Quantification of Mitochondria-Endoplasmic Reticulum Interactions in Single Cells via Super-Resolution Microscopy

Mitochondria (MT) and the endoplasmic reticulum (ER) maintain lipid and calcium homeostasis through membrane contacts, particularly MT-ER contacts (MERCs), spanning distances from 10 to 50 nm. However, the variation of different distance ranges and the metabolic factors influencing this variation remain poorly understood. This study employed microfluidic chip-based super-resolution microscopy in conjunction with a Moore-Neighbor tracing-incorporated organelle proximity analysis algorithm. This approach enabled precise three-dimensional localization of single-fluorescence protein molecules within narrow and irregular membrane proximities. It achieved lateral localization precision of less than 20 nm, resulting in a minimum MERC distance of approximately 8 nm in spatial and mean distances across multiple threshold ranges. Additionally, we demonstrated that the MERC distance variation was correlated with MT size rather than ER width. The proportion of each distance range varied significantly after the stimuli. Free cholesterol showed a negative correlation with various distances, while distances of 10-30 nm were associated with glucose, glutamine, and pyruvic acid. Furthermore, the 30-40 nm range was influenced by citric acid. These results underscore the role of advanced subcellular organelle analysis in elucidating the single-molecule behavior and organelle morphology in single-cell studies.

Method for nanoparticles uptake evaluation based on double labeled fluorescent cells scanned in enhanced darkfield microscopy

We present a method that integrates the standard imaging tools for locating and detecting unlabeled nanoparticles (NPs) with computational tools for partitioning cell volumes and NPs counting within specified regions to evaluate their internal traffic. The method uses enhanced dark field CytoViva optical system and combines 3D reconstructions of double fluorescently labeled cells with hyperspectral images. The method allows the partitioning of each cell image into four regions: nucleus, cytoplasm, and two neighboring shells, as well as investigations across thin layers adjacent to the plasma membrane. MATLAB scripts were developed to process the images and to localize NPs in each region. Specific parameters were computed to assess the uptake efficiency: regional densities of NPs, flow densities, relative accumulation indices, and uptake ratios. The results of the method are in line with biochemical analyses. It was shown that a sort of saturation limit for intracellular NPs density is reached at high extracellular NPs concentrations. Higher NPs densities were found in the proximity of the plasma membranes. A decrease of the cell viability with increasing extracellular NPs concentration was observed and explained the negative correlation of the cell eccentricity with NPs number.

Minimizing the Optical Illusion of Nanoparticles in Single Cells Using Four-Dimensional Cuboid Multiangle Illumination-Based Light-Sheet Super-Resolution Imaging

Although light-sheet-based super-resolution microscopy is an excellent detection technique for biological samples because of minimal photodamage, uneven light paths due to solid-angle illumination limits it, resulting in an optical illusion. Furthermore, the optical illusion limits the observations of individual molecules in diffraction. In this study, a four-dimensional cuboid multiangle illumination-based light-sheet super-resolution (4D CMLS) imaging system was developed to minimize optical illusions in cells. The lab-built 4D CMLS imaging system was integrated with total internal reflection fluorescence and a differential interference contrast microscope. A specially designed rotatable cuboid prism simply overcame the optical illusion by rotating a specimen on the prism to change the direction of light coming from an illumination lens. 4D CMLS reconstructed images of nanoparticles of different sizes were acquired in multi-illumination angles of 0°, 90°, 180°, and 270°. Additionally, a 4D multiangle illumination-based algorithm was created to select the optimal illumination angle by combining three-dimensional super-resolution imaging with multiangle observation, even in the presence of obstacles. The 4D CMLS imaging method demonstrates the in-depth 4D observation of samples at an optimum angle that can be used in various applications, such as single-molecule and subcellular organelle observations in single cells at subdiffraction limit resolutions that describe the scenario of nature.

Ultrasensitive Hypoxia Sensing at the Single-Molecule Level via Super-Resolution Quantum Dot-Linked Immunosandwich Assay

Activated hypoxia-inducible factor-1alpha (HIF-1α) plays an important role in the adaptive response of tumor cells to oxygen changes through the transcriptional activation of genes that regulate important biological processes required for tumor survival and progression. In this study, we developed an ultrasensitive hypoxia sensor based on read-out with quantum dots on a gold nanodisc (quantum dot-linked immunosandwich assay, QLISA) with excellent selectivity for HIF-1α. The immunoassay platform was established by comparing the immune response results using Qdot525 as a detection nanoprobe instead of a fluorescent dye (Alexa488) (fluorescent-linked immunosandwich assay, FLISA). In addition, using three-dimensional total internal reflection fluorescence microscopy, the platform was optically sectioned along the z-axis at 10 nm intervals to compare the height difference between the nanodisc and the nanoprobe following the QLISA and FLISA procedures and to localize the target location. Here, the super-resolution QLISA (srQLISA)-based hypoxia sensor exhibited high accuracy and precision for the detection of HIF-1α-extracted samples in cancer spheroids compared with the super-resolution FLISA (srFLISA) method. The developed nanobiosensor method demonstrated a wide dynamic linear detection range of 32.2 zM-8.0 pM with a limit of detection of 16 zM under optimal experimental conditions for HIF-1α, an approximate 10⁶-fold enhanced detection sensitivity compared with the conventional enzyme-linked immunosorbent assay method based on absorbance. The detection of HIF-1α using the newly developed srQLISA sensor allows for independently predicting tumor progression and early cancer onset increases in the microvasculature density of tumor lesions.

Quantifying intracellular trafficking of silica-coated magnetic nanoparticles in live single cells by site-specific direct stochastic optical reconstruction microscopy

Background

Nanoparticles have been used for biomedical applications, including drug delivery, diagnosis, and imaging based on their unique properties derived from small size and large surface-to-volume ratio. However, concerns regarding unexpected toxicity due to the localization of nanoparticles in the cells are growing. Herein, we quantified the number of cell-internalized nanoparticles and monitored their cellular localization, which are critical factors for biomedical applications of nanoparticles.

Methods

This study investigates the intracellular trafficking of silica-coated magnetic nanoparticles containing rhodamine B isothiocyanate dye [MNPs@SiO₂(RITC)] in various live single cells, such as HEK293, NIH3T3, and RAW 264.7 cells, using site-specific direct stochastic optical reconstruction microscopy (dSTORM). The time-dependent subdiffraction-limit spatial resolution of the dSTORM method allowed intracellular site-specific quantification and tracking of MNPs@SiO₂(RITC).

Results

The MNPs@SiO₂(RITC) were observed to be highly internalized in RAW 264.7 cells, compared to the HEK293 and NIH3T3 cells undergoing single-particle analysis. In addition, MNPs@SiO₂(RITC) were internalized within the nuclei of RAW 264.7 and HEK293 cells but were not detected in the nuclei of NIH3T3 cells. Moreover, because of the treatment of the MNPs@SiO₂(RITC), more micronuclei were detected in RAW 264.7 cells than in other cells.

Conclusion

The sensitive and quantitative evaluations of MNPs@SiO₂(RITC) at specific sites in three different cells using a combination of dSTORM, transcriptomics, and molecular biology were performed. These findings highlight the quantitative differences in the uptake efficiency of MNPs@SiO₂(RITC) and ultra-sensitivity, varying according to the cell types as ascertained by subdiffraction-limit super-resolution microscopy.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-021-01147-1.

Cubic spline-based depth-dependent localization of mitochondria-endoplasmic reticulum contacts by three-dimensional light-sheet super-resolution microscopy

The contact distance between mitochondria (Mito) and endoplasmic reticulum (ER) has received considerable attention owing to their crucial function in maintaining lipid and calcium homeostasis. Herein, cubic spline algorithm-based depth-dependent fluorescence-free three-dimensional light-sheet super-resolution microscopy (3D LSRM) with dual-wavelength illumination sources was investigated to study the distance of Mito-ER contacts in various live cells. To detect wavelength-dependent scattering, 12 nm gold nanoparticles (AuNPs) and 20 nm silver nanoparticles (AgNPs) as fluorescence-free nanoprobes were conjugated with Mito and ER. The cubic spline algorithm-based method showed improved localization precision in lateral and axial directions compared with that for previously used least squares and least cubic algorithms. The cubic spline-based depth-dependent localization was applied to the spatial localization of nanoprobes in super-resolution images, in which the average distance of Mito and ER was 22.4 nm in HeLa cells, 22.2 nm in RAW264.7 macrophage cells, 21.9 nm in AGS cells, 21.4 nm in HT29 cells, and 21.3 nm in HEK293 cells. The distances were ∼12% larger than those previously determined by electron microscopy, which demonstrated that this method was accessible and reliable for studying the intracellular structures of various live cells at the subdiffraction limit resolution.

Dark-field/hyperspectral microscopy for detecting nanoscale particles in environmental nanotoxicology research

Nanoscale contaminants (including engineered nanoparticles and nanoplastics) pose a significant threat to organisms and environment. Rapid and non-destructive detection and identification of nanosized materials in cells, tissues and organisms is still challenging, although a number of conventional methods exist. These approaches for nanoparticles imaging and characterisation both inside the cytoplasm and on the cell or tissue outer surfaces, such as electron or scanning probe microscopies, are unquestionably potent tools, having excellent resolution and supplemented with chemical analysis capabilities. However, imaging and detection of nanomaterials in situ, in wet unfixed and even live samples, such as living isolated cells, microorganisms, protozoans and miniature invertebrates using electron microscopy is practically impossible, because of the elaborate sample preparation requiring chemical fixation, contrast staining, matrix embedding and exposure into vacuum. Atomic force microscopy, in several cases, can be used for imaging and mechanical analysis of live cells and organisms under ambient conditions, however this technique allows for investigation of surfaces. Therefore, a different approach allowing for imaging and differentiation of nanoscale particles in wet samples is required. Dark-field microscopy as an optical microscopy technique has been popular among researchers, mostly for imaging relatively large specimens. In recent years, the so-called "enhanced dark field" microscopy based on using higher numerical aperture light condensers and variable numerical aperture objectives has emegred, which allows for imaging of nanoscale particles (starting from 5 nm nanospheres) using almost conventional optical microscopy methodology. Hyperspectral imaging can turn a dark-field optical microscope into a powerful chemical characterisation tool. As a result, this technique is becoming popular in environmental nanotoxicology studies. In this Review Article we introduce the reader into the methodology of enhanced dark-field and dark-field-based hyperspectral microscopy, covering the most important advances in this rapidly-expanding area of environmental nanotoxicology.

Three-Dimensional Orientation of Anisotropic Plasmonic Aggregates at Intracellular Nuclear Indentation Sites by Integrated Light Sheet Super-Resolution Microscopy

Three-dimensional (3D) orientations of individual anisotropic plasmonic nanoparticles in aggregates were observed in real time by integrated light sheet super-resolution microscopy ( iLSRM). Asymmetric light scattering of a gold nanorod (AuNR) was used to trigger signals based on the polarizer angle. Controlled photoswitching was achieved by turning the polarizer and obtaining a series of images at different polarization directions. 3D subdiffraction-limited super-resolution images were obtained by superlocalization of scattering signals as a function of the anisotropic optical properties of AuNRs. Varying the polarizer angle allowed resolution of the orientation of individual AuNRs. 3D images of individual nanoparticles were resolved in aggregated regions, resulting in as low as 64 nm axial resolution and 28 nm spatial resolution. The proposed imaging setup and localization approach demonstrates a convenient method for imaging under a noisy environment where the majority of scattering noise comes from cellular components. This integrated 3D iLSRM and localization technique was shown to be reliable and useful in the field of 3D nonfluorescence super-resolution imaging.

New microscopy technique based on position localization of scattering particles

We introduce the Holographic - Single Scatterer Localization Microscopy in which we combine dynamical laser speckle illumination with centroid localization of backscattered light spots in order to localize isolated scattering particles. The reconstructed centroid images show very accurate particle localization, with precision much better than the width of diffraction-limited image of the particles recorded by the CCD. Furthermore, the method provides an improved resolution in distinguishing two very close scattering objects compared to the standard laser scanning techniques and can be assimilated to a confocal technique in the ability of light background rejection in three-dimensional disposition of scattering objects. The illumination is controlled via a digital holography setup based on the use of a spatial light modulator. This allows not only a high level of versatility in the illumination patterns, but also the remarkable characteristics of absence of moving mechanical parts, typical of the laser scanning techniques, and the possibility of strongly miniaturizing the setup.