Multicolor Imaging Research Articles

Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates

Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to perform a wide range of critical cellular functions by maintaining spatiotemporal regulation and organizing intracellular biochemistry. However, aberrant phase transitions are implicated in a multitude of human diseases. Here, we demonstrate that two neuronal proteins, namely tau and prion, undergo complex coacervation driven by domain-specific electrostatic interactions to yield highly dynamic, mesoscopic liquid-like droplets. The acidic N-terminal segment of tau interacts electrostatically with the polybasic N-terminal intrinsically disordered segment of the prion protein (PrP). We employed a unique combination of time-resolved tools that encompass several orders of magnitude of timescales ranging from nanoseconds to seconds. These studies unveil an intriguing symphony of molecular events associated with the formation of heterotypic condensates comprising ephemeral, domain-specific, short-range electrostatic nanoclusters. Our results reveal that these heterotypic condensates can be tuned by RNA in a stoichiometry-dependent manner resulting in reversible, multiphasic, immiscible, and ternary condensates of different morphologies ranging from core-shell to nested droplets. This ternary system exhibits a typical three-regime phase behavior reminiscent of other membraneless organelles including nucleolar condensates. We also show that upon aging, tau:PrP droplets gradually convert into solid-like co-assemblies by sequestration of persistent intermolecular interactions. Our vibrational Raman results in conjunction with atomic force microscopy and multi-color fluorescence imaging reveal the presence of amorphous and amyloid-like co-aggregates upon maturation. Our findings provide mechanistic underpinnings of overlapping neuropathology involving tau and PrP and highlight a broader biological role of complex phase transitions in physiology and disease.

Tetra-color superresolution microscopy based on excitation spectral demixing

Multicolor imaging allows protein colocalizations and organelle interactions to be studied in biological research, which is especially important for single-molecule localization microscopy (SMLM). Here, we propose a multicolor method called excitation-resolved stochastic optical reconstruction microscopy (ExR-STORM). The method, which is based on the excitation spectrum of fluorescent dyes, successfully separated four spectrally very close far-red organic fluorophores utilizing three excitation lasers with cross-talk of less than 3%. Dyes that are only 5 nm apart in the emission spectrum were resolved, resulting in negligible chromatic aberrations. This method was extended to three-dimensional (3D) imaging by combining the astigmatic method, providing a powerful tool for resolving 3D morphologies at the nanoscale.

Multi-color live-cell fluorescence imaging of primary ciliary membrane assembly and dynamics.

The ciliary membrane is continuous with the plasma membrane but has distinct lipid and protein composition, which is key to defining the function of the primary cilium. Ciliary membranes dynamically assemble and disassemble in association with the cell cycle and directly transmit signals and molecules through budding membranes. Various imaging approaches have greatly advanced the understanding of the ciliary membrane function. In particular, fluorescence live-cell imaging has revealed important insights into the dynamics of ciliary membrane assembly by monitoring the changes of fluorescent-tagged ciliary proteins. Protein dynamics can be tracked simultaneously using multi-color live cell imaging by coupling ciliary-associated factors with different colored fluorescent tags. Ciliary membrane and membrane associated-proteins such as Smoothened, 5-HTr6, SSTR3, Rab8a, and Arl13b have been used to track ciliary membranes and centriole proteins like Centrin1/2, CEP164, and CEP83 are often used to mark the ciliary basal body. Here, we describe a method for studying ciliogenesis membrane dynamics using spinning disk confocal live-cell imaging.

Tunable emissive carbon polymer dots with solvatochromic behaviors for trace water detection and cell imaging

The solvatochromic behavior of CPDs in aprotic or protic solvents affected by hydrogen bonding (R = H, alkyl chain), which can be applied in trace water detection and multi-color imaging.

Critical Steps in DAPI and FISH Imaging of Chromosome Spread Preparations.

The final step in a long period of chromosome slide experiments is the publication of DAPI and multicolor fluorescence images. Quite often the result of published artwork is disappointing due to insufficient knowledge of image processing and presentation. In this chapter we describe some errors of fluorescence photomicrographs and how to avoid them. We include suggestions of processing chromosome images with simple examples of image processing in Photoshop® or the like, without the need of complex knowledge of the software programs.

Multimodal algorithm for differential diagnosis of tumors and tumor-like diseases of the ocular fundus

Diagnosing pathologies of the ocular fundus and performing differential diagnosis of intraocular tumors along with conventional ophthalmoscopy can involve additional visualization methods such as ultrasonography, fluorescein angiography and optical coherence tomography (OCT). Many researchers note the importance of employing a multimodal approach in differential diagnosis of intraocular tumors, but there is no universally established algorithm for a rational choice of both the combination of visualizing methods, and the sequence of their application with consideration of the ophthalmoscopy findings and the results of first-line diagnostic methods. The article presents author's own multimodal algorithm developed for differential diagnosis of tumors and tumor-like diseases of the ocular fundus. This approach involves the use of such methods as OCT and Multicolor fluorescence imaging, with exact sequence and combination determined on the basis of ophthalmoscopy and ultrasonography findings.

Fluorescence imaging analysis of the glioma microenvironment

Glioma is the most malignant brain cancer. The neurons, macrophages, T cells and other immune cells constitute the glioma immunosuppressive microenvironment. The accurate spatial distribution of these cells in the glioma microenvironment and its relationship with glioma metastasis is unknown. We constructed a mouse glioma cell line stably expressing the large Stokes-shifted yellow fluorescent protein and applied it to the multicolor immunofluorescence imaging. The imaging data revealed that the neurons were sparsely distributed in the glioma core and the number of neurons decreased by 90% compared with normal brain site. The spatial distribution of monocyte-macrophages and microglia is heterogeneous. The monocyte-macrophages and T cells were heavily recruited into the glioma core and metastasis. There was no significant difference in the distribution of microglia among glioma core, margin, and normal brain site. Our results provided new perspectives for targeting immune regulation cells and developing new immunotherapy strategies for glioma.

A comprehensive method to study the DNA's association with lamin and chromatin compaction in intact cell nuclei at super resolution.

Super-resolution fluorescence microscopy has revolutionized multicolor imaging of nuclear structures due to the combination of high labeling specificity and high resolution. Here we expanded the recently developed fBALM (DNA structure fluctuation-assisted binding activated localization microscopy) method by developing a stable methodological sequence that enables dual-color imaging of high-resolution genomic DNA together with an immunofluorescently labeled intranuclear protein. Our measurements of the nuclear periphery, imaging DNA and LaminB1 in biologically relevant samples, show that this novel dual-color imaging method is feasible for further quantitative evaluations. We were able to study the relative spatial signal organization between DNA and LaminB1 by means of highly specific colocalization measurements at nanometer resolution. Measurements were performed with and without the antifade embedding medium ProLong Gold, which proved to be essential for imaging of LaminB1, but not for imaging of SytoxOrange labeled DNA. The localization precision was used to differentiate between localizations with higher and lower amounts of emitting photons. We interpret high intensity localizations to be renatured DNA sections in which a high amount of Sytox Orange molecules were bound. This could give insight into the denaturation kinetics of DNA during fBALM. These results were further complemented by measurements of γH2AX and H3K9me3 signal organization to demonstrate differences within the chromatin landscape, which were quantified with image processing methods such as Voronoi segmentation.

Harmonizing the growing fluorogenic RNA aptamer toolbox for RNA detection and imaging.

The field of fluorogenic RNA aptamers is a burgeoning research area that aims to address the lack of naturally fluorescent RNA molecules for RNA detection and imaging. These small RNA tags bind to their fluorogenic ligands resulting in significant fluorescent enhancement, leading to a molar brightness comparable to or exceeding that of fluorescent proteins. In the past decade, multiple light-up RNA aptamer systems have been isolated that bind to a broad range of ligands involving several distinct mechanisms of fluorogenicity. This review discusses the selection methods used to isolate fluorogenic RNA aptamers. More than seventy fluorogenic aptamer:ligand pairs are evaluated using objective parameters (e.g., molar brightness, binding affinity, fluorophore exchange capabilities and other details). General guidelines for choosing fluorescent RNA tools, with an emphasis on single-molecule detection and multi-colour imaging applications are provided. Lastly the importance of global standards for evaluating fluorogenic RNA aptamer systems is discussed.

Super-resolution imaging of linearized chromatin in tunable nanochannels.

Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Furthermore, through careful selection of self-blinking fluorescent dyes and the design of the nanochannel system, we achieve direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging of the linearized chromatin. As an initial demonstration, rDNA chromatin extracted from Tetrahymena is analyzed by multi-color imaging of total DNA, newly synthesized DNA, and newly synthesized histone H3. Our analysis reveals a relatively even distribution of newly synthesized H3 across two halves of the rDNA chromatin with palindromic symmetry, supporting dispersive nucleosome segregation. As a proof-of-concept study, our work achieves super-resolution imaging of native chromatin fibers linearized and immobilized in tunable nanochannels. It opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.

Revisiting Pyronin Y, A Classical Photostable Xanthene Dye useful for Cost Effective Multimodal Fluorescence Microscopy

In search of cost-effective alternatives for developing high-throughput imaging methods for NETosis, several classical histology dyes were revisited. It was found that the second component of the marketed premix Methyl Green-Pyronin Y (Gurr’s Certistain) has several properties compatible with this aim. Therefore, a simple purification method was developed, and the obtained Pyronin Y fraction, dried and redissolved in a biocompatible medium, was found to be photostable, selectively internalized by non-viable cells, and had spectroscopic features that make it compatible with many common fluorophores for multicolor imaging. Under certain conditions, Pyronin Y has a maximum absorption at 548nm, so it can be excited by 514nm and 561nm Laser lines, with an emission peak at 571nm. Experiments with human polymorphonuclear leukocytes (PMN) enzymatically induced to NETosis confirmed the usefulness of Pyronin Y in detecting early NETotic nuclei. By super-resolution microscopy, the compound enhances the visualization of nuclear subdomains, enabling the reduction of assay duration by detecting morphological alterations indicative of initial NETosis steps. Also, in chemically fixed resting PMN, azurophilic granules were stained by Pyronin Y, suggesting a previously unappreciated nucleic acid-independent staining mechanism. In addition, fluorescence lifetime imaging microscopy (FLIM) followed by time domain phasor analysis demonstrates the utility of the dye in differentiating between NETs released into the extracellular space and the genetic material still remaining inside the cell.

Simultaneous labeling and multicolor fluorescence imaging of multiple immune cells on liver frozen section by polychromatic quantum dots below freezing points

A method for simultaneous labeling and multicolor fluorescence imaging of different hepatic immune cells below freezing point is established based on quantum dots. In the experiment, carbon quantum dots with emission wavelength of 435 nm, CdTe@CdS quantum dots at 542 nm and CdSe@ZnS quantum dots at 604 nm are synthesized respectively, it is found that when the mass fractions of KCl (as antifreeze) are 12 %, 14 %, and 12 %, respectively, the three quantum dot dispersion systems remain liquid state at −20 °C. After they are conjugated with the corresponding secondary antibodies, agarose gel electrophoresis, circular dichroism and capillary electrophoresis confirm the effectiveness of conjugation. By indirect immunofluorescence method, the above three quantum dot fluorescent probes are used to simultaneously and specifically target a variety of liver immune cells, and the multi-color simultaneous imaging of different liver immune cells is realized under the same excitation wavelength, it is found that hepatic macrophages are arranged radially in the liver, hepatic stellate cells present punctate distribution, and hepatic sinusoidal endothelial cells present circular distribution, which is consistent with the results of H&E staining and ultrathin section TEM. This study provides an important technical means for elucidating the structure and function of the liver.

Werner syndrome protein works as a dimer for unwinding and replication fork regression.

The determination of the oligomeric state of functional enzymes is essential for the mechanistic understanding of their catalytic activities. RecQ helicases have diverse biochemical activities, but it is still unclear how their activities are related to their oligomeric states. We use single-molecule multi-color fluorescence imaging to determine the oligomeric states of Werner syndrome protein (WRN) during its unwinding and replication fork regression activities. We reveal that WRN binds to a forked DNA as a dimer, and unwinds it without any change of its oligomeric state. In contrast, WRN binds to a replication fork as a tetramer, and is dimerized during activation of replication fork regression. By selectively inhibiting the helicase activity of WRN on specific strands, we reveal how the active dimers of WRN distinctly use the energy of ATP hydrolysis for repetitive unwinding and replication fork regression.

Acidic pH-Triggered Live-Cell Lysosome Specific Tracking, Ratiometric pH Sensing, and Multicolor Imaging by Visible to NIR Switchable Cy-7 Dyes.

We have demonstrated an efficient synthetic route with crystal structures for the construction of acidic pH-triggered visible-to-NIR interchangeable ratiometric fluorescent pH sensors. This bioresponsive probe exhibits pH-sensitive reversible absorption/emission features, low cytotoxicity, a huge 322 nm bathochromic spectral shift with augmented quantum yield from neutral to acidic pH, high sensitivity and selective targeting ability of live-cell lysosomes with ideal pKa , off-to-on narrow NIR absorption/fluorescence signals with high molar absorption coefficient at acidic lysosomal lumen, and in-situ live-cell pH-activated ratiometric imaging of lysosomal pH. Selective staining and ratiometric pH imaging in human carcinoma live-cell lysosomes were monitored by dual-channel confocal laser scanning microscope using a pH-activatable organic fluorescent dye comprising a morpholine moiety for lysosome targeting and an acidic pH openable oxazolidine ring. Moreover, real-time tracking of lysosomes, 3D, and multicolor live-cell imaging have been achieved using the synthesized pH-activatable probe.

SYNTHESIS OF THE SYMBOLOGIES OF MULTICOLOR INTERFERENCE-RESISTANT BAR CODES ON THE BASE OF MULTI-VALUED BCH CODES

Context. The problem of constructing a set of barcode patterns for multicolor barcodes that are resistant to distortions of one or two elements within each pattern is considered.
 Objective. The goal of the work is ensuring the reliability of the reading of multi-color barcode images.
 Method. A multicolor barcode pattern has the property of interference immunity if its digital equivalent (vector) is a codeword of a multi-valued (non-binary) correcting code capable to correct errors (distortions of the pattern elements). It is shown that the construction of barcode patterns should be performed on the basis of a multi-valued correcting BCH code capable to correct two errors. A method is proposed for constructing a set of interference-resistant barcode patterns of a given capacity, which ensure reliable reproduction of data when they are read from a carrier. A procedure for encoding data with a multi-valued BCH code based on the generator matrix of the code using operations by the modulo of a prime number has been developed. A new method of constructing the check matrix of the multivalued BCH code based on the vector representation of the elements of the finite field is proposed. A generalized algorithm for generating symbologies of a multi-color barcode with the possibility of correcting double errors in barcode patterns has been developed. The method also makes it possible to build symbology of a given capacity based on shortened BCH codes. A method of reducing the generator and check matrices of a multi-valued full BCH code to obtain a shortened code of a given length is proposed. It is shown that, in addition to correction double errors, multi-valued BCH codes also make it possible to detect errors of higher multiplicity – this property is enhanced when using shortened BCH codes. The method provides for the construction of a family of multicolor noise-immune barcodes.
 Results. On the basis of the developed software tools, statistical data were obtained that characterize the ability of multi-valued BCH codes to detect and correct errors, and on their basis to design multi-color interference-resistant bar codes.
 Conclusions. The conducted experiments have confirmed the operability of the proposed algorithmic tools and allow to recommend it for use in practice for developing interference-resistant multi-color barcodes in automatic identification systems.

Super-Resolution Live Imaging of Cargo Traffic Through the Golgi Apparatus in Mammalian Cells.

Super-resolution confocal live imaging microscopy (SCLIM) we developed provides high-speed, high-resolution, three- and four-dimensional, and multicolor simultaneous imaging. Using this technology, we are now able to observe the fine details of various dynamic events going on in living cells, such as membrane traffic and organelle dynamics. The retention using selective hooks (RUSH) system is a powerful tool to control synchronous release of natural cargo proteins of interest from the endoplasmic reticulum in mammalian cells. In this chapter, we describe a method for visualizing secretory cargo traffic within and around the Golgi apparatus in HeLa cells using SCLIM in combination with the RUSH assay.

Comparison of Multicolor Scanning Laser Imaging and Color Fundus Photography in Evaluating Vessel Whitening in Branch Retinal Vein Occlusion

Introduction: Few studies have explored MultiColor™ imaging (MCI) in evaluating retinal vascular diseases, particularly branch retinal vein occlusion (BRVO). This study aimed to compare the identification of retinal vessel whitening in BRVO using MCI by scanning confocal laser versus conventional white-flash color fundus photography (CFP). Methods: Paired images of consecutive patients diagnosed with BRVO who underwent same-day MCI and CFP were reviewed. Visualization of vessel whitening on MCI and CFP was graded and scored using a scale by two masked graders. A longitudinal analysis of the vessel grading score was performed to evaluate the vessel whitening detection by MCI. A correlation analysis was conducted between vessel whitening on MCI and the measured area of retinal ischemia on fluorescein angiography to evaluate the MCI performance. Results: Forty-four eyes of 41 patients (mean age 69 ± 14 years; 61% female) were analyzed. MCI demonstrated superior vessel whitening visibility score than CFP (p < 0.001). Longitudinal analysis showed no significant changes in vessel whitening visibility scores over a mean follow-up time of 430 ± 648 days (p = 0.655). There was a significantly positive correlation between the grading score of vessels whitening by MCI and the area of ischemia by fluorescein angiography (r2 = 0.15; p = 0.036). Conclusion: MCI appears to provide a superior detection of whitening BRVO compared to CFP, serving as a rapid and non-invasive correlate of retinal ischemia.

Multicolor fluorescence digital mapping of rare-earth ion-labeled porous silica nanoprobes for the recognition of various antibiotic residues in milk

• Three fluorescence-enhanced rare-earth ions labeled porous silica nanoprobes were developed. • Multicolor fluorescence responses allow for sensitive and selective detection of antibiotics. • Digital mapping of fluorescence array enables rapid identification of multiple antibiotics. • Applicability of method was demonstrated for detecting multiple residues in milk. The misuse of antibiotics not only has adverse effects on the environment but also has become a serious problem that threatens human health. However, the simultaneous, rapid, and accurate detection of various antibiotic residues remains a challenge for actual samples. Herein, a new sensing strategy was developed by using fluorescence-enhanced rare-earth ion-labeled mesoporous silica nanoprobes (MSN–COOH–Eu 3+ , MSN–COOH–Tb 3+ , and MSN–COOH–La 3+ ) and their array to detect three representative antibiotics, namely, oxytetracycline (OTC), norfloxacin (NFX), and gatifloxacin (GTFX). The three rare-earth ion-labeled nanoprobes exhibited red, green, and blue fluorescence when reacting with OTC, NFX, and GTFX, respectively, because of the antenna effect of rare-earth ions or restricted conformational rotation of antibiotics. The multicolor digital imaging pattern generated from the three-nanoprobe array also enables the rapid identification of OTC, NFX, and GTFX in various combinations. Meanwhile, the linear detection ranges for OTC, NFX, and GTA were 11–30, 0–0.9, and 0–1.4 μM, respectively, and their detection limits were 0.016, 0.007, and 0.005 μM, respectively. Furthermore, satisfactory recoveries of 90.1%–107.8% were obtained in OTC, NFX, or GTFX-spiked raw milk, indicating the potential application of our method for monitoring various antibiotic residues in daily food safety controls.

Comparison of Multimodal Imaging for the Characterization of Geographic Atrophy.

The purpose of this study was to compare the performances of infrared (IR), fundus autofluorescence (FAF), and multicolor (MC) imaging in the characterization of geographic atrophy, with a focus on the possibility to detect incomplete retinal pigmented and outer retinal atrophy (iRORA) on en face imaging. The ground truth was established by two graders evaluating atrophy on spectral-domain optical coherence tomography (SD-OCT) images. A score for visibility of foveal sparing and margins of atrophy was attributed. Measurement of the atrophic area and the fovea-to-margin distance were performed. Accuracy of detection of foveal sparing was evaluated through comparison with B-scan images ground truth, with/without the inclusion of patients with foveal iRORA. Seventy patients were included in this study. Foveal sparing and atrophy's margins subjective visibility were significantly higher rated on MC images compared to IR and FAF (P < 0.005 and P < 0.001). Agreement with OCT B-scan assessed foveal sparing revealed a significantly higher area under receiver operating characteristic curves (AUROC) for MC images at the analysis performed both with (0.876) and without (0.853) inclusion of patients with foveal iRORA (P < 0.001 and P = 0.006). Quantitative measurements revealed lower atrophy extension (P = 0.026) and fovea-to-margin distance (P = 0.019) with MC imaging. MC imaging performed better at foveal sparing assessment, especially in the setting of foveal iRORA. MC also resulted in higher visibility of atrophy's margins, lower atrophy extension measurements, and lower distance from the fovea to atrophy's margins compared to both FAF and IR. MC rated significantly higher in foveal sparing and atrophy detection, higher visibility of atrophy's margins, lower atrophy extension measurements, and lower distance from the fovea to atrophy's margins, compared to FAF and IR.

Application of multicolour reflectance imaging for the characterisation of inherited retinal disorders.

To describe the role of multicolour reflectance images (MCI) in the phenotypic diagnosis of inherited retinal disorders (IRDs). A retrospective review of consecutive patients affected by IRDs examined with MCI techniques from January to December 2019 at a tertiary care referral centre. All patients had MCI, fundus autofluorescence and optical coherence tomography taken at the same time point. The ability of each modality to highlight clinical features was assessed. Lesions' size was also measured and compared among imaging modalities. Thirty eyes of 15 patients were included in the study, 6 males and 9 females, with a mean age of 44 years (range: 19-57.5). The most frequent clinical diagnosis were: pattern dystrophies, and late-onset retinal degeneration. Next-generation or Sanger sequencing analysis was carried out in all patients. Blue and green reflectance were relevant in highlighting peripheral mottling in fundus albipunctatus, pseudoreticular drusen in late-onset retinal degeneration, parafoveal hyperreflective area in bull's eye maculopathy and crystals in Bietti's crystalline dystrophy. Likewise, it is to mention the ability of infrared reflectance to detect hyperreflective patches in posterior pole in neurofibromatosis type 1 and retinal changes in pattern dystrophies and cone dystrophies. Multicolour imaging technique enables the detection of clinical features that could be overlooked by other imaging modalities, allowing accurate phenotypic characterisation of IRDs and guiding genetic diagnose, and may become a meaningful monitoring tool for future treatments.