Microscopy methods for Clostridioides difficile

Microscopic technologies including light and fluorescent, transmission electron microscopy (TEM), scanning electron microscopy (SEM), and cryo-electron microscopy have been widely utilized to visualize Clostridioides difficile at the molecular, cellular, community, and structural biology level. This comprehensive review summarizes the microscopy tools (fluorescent and reporter system) in their use to study different aspects of C. difficile life cycle and virulence (sporulation, germination) or applications (detection of C. difficile or use of antimicrobials). With these developing techniques, microscopy tools will be able to find broader applications and address more challenging questions to study C. difficile and C. difficile infection.

A comparison of confocal and epifluorescence microscopy for quantification of RNAScope and immunohistochemistry fluorescent images

BACKGROUND

Quantification of RNA expression and protein production in fluorescent stainings provides critical information concerning neurodevelopment. A trustable independent quantification technique requires acquisition of reliable images prior to image processing. There is uncertainty in existing literature regarding the use of confocal microscopy compared to standard epifluorescence microscopy, especially in the context of RNA in situ hybridization protocols.

NEW METHOD

The hindbrains of developing rat embryos from embryologic day 14 (E14) to E20 were sectioned and stained for expression of Hoxb1, Hoxb2, and Phox2b using both RNAScope and immunohistochemistry. Islet1 was used for identification of hindbrain motoneuron cell bodies. Slides were imaged using both confocal and epifluorescence microscopy.

RESULTS

Expression patterns of both mRNA and protein were similar in both imaging modalities. Analyses of Hoxb1 and Hoxb2 mRNA expression were particularly concordant between-scopes, with similar p-values and posthoc differences between timepoints. Confocal imaging of Hoxb2 protein yielded a significant peak at E18, but this level of significance was not reached using epifluorescence microscopy. Although similar trends were observed, only Phox2b RNAScope results were statistically significant when analyzed with confocal microscopy. In contrast, Phox2b immunostaining analyses showed significant differences using both microscopes.

COMPARISON WITH EXISTING METHODS

Researchers may save time and financial resources if epifluorescence microscopy provides comparable or equal results as confocal.

CONCLUSIONS

Epifluorescence microscopy appears sufficient for quantification of RNAScope experiments with relatively low puncta per cell, while confocal microscopy gives clearer definition to immunohistochemical protein relationships and may be preferable especially in targets with low protein production.

Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA-FISH

Plant small RNAs are 21-24 nucleotide, noncoding RNAs that function as regulators in plant growth and development. Colorimetric detection of plant small RNAs was made possible with the introduction of locked nucleic acid probes. However, fluorescent detection of plant small RNAs has been challenging due to the high autofluorescence from plant tissue. Here we report a fluorescent in situ detection method for plant small RNAs. This method can be applied to most plant samples and tissue types and also can be adapted for single-molecule detection of small RNAs with super-resolution microscopy.

Brain Imaging and Registration in Larval Zebrafish

Registration of larval zebrafish brain scans to a common reference brain enables comparison of transgene and gene expression patterns, neuroanatomy, and morphometry. Here we describe methods for staining and mounting larval zebrafish to facilitate whole-brain fluorescence imaging. Following image acquisition, we provide a template for aligning brain images to a reference atlas using nonlinear registration with the ANTs software package.

Examining Phosphatases Through Immunofluorescent Microscopy

Immunofluorescent microscopy enables the examination of cellular expression and localization of proteins. Cellular localization can often impact protein function, as certain molecular interactions occur in specific cellular compartments. Here we describe in detail the processes necessary for identifying phosphatases in the cell through immunofluorescent microscopy. Identification of phosphatase expression and localization could lead to the discovery of protein function in disease states along with potential substrates and binding partners.

A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging

The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.

Subcellular Colocalization Assay of Host Factors with Viral Replication Complex in the dsRNA Reporter Nicotiana benthamiana

As obligate pathogens, plant viruses co-opt several host factors for viral replication. Double-stranded RNA (dsRNA) plays important roles in plants, including eliciting innate immune responses and RNA interference. dsRNA also represents the genetic entities of a number of viruses and is a marker of infection by positive-sense single-stranded RNA viruses. Previous detection methods for RNA viruses basically relied on immunological methods, but later researchers discovered that the dsRNA-binding domain of the Flock house virus B2 protein is a perfect alternative to the J2 mAb for sensitive and rapid detection of long dsRNA in vitro and in vivo, and developed B2:GFP transgenic Nicotiana benthamiana line. This method describes in detail how to visualize host factors in the viral replication complex in time and space with the help of B2:GFP transgenic plants, exemplified by Turnip mosaic virus (TuMV), a representative virus member of the Potyviruses.

The Use of In Vivo Reflectance Confocal Microscopy for the Diagnosis and Classification of Melasma

In recent years, in vivo reflectance confocal microscopy (RCM) draws attention as a noninvasive method to precisely detect abnormal pigment deposits, providing additional cytological details for the diagnosis, classification, and treatment monitoring of melasma. This article aims to review the RCM findings of melasma and classify melasma with RCM findings.

Uncovering the synergistic interplay of melatonin and spermidine in the alleviation of nematode stress in Solanum lycopersicum

Worldwide, biotic stress severely degrades agricultural output and increases the risk of starvation. Root-knot nematodes (Meloidogyne incognita) are one of the important endoparasites that adversely affect the growth and development in plants, thus affecting their productivity. Contrarily, humans employ a number of unfriendly techniques, such as chemical applications, to manage biotic stressors. Use of Plant Growth Regulators is an environmentally safe alternative method against chemical pesticides that can be used to defend plants from biotic stressors. Melatonin and polyamines have been broadly found in multiple physiological processes and in diverse biotic and abiotic stresses faced by plants. In the contemporaneous study, we conducted an in vitro experiment which disclosed that pretreated seeds with melatonin and spermidine (a polyamine), decreased root galls in afflicted plants and uplifted the growth of Solanum lycopersicum seedlings. According to our findings, tomato plants' photosynthetic efficiency dropped and reactive oxygen species levels dramatically rose after nematode inoculation. On the other hand, melatonin and spermidine decreased oxidative stress by scavenging hydrogen peroxide and decreased malonaldehyde. The present work investigated improvement in growth characteristics, photosynthetic pigments, antioxidative enzymes and non-antioxidative enzymes in PGR treated tomato seedlings even during the nematode stress. Confocal studies evaluated nuclear damage within root apices and intensity of blue colour was directly proportional to nuclear damage. The findings of the present investigation support the use of plant growth regulators, melatonin and spermidine as seed priming agent to manage nematode stress in plants.

Confocal micro X-ray fluorescence analysis for the non-destructive investigation of structured and inhomogeneous samples

Confocal micro X-ray fluorescence (CMXRF) spectroscopy is a non-destructive, depth-resolved, and element-specific technique that is used to analyze the elemental composition of a sample. For this, a focused beam of mono- or polychromatic X-rays is applied to excite the atoms in the sample, causing them to emit fluorescence radiation which is detected with focusing capillary optics. The confocal design of the instrument allows for depth-resolved analysis, in most cases with a resolution in the lower micrometer dimension after collecting X-rays from a predefined volume within the sample. The element-specific nature of the technique allows information to be obtained about the presence and concentration of specific elements in this volume. This makes CMXRF spectroscopy a valuable tool for a wide range of applications, especially when samples with an inhomogeneous distribution of elements and a relatively light matrix have to be analyzed, which are typical examples in materials science, geology, and biology. The technique is also commonly used in the art and archaeology fields to analyze the elemental composition of historical artifacts and works of art, helping to provide valuable insights into their provenance, composition, and making. Recent technical developments to increase sensitivity and efforts to improve quantification in three-dimensional samples will encourage wider use of this method across a multitude of fields of application in the near future. Confocal micro X-ray fluorescence (CMXRF) is based on the confocal overlap of two polycapillary lens foci, creating a depth-sensitive and non-destructive probing volume. Three-dimensional resolved element distribution images can be obtained by measuring the fluorescence intensity as function of the three-dimensional position.

Effect of continuous chelation on the dentinal tubule penetration of a calcium silicate-based root canal sealer: a confocal laser microscopy study

BACKGROUND

This study aimed to evaluate the effect of various irrigation protocols on the penetration depth of a calcium silicate-based sealer into dentinal tubules using confocal laser scanning microscopy (CLSM).

METHODS

Twenty single-rooted mandibular premolars were endodontically prepared and divided into the following two groups according to the irrigation protocol used (n = 10): Group I: NaOCl + EDTA and Group II: continuous chelation (NaOCl/Dual Rinse). Obturation was performed with the warm vertical compaction technique using TotalFill HiFlow bioceramic sealer mixed with a fluorophore dye. Samples were observed using CLSM at 10× to measure the percentage of sealer penetration and its maximum depth into the dentinal tubules. Data were analysed using one-way ANOVA followed by Tukey's post-hoc test. The significance level was set at p < 0.05 within all tests.

RESULTS

Comparing the overall results of all sections tested, no statistically significant differences existed between the groups regarding the percentage of sealer penetration (p = 0.612) and maximum depth of penetration (p > 0.05).

CONCLUSIONS

With both types of irrigation used, dentinal tubule penetration was higher in the coronal section than in the apical section. Continuous chelation using NaOCl/Dual Rinse HEDP performed better in the coronal segments, while irrigation using NaOCl + EDTA promoted a higher percentage of sealer penetration in the apical segment.

Recent Applications of Deconvolution Microscopy in Medicine

Deconvolution microscopy is a computational image-processing technique used in conjunction with fluorescence microscopy to increase the resolution and contrast of three-dimensional images. Fluorescence microscopy is a widely used technique in biology and medicine that involves labeling specific molecules or structures within a sample with fluorescent dyes and then electronically photographing the sample through a microscope. However, the resolution of conventional fluorescence microscopy is limited by diffraction within the microscope's optical path, which causes blurring of the image and reduces the ability to resolve structures in close proximity with one another. Deconvolution microscopy overcomes this limitation by means of computer-based image processing whereby mathematical algorithms are used to eliminate the blurring caused by the microscope's optics and thus obtain a higher-resolution image that reveals the fine details of the sample with greater accuracy. Deconvolution microscopy, which can be applied to a range of image acquisition modalities, including widefield, confocal, and super-resolution microscopy, has become an essential tool for studying the structure and function of biological systems at the cellular and molecular levels. In this perspective, the latest deconvolution techniques have been introduced and image-processing methods for medical purposes have been presented.

CAR T-cell behavior and function revealed by real-time imaging

Adoptive transfer of T-cells expressing chimeric antigen receptors (CAR) has shown remarkable clinical efficacy against advanced B-cell malignancies. Nonetheless, the field of CAR T-cells is currently facing several major challenges. In particular, the CAR T-cell strategy has not yet produced favorable clinical responses when targeting solid tumors. In this context, it is of paramount importance to understand the determinants that limit the efficacy of T-cell-based immunotherapy. Characterization of CAR T-cells is usually based on flow cytometry and whole-transcriptome profiling. These approaches have been very valuable to determine intrinsic elements that condition T-cell ability to proliferate and expand. However, they do not take into account spatial and kinetic aspects of T-cell responses. In particular, in order to control tumor growth, CAR T-cells need to enter into the tumor, migrate within a complex tumor environment, and form productive conjugates with their targets. Advanced imaging techniques combined with innovative preclinical models represent promising tools to uncover the dynamics of CAR T-cells. In this review, we will discuss recent results on the biology of engineered T-cells that have been obtained with real-time imaging microscopy. Important notions have emerged from these imaging-based studies, such as the multi-killing potential of CAR T-cells. Finally, we will highlight how imaging techniques combined with other tools can solve remaining unresolved questions in the field of engineered T-cells.

Time-Lapse Imaging and Morphometric Analysis of Tracheal Development in Drosophila

Detailed and quantitative analyses of the cellular events underlying the formation of specific organs or tissues is essential to understand the general mechanisms of morphogenesis and pattern formation. Observation of live tissues or whole-mount fixed specimens has emerged as the method of choice for identifying and quantifying specific cellular and tissular structures within the organism. In both cases, cell and subcellular structure identification and good quality image acquisition for these analyses are essential. Many markers for live imaging and fixed tissue are now available for detecting cell membranes, subcellular structures, and extracellular structures like the extracellular matrix (ECM). Combination of live imaging and analysis of fixed tissue is ideal to obtain a general and detailed picture of the events underlying embryonic development. By applying morphometric methods to both approaches, we can, in addition, obtain a quantitative evaluation of the specific parameters under investigation in morphogenetic and cell biological studies. In this chapter, we focus on the development of the tracheal system of Drosophila melanogaster, which provides an ideal paradigm to understand the formation of branched tubular organs. We describe the most used methods of imaging and morphometric analysis in tubulogenesis using mainly (but not exclusively) examples from embryonic development. We cover embryo preparation for fixed and live analysis of tubulogenesis, together with methods to visualize larval tracheal terminal cell branching and lumen formation. Finally, we describe morphometric analysis and quantification methods using fluorescent images of tracheal cells.

Visualizing Metal Distribution in Plants Using Synchrotron X-Ray Fluorescence Microscopy Techniques

Recent improvements in synchrotron-based X-ray fluorescence (SXRF) microscopy established it as an advanced analytical tool for analyzing 2D- and 3D distribution of mineral elements in plants. Among existing imaging techniques, SXRF microscopy offers several unique capabilities, including in situ metal quantification in plant tissues and high sensitivity, as low as 1 mg kg^-1, at the nanoscale spatial resolution. SXRF is increasingly utilized in different plant science disciplines to provide a fundamental understanding of metal homeostasis, and the function of trace elements in plant metabolism and development. Here, we describe methods for SXRF imaging, including sample preparation, the optimization of conventional SXRF for analyzing trace elements, and the development of confocal SXRF (C-SXRF).

Monitoring Plasma Membrane Injury-Triggered Endocytosis at Single-Cell and Single-Vesicle Resolution

Plasma membrane injury activates membrane trafficking and remodeling events that are required for the injured membrane to repair. With the rapidity of the membrane repair process, the repair response needs to be monitored at high temporal and spatial resolution. In this chapter, we describe the use of live cell optical imaging approaches to monitor injury-triggered bulk and individual vesicle endocytosis. Use of these approaches allows quantitatively assessment of the rate of retrieval of the injured plasma membrane by bulk endocytosis as well as by endocytosis of individual caveolae following plasma membrane injury.

Confocal Laser Scanning Imaging of Cell Junctions in Human Colon Cancer Cells

The intestinal epithelium is formed by a single layer of cells. These cells originate from self-renewal stem cells that give rise to various lineages of cells: Paneth, transit-amplifying, and fully differentiated cells (as enteroendocrine, goblet cells, and enterocytes). Enterocytes, also known as absorptive epithelial cells, are the most abundant cell type in the gut. Enterocytes have the potential to polarize as well as form tight junctions with neighbor cells which altogether serve to ensure both the absorption of "good" substances into the body and the blockage of "bad" substances, among other functions. Culture cell models such as the Caco-2 cell line have been proved to be valuable tools to study the fascinating functions of the intestine. In this chapter we outline some experimental procedures to grow, differentiate, and stain intestinal Caco-2 cells, as well as image them using two modes of confocal laser scanning microscopy.

Confocal Endomicroscopy Monitoring of Tumor Formation

The utilization of preclinical murine models of colorectal cancer (CRC) has been essential to our understanding of the onset and progression of disease. As the genetic complexity of these models evolves to better recapitulate emerging CRC subtypes, our ability to utilize these models to discover and validate novel therapeutic targets will also improve. This will be aided, in part, by the development of live animal imaging techniques, including confocal endomicroscopy for mice. Here in this chapter, we describe the combined use of standard white light endoscopy and confocal endomicroscopy thereby providing a method to rapidly image and assess changes in the colon of an individual live mouse in real time. These methods permit the generation of high-resolution cross-sectional images of the tumor microenvironment for immediate visualization of cells of interest, avoiding the need for euthanasia and tissue collection across multiple cohorts of mice.

Nano-microbial based technology employing polyvalent phage conjugate: A next generation weapon for antimicrobial resistance lurking behind wastewater

Worldwide, due to a dearth of innovative interventions, new forms of antimicrobial resistance (AMR) are being discovered every day in clinical and environmental settings. Therefore, it is necessary to remove these contaminants directly or indirectly from the environment. Nanomicrobial-based technology employing nanomaterials with microbes is a new paradigm that finds a place in the antimicrobial crisis. Microbial entities such as phages can be used to treat antimicrobial resistance, but phage resistance is challenging and limits its applicability. Similarly, nanotechnology will not be able to selectively remove resistant strains from the environment individually. Therefore, we employ nanomicrobial-based technology that aims to fill these gaps. In the present study, polyvalent phages were isolated from wastewater with an easy-to-use modified multi-host sequential approach, characterized and conjugated with magnetite (Fe₃O₄) nanoparticles with the modified formulation to form nanomicrobial conjugates (NMCs). These NMCs were subjected to characterization and in vitro antibacterial studies. The results indicated a significant polyvalency of phages in the order of Caudovirales. Transmission electron microscopy (TEM) analysis of Fe₃O₄ nanoparticles formed by the co-precipitation method showed a particle size of 30 ± 5 nm and the selected area electron diffraction (SAED) pattern indicates a single-phase crystalline structure. To form NMCs, isolated phages (10⁵ PFU/mL) were immobilized onto Fe₃O₄ nanoparticles. Further, surface modification of Fe₃O₄ nanoparticles enables the covalent association of phages. Biosurfactant-functionalized Fe₃O₄ nanoparticles (FNMCs) were found to have higher phage loading capacity, with a significant value of p < 0.0127 and a zeta potential of -22.2 mV. TEM studies and in vitro biofilm assay showed that NMCs exhibit promising antibacterial activity against various resistant bacterial strains. Pilot studies showed that NMCs can selectively eliminate up to 98.3% of AMR in wastewater. Thus, these findings indicate a synergistic effect of both phage and nanomaterial and this technology is expected to be a new lead in wastewater management.

Scanning laser ophthalmoscopy retroillumination: applications and illusions

Scanning laser ophthalmoscopes (SLOs) are used widely for reflectance, fluorescence or autofluorescence photography and less commonly for retroillumination imaging. SLOs scan a visible light or near-infrared radiation laser beam across the retina, collecting light from each retinal spot as it’s illuminated. An SLO’s clinical applications, image contrast and axial resolution are largely determined by an aperture overlying its photodetector. High contrast, reflectance images are produced using small diameter, centered apertures (confocal apertures) that collect retroreflections and reject side-scattered veiling light returned from the fundus. Retroillumination images are acquired with annular on-axis or laterally-displaced off-axis apertures that capture scattered light and reject the retroreflected light used for reflectance imaging. SLO axial resolution is roughly 300 μm, comparable to macular thickness, so SLOs cannot provide the depth-resolved chorioretinal information obtainable with optical coherence tomography’s (OCT’s) 3 μm axial resolution. Retroillumination highlights and shades the boundaries of chorioretinal tissues and abnormalities, facilitating detection of small drusen, subretinal drusenoid deposits and subthreshold laser lesions. It also facilitates screening for large-area chorioretinal irregularities not readily identified with other en face retinal imaging modalities. Shaded boundaries create the perception of lesion elevation or depression, a characteristic of retroillumination but not reflectance SLO images. These illusions are not reliable representations of three-dimensional chorioretinal anatomy and they differ from objective OCT en face topography. SLO retroillumination has been a useful but not indispensable retinal imaging modality for over 30 years. Continuing investigation is needed to determine its most appropriate clinical roles in multimodal retinal imaging.

Loss of Corneal Nerves and Corneal Haze in Patients with Fuchs' Endothelial Corneal Dystrophy with the Transcription Factor 4 Gene Trinucleotide Repeat Expansion

Objective

Seventy percent of Fuchs' endothelial corneal dystrophy (FECD) cases are caused by an intronic trinucleotide repeat expansion in the transcription factor 4 gene (TCF4). The objective of this study was to characterize the corneal subbasal nerve plexus and corneal haze in patients with FECD with (RE+) and without the trinucleotide repeat expansion (RE-) and to assess the correlation of these parameters with disease severity.

Design

Cross-sectional, single-center study.

Participants

Fifty-two eyes of 29 subjects with a modified Krachmer grade of FECD severity from 1 to 6 were included in the study. Fifteen of the 29 subjects carried an expanded TCF4 allele length of ≥ 40 cytosine-thymine-guanine repeats (RE+).

Main Outcomes Measures

In vivo confocal microscopy assessments of corneal nerve fiber length (CNFL), corneal nerve branch density, corneal nerve fiber density (CNFD), and anterior corneal stromal backscatter (haze); Scheimpflug tomography densitometry measurements of haze in anterior, central, and posterior corneal layers.

Results

Using confocal microscopy, we detected a negative correlation between FECD severity and both CNFL and CNFD in the eyes of RE+ subjects (Spearman ρ = -0.45, P = 0.029 and ρ = -0.62, P = 0.0015, respectively) but not in the eyes of RE- subjects. Additionally, CNFD negatively correlated with the repeat length of the expanded allele in the RE+ subjects (Spearman ρ = -0.42, P = 0.038). We found a positive correlation between anterior stromal backscatter and severity in both the RE+ and RE- groups (ρ = 0.60, P = 0.0023 and ρ = 0.44, P = 0.024, respectively). The anterior, central, and posterior Scheimpflug densitometry measurements also positively correlated with severity in both the RE+ and RE- groups (P = 5.5 × 10^-5, 2.5 × 10^-4, and 2.9 × 10^-4, respectively, after adjusting for the expansion status in a pooled analysis. However, for patients with severe FECD (Krachmer grades 5 and 6), the posterior densitometry measurements were higher in the RE+ group than in the RE- group (P < 0.05).

Conclusions

Loss of corneal nerves in FECD supports the classification of the TCF4 trinucleotide repeat expansion disorder as a neurodegenerative disease. Haze in the anterior, central, and posterior cornea correlate with severity, irrespective of the genotype. Quantitative assessments of corneal nerves and corneal haze may be useful to gauge and monitor FECD disease severity in RE+ patients.

In vivo confocal microscopic study of corneal innervation in Sjögren's Syndrome with or without small fiber neuropathy

PURPOSE

To study changes in the subbasal nerve plexus by In vivo confocal microscopy (IVCM) in Sjögren's Syndrome (SS) with or without associated Small Fiber Neuropathy (SFN), in order to prevent diagnostic delay.

METHODS

Seventy-one patients with SS, including 19 with associated SFN, 20 healthy volunteers and 20 patients with Meibomian gland dysfunction (MGD) were included in this retrospective case-control study. IVCM was used to investigate subbasal nerve plexus density and morphology.

RESULTS

Corneal sensitivity as evaluated with the Cochet-Bonnet aesthesiometer was significantly reduced in the SS group versus the control group (P = 0.026) and the MGD group (P = 0.037). The number of inflammatory cells was significantly increased in the SS group to 86.2 ± 82.1 cells/mm² compared to the control group (P < 0.001). The density of the subbasal nerve plexus was significantly reduced to 16.7 ± 6.5 mm/mm² in the SS group compared to the control group (P < 0.005) and the MGD group (P = 0.042). The tortuosity of the nerves in the SS group was significantly increased compared to the control group (P < 0.001) and the MGD group (P = 0.025). The average number of subbasal nerve plexus neuromas was significantly increased in the SS group compared to the control group (P = 0.001), with a significant increase in the average number of neuromas in SS patients with associated SFN compared to SS patients without SFN (P = 0.008).

CONCLUSION

IVCM can be useful to detect corneal nerve changes in SS patients and may allow earlier diagnosis of the disease and to consider new therapeutic approaches.

Bonding effects of cleaning protocols and time-point of acid etching on dentin impregnated with endodontic sealer

Objectives

This study aimed to investigate the bonding effects of cleaning protocols on dentin impregnated with endodontic sealer residues using ethanol (E) or xylol (X). The effects of dentin acid etching immediately (I) or 7 days (P) after cleaning were also evaluated. For bonding to dentin, universal adhesive (Scotchbond Universal; 3M ESPE) was used. The persistence of sealer residues, hybrid layer formation and microshear bond strength were the performed analysis.

Materials and Methods

One hundred and twenty bovine dentin specimens were allocated into 4 groups (n = 10): G1 (E+I); G2 (X+I); G3 (E+P); and G4 (X+P). The persistence of sealer residues was evaluated by SEM. Confocal laser scanning microscopy images were taken to measure the formed hybrid layer using the Image J program. For microshear bond strength, 4 resin composite cylinders were placed over the dentin after the cleaning protocols. ANOVA followed by Tukey test and Kruskal-Wallis followed by Dunn test were used for parametric and non-parametric data, respectively (α = 5%).

Results

G2 and G4 groups showed a lower persistence of residues (p < 0.05) and thicker hybrid layer than the other groups (p < 0.05). No bond strength differences among all groups were observed (p > 0.05).

Conclusions

Dentin cleaning using xylol, regardless of the time-point of acid etching, provided lower persistence of residues over the surface and thicker hybrid layer. However, the bond strength of the universal adhesive system in etch-and-rinse strategy was not influenced by the cleaning protocols or time-point of acid etching.

Is Real-Time Microscopy on the Horizon? A Brief Review of the Potential Future Directions in Clinical Breast Tumor Microscopy Implementation

We will briefly review the current paradigm and some recent developments in the area of clinical breast microscopy, highlighting several promising commercially available, and research-based platforms. Confocal microscopy (reflectance, fluorescence, and spectrally encoded), optical coherence tomography (wide field and full field), stereomicroscopy, open-top light sheet microscopy, microscopy with ultraviolet surface excitation, nonlinear microscopy, Raman scattering microscopy, photoacoustic microscopy, and needle microendoscopy will be discussed. Non-microscopic methods for breast pathology assessment are beyond the scope of this review. These microscopic technologies have to varying degrees the potential for transforming breast cancer care, but in order for any of these to be integrated into clinical practice there are several hurdles to overcome. In our review we will focus on what needs to be done in order for the commercially available technologies to become more established, what the technologies in the research domain need to do in order to reach the commercial realm; and finally, what the field of breast pathology might look like if these technologies were to be widely adopted.

Mesenchymal stem cell secretome protects against oxidative stress-induced ocular blast visual pathologies

Visual deficits are a common concern among subjects with head trauma. Stem cell therapies have gained recent attention in treating visual deficits following head trauma. Previously, we have shown that adipose-derived stem cell (ASC) concentrated conditioned medium (ASC-CCM), when delivered via an intravitreal route, yielded a significant improvement in vision accompanied by a decrease in retinal neuroinflammation in a focal cranial blast model that indirectly injures the retina. The purpose of the current study is to extend our previous studies to a direct ocular blast injury model to further establish the preclinical efficacy of ASC-CCM. Adult C57BL/6J mice were subjected to repetitive ocular blast injury (rOBI) of 25 psi to the left eye, followed by intravitreal delivery of ASC-CCM (∼200 ng protein/2 μl) or saline within 2-3 h. Visual function and histological changes were measured 4 weeks after injury and treatment. In vitro, Müller cells were used to evaluate the antioxidant effect of ASC-CCM. Visual acuity, contrast sensitivity, and b-wave amplitudes in rOBI mice receiving saline were significantly decreased compared with age-matched sham blast mice. Immunohistological analyses demonstrated a significant increase in glial fibrillary acidic protein (a retinal injury marker) in Müller cell processes, DNA/RNA damage, and nitrotyrosine (indicative of oxidative stress) in the retina, while qPCR analysis revealed a >2-fold increase in pro-inflammatory cytokines (TNF-α, ICAM1, and Ccl2) in the retina, as well as markers for microglia/macrophage activation (IL-1β and CD86). Remarkably, rOBI mice that received ASC-CCM demonstrated a significant improvement in visual function compared to saline-treated rOBI mice, with visual acuity, contrast sensitivity, and b-wave amplitudes that were not different from those in sham mice. This improvement in visual function also was associated with a significant reduction in retinal GFAP, neuroinflammation markers, and oxidative stress compared to saline-treated rOBI mice. In vitro, Müller cells exposed to oxidative stress via increasing doses of hydrogen peroxide demonstrated decreased viability, increased GFAP mRNA expression, and reduced activity for the antioxidant catalase. On the other hand, oxidatively stressed Müller cells pre-incubated with ASC-CCM showed normalized GFAP, viability, and catalase activity. In conclusion, our study demonstrates that a single intravitreal injection of ASC-CCM in the rOBI can significantly rescue retinal injury and provide significant restoration of visual function. Our in vitro studies suggest that the antioxidant catalase may play a major role in the protective effects of ASC-CCM, uncovering yet another aspect of the multifaceted benefits of ASC secretome therapies in neurotrauma.

Image-Based Single-Molecule Analysis of Notch-Dependent Transcription in Its Natural Context

Notch signaling is crucial to animal development and homeostasis. Notch triggers the transcription of its target genes, which produce diverse outcomes depending on context. The high resolution and spatially precise assessment of Notch-dependent transcription is essential for understanding how Notch operates normally in its native context in vivo and how Notch defects lead to pathogenesis. Here we present biological and computational methods to assess Notch-dependent transcriptional activation in stem cells within their niche, focusing on germline stem cells in the nematode Caenorhabditis elegans. Specifically, we describe visualization of single RNAs in fixed gonads using single-molecule RNA fluorescence in situ hybridization (smFISH), live imaging of transcriptional bursting in the intact organism using the MS2 system, and custom-made MATLAB codes, implementing new image processing algorithms to capture the spatiotemporal patterns of Notch-dependent transcriptional activation. These methods allow a powerful analysis of in vivo transcriptional activation and its dynamics in a whole tissue. Our methods can be adapted to essentially any tissue or cell type for any transcript.

Imaging Fluorescent Nuclear Pore Complex Proteins in C. elegans

C. elegans is a well-characterized and relatively simple model organism, making it attractive for studying nuclear pore complex proteins in cell and developmental biology. C. elegans is transparent and highly amendable to genetic manipulation. Therefore, it is possible to generate fluorescently tagged proteins and combine this with various light microscopy techniques to study protein behavior in space and time. Here, we provide protocols to prepare both fixed and live C. elegans for confocal and light sheet microscopy. This enables the analysis of nuclear pore complex proteins from embryonic stages to the aging adult.

Span 80/TPGS modified lipid-coated chitosan nanocomplexes of acyclovir as a topical delivery system for viral skin infections

Acyclovir (ACR) is considered the gold standard drug for the treatment of skin viral infections caused by the herpes simplex or varicella-zoster virus. However, topical therapy with ACR is hindered by its poor skin penetrability, thus necessitating high doses and frequent administrations. This study was proposed to formulate a modified lipid-coated chitosan nanocomplexes (LCNCs) of acyclovir (ACR), containing span 80 and TPGS, to boost the dermal delivery of ACR and improve the therapeutic outcomes. LCNCs were formulated through a self-assembly method, and the statistical analysis and the optimization were performed via a general 2³ factorial design. Three formulation variables were selected; namely, the amount of chitosan (A), the amount of glyceryl monooleate (GMO) (B), and span 80: D-α-tocopheryl polyethylene glycol succinate (Vitamin ETPGSorTPGS) ratio (C). Four measured attributes were determined; viz., the particle size (PS) in nm, the polydispersity index (PDI), the zeta potential (ZP) in mV, and the entrapment efficiency percentages (EE%). The optimal formulation (LCNCs 8), formulated with 600 mg chitosan, 120 mg GMO, and 3:1 span 80: TPGS ratio, possessed PS of 177.50 ± 1.41 nm, PDI value of 0.28 ± 0.02, ZP of -10.70 ± 0.85 mV, and EE% of 77.20 ± 2.40 %, and was able to sustain ACR release over 24 h. Transmission electron microscopy displayed LCNCs architecture as a polymeric core of chitosan with a lipid coat of GMO, and the solid-state characterization results confirmed the dispersion of ACR in LCNCs. The ex vivo permeation study and the in vivo dermatokinetics profile verified the boosted accumulation of ACR in the skin via LCNCs, while the confocal laser scanning microscopy revealed the heightened penetrability of LCNCs. The topical application of LCNCs demonstrated a safe profile via the modified Draize test and histopathological examinations. Inclusively, ACR-loaded LCNCs could be a promising topical formulation with an advanced dermal delivery status for the treatment of skin viral infections.

Investigating molecular crowding during cell division and hyperosmotic stress in budding yeast with FRET

Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear how these events are coordinated and how they integrate with regulation of molecular crowding. We use the budding yeast Saccharomyces cerevisiae as a model system to study these questions using recent progress in optical fluorescence microscopy and crowding sensing probe technology. We used a Förster Resonance Energy Transfer (FRET) based sensor, illuminated by confocal microscopy for high throughput analyses and Slimfield microscopy for single-molecule resolution, to quantify molecular crowding. We determine crowding in response to cellular growth of both mother and daughter cells, in addition to osmotic stress, and reveal hot spots of crowding across the bud neck in the burgeoning daughter cell. This crowding might be rationalized by the packing of inherited material, like the vacuole, from mother cells. We discuss recent advances in understanding the role of crowding in cellular regulation and key current challenges and conclude by presenting our recent advances in optimizing FRET-based measurements of crowding while simultaneously imaging a third color, which can be used as a marker that labels organelle membranes. Our approaches can be combined with synchronized cell populations to increase experimental throughput and correlate molecular crowding information with different stages in the cell cycle.

Multicolor 3D Confocal Imaging of Thick Tissue Sections

In multicellular organisms, most physiological and pathological processes involve an interplay between various cells and molecules that act both locally and systemically. To understand how these complex and dynamic processes occur in time and space, imaging techniques are key. Advances in tissue processing techniques and microscopy now allow us to probe these processes at a large scale and at the same time at a level of detail previously unachievable. Indeed, it is now possible to reliably quantify multiple protein expression levels at single-cell resolution in whole organs using three-dimensional fluorescence imaging techniques. Here we describe a method to prepare adult mouse bone tissue for multiplexed confocal imaging of thick tissue sections. Up to eight different fluorophores can be multiplexed using this technique and spectrally resolved using standard confocal microscopy. The optical clearing method described allows detection of these fluorophores up to a depth of >700 μm in the far-red. Although the method was initially developed for bone tissue imaging, we have successfully applied it to several other tissue types.

Parameter estimation in fluorescence recovery after photobleaching: quantitative analysis of protein binding reactions and diffusion

Fluorescence recovery after photobleaching (FRAP) is a common experimental method for investigating rates of molecular redistribution in biological systems. Many mathematical models of FRAP have been developed, the purpose of which is usually the estimation of certain biological parameters such as the diffusivity and chemical reaction rates of a protein, this being accomplished by fitting the model to experimental data. In this article, we consider a two species reaction–diffusion FRAP model. Using asymptotic analysis, we derive new FRAP recovery curve approximation formulae, and formally re-derive existing ones. On the basis of these formulae, invoking the concept of Fisher information, we predict, in terms of biological and experimental parameters, sufficient conditions to ensure that the values all model parameters can be estimated from data. We verify our predictions with extensive computational simulations. We also use computational methods to investigate cases in which some or all biological parameters are theoretically inestimable. In these cases, we propose methods which can be used to extract the maximum possible amount of information from the FRAP data.

Parasitemia Evaluation in Mice Infected with Schistosoma mansoni

Schistosomiasis is a neglected tropical disease. Its treatment relies on the use of a single drug, praziquantel. Due to treatment limitations, an alternative for schistosomiasis chemotherapy is required; thus, a better understanding of parasite biology and host-parasite interactions is valuable to aid the identification of new anti-Schistosoma drugs. The parasite has a complex life cycle, which results in challenges regarding the evaluation of Schistosoma mansoni development and mammalian infection establishment. Accordingly, this protocol describes methodologies to evaluate: (1) adult worm growth; (2) reproduction; and (3) granuloma formation; and consequently allows more comprehensive knowledge of S. mansoni development in a natural biological system.

A novel non-destructive technique for qualitative and quantitative measurement of dental erosion in its entirety by porosity and bulk tissue-loss

OBJECTIVE

To explore the potential of combining non-contact profilometry (NCP) and confocal laser scanning microscopy (CLSM) data to measure the entire erosive process non-destructively and to validate findings using inductively coupled plasma-atomic emission spectroscopy (ICP-AES), scanning electron microscopy (SEM) and surface microhardness (SMH) using the same samples throughout.

METHODS

Polished bovine enamel samples (n = 35) were divided into groups (7/group) with similar SMH values. Samples underwent individual erosive challenges (1 % citric acid, pH3.8) for 1, 5, 10, 15 or 30 min under stirring and aliquot extracts were analysed for Ca and P by ICP-AES. SMH was used to measure erosive softening. Profilometry was used to assess bulk volume loss (BVL). Images were captured by SEM. Samples were stained with rhodamine-B (0.1 mM, 24 h) and images captured by CLSM. Image processing was used to determine changes in fluorescent volume for the first 10 μm (ΔFV₁₀) for each enamel sample which were combined with BVL to calculate total lesion volume (TLV). ANOVA, linear regression and Pearson correlation analysis were used where applicable.

RESULTS

Surface softening, [Ca], [P], BVL and ΔFV_10μm increased with acid erosion duration which were significant by 10 min (P < .01). The Ca:P ratio increased to 1.57 then decreased after 5 min erosion suggesting a sub/surface phase change, which was observed by SEM and CLSM showing significant changes to the enamel surface and subsurface morphology with time. Combination of BVL and ΔFV₁₀ as TLV strengthened the significant correlations with [Ca], [P], and SMH (P < .01).

CONCLUSION

This novel combination of CLSM and NCP allows for concurrent non-destructive quantification of the entire erosive process by mineral loss, and qualitatively characterise microstructural changes during dental erosion.

The effect of dough mixing speed and work input on the structure, digestibility and celiac immunogenicity of the gluten macropolymer within bread

Modern high-speed mechanical dough development (MDD) alters the gluten macropolymer's (GMP) structure. Changes to both the protein and food matrix structure can influence protein digestibility and immunogenicity. This study investigated the relationship between protein structural changes imparted by MDD and gluten's digestibility plus celiac reactivity. Dough was prepared at three mixing speeds (63 rpm, 120 rpm and 200 rpm) to different degrees of development (between 10 and 180% wh.kg^-1). Protein structural changes were characterised by confocal microscopy, free thiol determination and protein extractability assays. MDD altered the structure of gluten within bread, changing the protein's surface area and macrostructure. Breads were digested using the INFOGEST in vitro protocol. Gluten's antigenicity and digestibility were monitored using ELISA and mass spectrometry, by monitoring the concentration of six immunogenic peptides causative of celiac disease. The structural changes imparted by mixing did not affect bread's digestibility or celiac reactivity.

Intrinsic sources of tachykinin-related peptide in the thoracic ganglion mass of the crab, Cancer borealis

Neuropeptides comprise the largest class of neural and neuroendocrine signaling molecules. Vertebrate tachykinins (TKs) and the structurally-related invertebrate tachykinin-related peptides (TRPs) together form the largest neuropeptide superfamily, with a number of conserved neural and neuroendocrine functions across species. Arthropods, including crustaceans, have provided many insights into neuropeptide signaling and function. Crustacean tachykinin-related peptide occurs in endocrine organs and cells and in two of the major crustacean CNS components, the supraoesophageal ganglion ("brain") and the stomatogastric nervous system. However, little is known about TRP sources in the remaining major CNS component, the thoracic ganglion mass (TGM). To gain further insight into the function of this peptide, we aimed to identify intrinsic TRP sources in the TGM of the Jonah crab, Cancer borealis. We first adapted a clearing protocol to improve TRP immunoreactivity specifically in the TGM, which is a dense, fused mass of multiple ganglia in short-bodied crustaceans such as Cancer species of crabs. We verified that the clearing protocol avoided distortion of cell body morphology yet increased visibility of TRP immunoreactivity. Using confocal microscopy, we found TRP-immunoreactive (TRP-IR) axon tracts running the length of the TGM, TRP-IR neuropil in all ganglia, and approximately 110 TRP-IR somata distributed throughout the TGM, within and between ganglia. These somata likely represent both neural and neuroendocrine sources of TRP. Thus, there are many potential intrinsic sources of TRP in the TGM that are positioned to regulate behaviors such as food intake, locomotion, respiration, and reproduction.

Microscopic Analysis of Viral Infection

Viruses engineered to express fluorescent proteins can be used with live-cell imaging techniques to monitor the progression of infection in real time. Here we describe a set of methods to track infection spreading from one cell population to another as well as to visualize transfer of virions between cells. This approach is extended to multiplexing with physiological readouts of cell death, which can be correlated with single-cell resolution to viral infection.

Live Imaging of Arabidopsis Leaf and Vegetative Meristem Development

Plants develop lateral organs such as leaves and flowers throughout their post-embryonic life from a structure called the shoot apical meristem (SAM), located at the plant shoot apex. This process is highly dynamic, and therefore in order to understand meristem and organ development, it is critical to be able to analyze these processes with high temporal and spatial resolution. Although several protocols have been published for imaging the Arabidopsis inflorescence meristem, gaining access to the vegetative meristem for imaging has been considered more difficult. Here we describe a method to dissect young Arabidopsis seedlings in order to obtain a clear view of the vegetative meristem and young leaf primordia using confocal microscopy.

Studying cell wall mechanics using an automated confocal micro-extensometer

Recently there has been a lot of interest in quantifying mechanical properties and responses to mechanical stress. This type of data can provide insight into how growth is regulated, the processes that enable it to occur and how stresses that build up during development feedback onto development itself. However, quantifying mechanical properties of plant cell walls is difficult as the material is heterogeneous, anisotropic and shows complex time-dependent properties as well as being subject to the complex geometries of plant tissues. It is therefore necessary to have a range of methods to enable the quantification of these properties at different resolutions and time-scales. Here we provide a guide to quantifying mechanical properties in Arabidopsis thaliana hypocotyls using a tensile testing device an automated confocal micro-extensometer (ACME). In contrast to indentation methods, tensile testing provides information on the tissue as a whole and in the plane of the sample. We also detail how to adapt the method to use it for quantifying responses to mechanical stress.

Computational Analysis of DNA Modifications in Confocal Images

Computational analysis of digital images provides a robust and unbiased way to compare and investigate the amount (pixel intensity) and spatial distribution of DNA modifications. The DNA modifications in the cells are visualized by fluorescence labeling and the images are captured by confocal microscopy. The key advantage of the confocal over conventional microscope is that it images only a thin optical section around the focal plane of the microscope therefore it can precisely record signals only from the focal plane inside the nucleus. In this chapter, we will describe in detail several analysis methods to visualize and quantify the DNA modification signals including how to investigate codistribution of such signals when using dual labeling.

Imaging tools for assessment of myocardial fibrosis in humans: the need for greater detail

Myocardial fibrosis is recognized as a key pathological process in the development of cardiac disease and a target for future therapeutics. Despite this recognition, the assessment of fibrosis is not a part of routine clinical practice. This is primarily due to the difficulties in obtaining an accurate assessment of fibrosis non-invasively. Moreover, there is a clear discrepancy between the understandings of myocardial fibrosis clinically where fibrosis is predominately studied with comparatively low-resolution medical imaging technologies like MRI compared with the basic science laboratories where fibrosis can be visualized invasively with high resolution using molecularly specific fluorescence microscopes at the microscopic and nanoscopic scales. In this article, we will first review current medical imaging technologies for assessing fibrosis including echo and MRI. We will then highlight the need for greater microscopic and nanoscopic analysis of human tissue and how this can be addressed through greater utilization of human tissue available through endomyocardial biopsies and cardiac surgeries. We will then describe the relatively new field of molecular imaging that promises to translate research findings to the clinical practice by non-invasively monitoring the molecular signature of fibrosis in patients.

Ultrastructural changes of smooth and rough titanium implant surfaces induced by metal and plastic periodontal probes

Objectives

To determine the ultrastructural changes of titanium surfaces of dental implants induced by the tip of periodontal probes.

Materials and methods

A total of 40 samples of smooth and rough surfaces of titanium implants were randomly assigned for the treatment with metal or plastic periodontal probes under application angles of 20° and 60°. Titanium surfaces have been evaluated with CLSM prior and following to experimental probing determining various standardized 2D and 3D roughness parameters.

Results

The average profile and surface roughness (Ra and Sa) showed no significant difference between treated and untreated samples on smooth and rough surface areas irrespective of the probe material. On smooth surfaces several amplitude roughness parameters were increased with metal probes but reached significance only for Rp (p = 0.007). Rough surface parts showed a slight but not significant reduction of roughness following to the contact with metal probes. The surface roughness remained almost unchanged on smooth and rough implant surfaces using plastic probes. The surface roughness on implant surfaces was not dependent on the application angle irrespective of the probe material.

Conclusion

Probing of titanium implants with metal probes and even less with plastic probes causes only minor changes of the surface roughness. The clinical significance of these changes remains to be elucidated.

Clinical relevance

Using plastic probes for the clinical evaluation of the peri-implant sulcus might avoid ultrastructural changes to titanium implant surfaces.

Didactic approach recounting advances and limitations in novel glutathione and cysteine detection (reduced GSH probe) with mixed coumarin, aldehyde, and phenyl-selenium chemistry

We describe the pertinent research steps and analysis, many of which are chemical, to achieve a novel molecular probe for glutathione (GSH) which has been published and patented based on two recent articles: "Exceptional time response, stability and selectivity in doubly-activated phenyl selenium-based glutathione-selective platform" and "Enhanced Doubly Activated Dual Emission Fluorescent Probes for Selective Imaging of Glutathione or Cysteine in Living Systems" (Kim et al., 2015; Mulay et al., 2018). The papers involve coumarin probes. Reaction/detection unfolds with aminothiol attack at an electrophilic ring carbon position. An adjacent -CHO group is heavily involved in resonance aspects of the C-Se position, as well as the binding of the pendant N-group; the coumarin lactone carbonyl also allows for resonance to be achieved (vide infra). The leaving group, -SePh, while precedented in some systems, depends on electronic tuning (Fig. 1). For 1, the response times with GSH was ~100ms; a 100-fold fluorescence increase is observed (Compound 1). The probe also reacts with cysteine (Cys) and homocysteine (Hcy), albeit differently. For glutathione probing, the greater wavelength maxima (1: 550nm, DACP-1: 555nm, DACP-2: 590nm) enabled eventual cell studies (confocal microscopy) and animal studies. The limits of detection (LOD, 1: 270nM DACP-1: 10.1nM DACP-2: 17.0nM), as measured using the 3σ/k method. We provide a didactic presentation from probe conception to probe in vivo testing, etc., with additional considerations presented; a variety of factors/issues (2.1-2.28) help maintain a realistic sequence, a flow from wider to narrower, of the factors that go into developing medical, biological and neurodegenerative disease-related probes, meant to help other researchers follow our intention, gain perspective, and overcome current limitations.

Confocal lens focused piezoelectric lithotripter

This work focuses on the evaluation of a type of piezoelectric lithotripter with similar dimensions of a commercial lithotripter and composed of either 3 or 4 large lens focused piezoelectric transducers set either in a confocal coplanar C-shape or a confocal spherical shape. Each transducer is made with a 92 mm diameter 220 kHz flat piezoelectric ceramic disc and a 3D printed acoustic lens. Both confocal setups pressure field were measured with a fiber optic hydrophone, and in vitro fragmentations of 13 mm diameter and 14 mm length cylindrical model stones were done in a 2 mm mesh basket. The acoustic characterization of the three transducers confocal setup revealed a disc shaped focal volume, with a 2.2 mm width on one axis and a 9.6 mm width on the other, and a peak positive pressure of 40.9 MPa and a peak negative pressure of -16.9 MPa, while the focus of the four transducers confocal setup was similar to a traditional narrow focus high pressure lithotripter with a focus width of 2.1 mm, and a peak positive pressure of 71.9 MPa and peak negative pressure of -24.3 MPa. Both confocal setups showed in vitro fragmentation efficiency close to a commercial electroconductive lithotripter.

Airyscan Superresolution Microscopy to Study Trypanosomatid Cell Biology

The recent introduction by Carl Zeiss Ltd. of the Airyscan detector module for their LSM880 confocal laser-scanning microscope has enabled routine superresolution microscopy to be combined with the advantages of confocal-based fluorescence imaging. Resulting enhanced spatial resolution in X, Y, and Z provides tractable opportunity to derive new insight into protein localization(s), organelle dynamics, and thence protein function within trypanosomatids or other organisms. Here, we describe methods for preparing slides, cells, and basic microscope setup for fluorescence imaging of trypanosomatids using the LSM-880 with Airyscan platform.

Live Imaging of Arabidopsis Axillary Meristems

Axillary meristems (AMs) are established postembryonically at the leaf axils and can develop into lateral branches. The initiation of AMs establishes new growth axis and is of primary importance for understanding plant development. Understanding plant development requires live imaging of morphogenesis and gene expression. However, AMs are embedded in the leaf axil, making it challenging to perform live imaging. In this chapter, we describe how to prepare and culture Arabidopsis thaliana leaves in vitro, to perform one-time or time-lapse imaging of AM initiation with a confocal microscope.

Imaging and quantifying drug delivery in skin - Part 2: Fluorescence andvibrational spectroscopic imaging methods

Understanding the delivery and diffusion of topically-applied drugs on human skin is of paramount importance in both pharmaceutical and cosmetics research. This information is critical in early stages of drug development and allows the identification of the most promising ingredients delivered at optimal concentrations to their target skin compartments. Different skin imaging methods, invasive and non-invasive, are available to characterize and quantify the spatiotemporal distribution of a drug within ex vivo and in vivo human skin. The first part of this review detailed invasive imaging methods (autoradiography, MALDI and SIMS). This second part reviews non-invasive imaging methods that can be applied in vivo: i) fluorescence (conventional, confocal, and multiphoton) and second harmonic generation microscopies and ii) vibrational spectroscopic imaging methods (infrared, confocal Raman, and coherent Raman scattering microscopies). Finally, a flow chart for the selection of imaging methods is presented to guide human skin ex vivo and in vivo drug delivery studies.

Tissue Clearing and Deep Imaging of the Kidney Using Confocal and Two-Photon Microscopy

Microscopic and macroscopic evaluation of biological tissues in three dimensions is becoming increasingly popular. This trend is coincident with the emergence of numerous tissue clearing strategies, and advancements in confocal and two-photon microscopy, enabling the study of intact organs and systems down to cellular and sub-cellular resolution. In this chapter, we describe a wholemount immunofluorescence technique for labeling structures in renal tissue. This technique combined with solvent-based tissue clearing and confocal imaging, with or without two-photon excitation, provides greater structural information than traditional sectioning and staining alone. Given the addition of paraffin embedding to our method, this hybrid protocol offers a powerful approach to combine confocal or two-photon findings with histological and further immunofluorescent analysis within the same tissue.

Quantitative Fluorescence In Situ Hybridization Detection of Plant mRNAs with Single-Molecule Resolution

Single-molecule FISH (smFISH) has been widely used in animal tissue to localize and quantify RNAs with high specificity. This protocol describes an smFISH method optimized for highly autofluorescent plant tissue. It provides details on fixation buffers and protocols to protect the integrity of plant samples. We also provide smFISH hybridization conditions to detect plant RNA with ~50 fluorescently labeled DNA oligonucleotides. In addition, this protocol provides instructions on linear spectral unmixing of smFISH signal from background autofluorescence by confocal microscopy and a method to quantify the smFISH spots that reflect the copy number of target RNA.

Preserving Cytonemes for Immunocytochemistry of Cultured Adherent Cells

Cytonemes are specialized signalling filopodia that have a role in development and cellular differentiation. However, they are not well preserved by standard fixation techniques to study protein localization and interactions. A recent methodological advance has yielded improvements in cytoneme preservation using glutaraldehyde fixation and sodium borohydride treatment to reduce background. We herein describe a safer method for effective blocking using glycine following glutaraldehyde fixation of cytonemes on cultured adherent cells and demonstrate its effectiveness in immunocytochemistry.

Staining MIF in Cells for Confocal Microscopy

Confocal microscopy is a powerful technique for immunofluorescence imaging of cells and tissues. The technique allows for detailed analysis of intracellular localization of molecules, as well as three-dimensional representation and analysis of samples, and can be used as a gateway to more advanced techniques, including FLIM-FRET and super-resolution microscopy. Relatively few studies have used confocal microscopy to study intracellular localization of macrophage migration inhibitory factor (MIF) in detail. This chapter outlines basic protocols and tips for staining MIF in fixed cells for confocal analysis.