Search

Correlative light and electron microscopy (CLEM) combines the advantages of protein localization by fluorescence microscopy with the high resolution of electron microscopy. Here, we describe a protocol that we developed for yeast peroxisome research. First, cells are fixed, using conditions that preserve the properties of fluorescent proteins and avoid the introduction of autofluorescence. Next, cryosections are prepared and imaged by fluorescence microscopy. The same sections are used for electron microscopy. Both images are aligned and merged, allowing to localize fluorescent proteins in electron microscopy images. This method was successfully used for peroxisomal membrane contact site research and allows to precisely localize contact site resident proteins at regions where membranes are closely associated at distances far below the resolution of conventional fluorescence microscopy.

The u-serrated immunodeposition pattern in direct immunofluorescence (DIF) microscopy is a recognizable feature and confirmative for the diagnosis of epidermolysis bullosa acquisita (EBA). Due to unfamiliarity with serrated patterns, serration pattern recognition is still of limited use in routine DIF microscopy. The objective of this study was to investigate the feasibility of using convolutional neural networks (CNNs) for the recognition of u-serrated patterns that can assist in the diagnosis of EBA. The nine most commonly used CNNs were trained and validated by using 220,800 manually delineated DIF image patches from 106 images of 46 different patients. The data set was split into 10 subsets: nine training subsets from 42 patients to train CNNs and the last subset from the remaining four patients for a validation data set of diagnostic accuracy. This process was repeated 10 times with a different subset used for validation. The best-performing CNN achieved a specificity of 89.3% and a corresponding sensitivity of 89.3% in the classification of u-serrated DIF image patches, an expert level of diagnostic accuracy. Experiments and results show the effectiveness of CNN approaches for u-serrated pattern recognition with a high accuracy. The proposed approach can assist clinicians and pathologists in recognition of u-serrated patterns in DIF images and facilitate the diagnosis of EBA.

SIGNIFICANCE: The combination of reflectance and fluorescence spectroscopy allows the determination of tissue optical properties and the calculation of the intrinsic fluorescence in vivo. These parameters can discriminate between tissues and may allow the discrimination of malignant from benign tissue. While this approach has significant clinical potential, the lack of standardization and quality assessment prevents the upscaling of research.AIM: Investigate which factors influence device calibration and tissue optical property determination. Improve system quality assessment and allow upscaling of the clinical research using multidiameter single fiber reflectance/singe fiber fluorescence spectroscopy.APPROACH: Two studies, one phantom based on uniform calibrations and skin measurements and a clinical study including clinical calibrations. The first validates the effect of factors under identical conditions and the effect of calibration quality on the optical property determination of skin. The second shows the effect of different system configurations and the performance of the system and probe over an extended period.RESULTS: Phantom calibrations showed stability over a period of 20 weeks except for a 16-week-old intralipid phantom which showed a significant difference (at least p = 0.0032) for all five probes evaluated. For clinical calibrations, only the fiber tree had a significant influence (probe 4: p CONCLUSIONS: Intralipid phantom quality and fiber tree performance are the main factors influencing the calibration quality. Probe and user performance did not show any effect, which makes the upscaling of research to multicenter trials easier. A high-quality assessment procedure should be implemented to track changes during clinical trials.

More than 400,000 people each year suffer adverse effects following bites from venomous snakes. However, snake venom is also a rich source of bioactive molecules with known or potential therapeutic applications. Manually ‘milking’ snakes is the most common method to obtain venom. Safer alternative methods to produce venom would facilitate the production of both antivenom and novel therapeutics. This protocol describes the generation, maintenance and selected applications of snake venom gland organoids. Snake venom gland organoids are 3D culture models that can be derived within days from embryonic or adult venom gland tissues from several snake species and can be maintained long-term (we have cultured some organoids for more than 2 years). We have successfully used the protocol with glands from late-stage embryos and recently deceased adult snakes. The cellular heterogeneity of the venom gland is maintained in the organoids, and cell type composition can be controlled through changes in media composition. We describe in detail how to derive and grow the organoids, how to dissociate them into single cells, and how to cryopreserve and differentiate them into toxin-producing organoids. We also provide guidance on useful downstream assays, specifically quantitative real-time PCR, bulk and single-cell RNA sequencing, immunofluorescence, immunohistochemistry, fluorescence in situ hybridization, scanning and transmission electron microscopy and genetic engineering. This stepwise protocol can be performed in any laboratory with tissue culture equipment and enables studies of venom production, differentiation and cellular heterogeneity.

Over the past years several forms of superresolution fluorescence microscopy have been developed that offer the possibility to study cellular structures and protein distribution at a resolution well below the diffraction limit of conventional fluorescence microscopy (

In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens., Preservation of cancer biopsies by FFPE introduces DNA fragmentation, hindering analysis of rearrangements. Here the authors introduce FFPE Targeted Locus Capture for identification of translocations in preserved samples.

Fluorogenic RNA aptamers bind and activate the fluorescence of otherwise nonfluorescent dyes. However, fluorogenic aptamers are limited by the small number of fluorogenic dyes suitable for use in live cells. In this communication, fluorogenic proteins whose fluorescence is activated by RNA aptamers are described. Fluorogenic proteins are highly unstable until they bind RNA aptamers inserted into messenger RNAs, resulting in fluorescent RNA–protein complexes that enable live imaging of mRNA in living cells.

In vitro 3D organoid systems have revolutionized the modeling of organ development and diseases in a dish. Fluorescence microscopy has contributed to the characterization of the cellular composition of organoids and demonstrated organoids' phenotypic resemblance to their original tissues. Here, we provide a detailed protocol for performing high-resolution 3D imaging of entire organoids harboring fluorescence reporters and upon immunolabeling. This method is applicable to a wide range of organoids of differing origins and of various sizes and shapes. We have successfully used it on human airway, colon, kidney, liver and breast tumor organoids, as well as on mouse mammary gland organoids. It includes a simple clearing method utilizing a homemade fructose-glycerol clearing agent that captures 3D organoids in full and enables marker quantification on a cell-by-cell basis. Sample preparation has been optimized for 3D imaging by confocal, super-resolution confocal, multiphoton and light-sheet microscopy. From organoid harvest to image analysis, the protocol takes 3 d.

WOS:000765832200001 OBJECTIVE: Direct immunofluorescence (DIF)-stained slides are archived in the dark to prevent fading. Reevaluation of slides for clinical evaluation and training may be needed. In this study we aimed to determine the duration of archiving in dark environment (DE) versus bright environment (BE) in order to evaluate DIF positive stained slides. STUDY DESIGN: A total of 56 immunofluorescence slides consisting of 35 kidney and 21 skin biopsies were included in the study. RESULTS: The mean wilting time of the slides was 7.5 weeks for those left in the BE and 7.1 weeks for those in the DE. The mean wilting times of the kidney slides left in BE and DE were 6.8 and 7.2 weeks, respectively. The mean wilting times of the skin slides left in a BE and DE were 8.2 and 7 weeks, respectively. CONCLUSION: We did not observe a significant difference between immunofluorescence (IF) slides archived in light versus dark media. The fact that there was no difference between the fading times between immunofluorescence slides stored in BE and DE showed that the duration of exposure to immunofluorescence microscopy light was more important than the environments where they were kept from fading on slides.

Saliva is a matrix which may act as a vector for pathogen transmission and may serve as a possible proxy for SARS-CoV-2 contagiousness. Therefore, the possibility of detection of intracellular SARS-CoV-2 in saliva by means of fluorescence in situ hybridization is tested, utilizing probes targeting the antisense or sense genomic RNA of SARS-CoV-2. This method was applied in a pilot study with saliva samples collected from healthy persons and those presenting with mild or moderate COVID-19 symptoms. In all participants, saliva appeared a suitable matrix for the detection of SARS-CoV-2. Among the healthy, mild COVID-19-symptomatic and moderate COVID-19-symptomatic persons, 0%, 90% and 100% tested positive for SARS-CoV-2, respectively. Moreover, the procedure allows for simultaneous measurement of viral load (‘presence’, sense genomic SARS-CoV-2 RNA) and viral replication (‘activity’, antisense genomic SARS-CoV-2 RNA) and may yield qualitative results. In addition, the visualization of DNA in the cells in saliva provides an additional cytological context to the validity and interpretability of the test results. The method described in this pilot study may be a valuable diagnostic tool for detection of SARS-CoV-2, distinguishing between ‘presence’ (viral load) and ‘activity’ (viral replication) of the virus. Moreover, the method potentially gives more information about possible contagiousness.

Probes are essential to visualize proteins in their cellular environment, both using light microscopy as well as electron microscopy (EM). Correlated light microscopy and electron microscopy (CLEM) requires probes that can be imaged simultaneously by both optical and electron-dense signals. Existing combinatorial probes often have impaired efficiency, need ectopic expression as a fusion protein, or do not target endogenous proteins. Here, we present FLIPPER-bodies to label endogenous proteins for CLEM. Fluorescent Indicator and Peroxidase for Precipitation with EM Resolution (FLIPPER), the combination of a fluorescent protein and a peroxidase, is fused to a nanobody against a target of interest. The modular nature of these probes allows an easy exchange of components to change its target or color. A general FLIPPER-body targeting GFP highlights histone2B-GFP both in fluorescence and in EM. Similarly, endogenous EGF receptors and HER2 are visualized at nm-scale resolution in ultrastructural context. The small and flexible FLIPPER-body outperforms IgG-based immuno-labeling, likely by better reaching the epitopes. Given the modular domains and possibilities of nanobody generation for other targets, FLIPPER-bodies have high potential to become a universal tool to identify proteins in immuno-CLEM with increased sensitivity compared to current approaches. Electronic supplementary material The online version of this article (10.1007/s00418-018-1632-6) contains supplementary material, which is available to authorized users.

Fibrin-based sealants consist of natural coagulation factors involved in the final phase of blood coagulation, during which fibrinogen is enzymatically converted by thrombin to form a solid-phase fibrin clot. For applications in tissue regeneration, a controlled process of matrix degradation within a certain period of time is essential for optimal wound healing. Hence, it is desirable to follow the kinetics of fibrinolysis at the application site. Non-invasive molecular imaging systems enable real-time tracking of processes in the living animal. In this study, a non-invasive fluorescence based imaging system was applied to follow and quantify site-specific degradation of fibrin sealant. To enable non-invasive tracking of fibrin in vivo, fibrin-matrix was labelled by incorporation of a fluorophore-conjugated fibrinogen component. Protein degradation and release of fluorescence were, in a first step, correlated in vitro. In vivo, fluorophore-labelled fibrin was subcutaneously implanted in mice and followed throughout the experiment using a multispectral imaging system. For the fluorescent fibrin, degradation correlated with the release of fluorescence from the clots in vitro. In vivo it was possible to follow and quantify implanted fibrin clots throughout the experiment, demonstrating degradation kinetics of approximately 16 days in the subcutaneous compartment, which was further confirmed by histological evaluation of the application site.

Involvement of the immune system in tumour progression is at the forefront of cancer research. Analysis of the tumour immune microenvironment has yielded a wealth of information on tumour biology, and alterations in some immune subtypes, such as tumour-associated macrophages (TAM), can be strong prognostic indicators. Here, we use optical tissue clearing and a TAM-targeting injectable fluorescent nanoparticle (NP) to examine three-dimensional TAM composition, tumour-to-tumour heterogeneity, response to colony-stimulating factor 1 receptor (CSF-1R) blockade and nanoparticle-based drug delivery in murine pulmonary carcinoma. The method allows for rapid tumour volume assessment and spatial information on TAM infiltration at the cellular level in entire lungs. This method reveals that TAM density was heterogeneous across tumours in the same animal, overall TAM density is different among separate pulmonary tumour models, nanotherapeutic drug delivery correlated with TAM heterogeneity, and successful response to CSF-1R blockade is characterized by enhanced TAM penetration throughout and within tumours., Tumour-associated macrophages (TAM) can be used as prognostic indicators in cancer. Here, the authors establish a platform for high-throughput 3D microscopy in murine lung carcinoma that allows to visualize TAMs infiltration throughout the entire lung, response to CSF-1R blockade and nanoparticle drug delivery.

Phospholipase C (PLC) regulates various cellular processes by catalyzing the formation of inositol-1,4,5-trisphosphate (IP3) and diacylglycerol from phosphatidylinositol-4,5-bisphosphate (PIP2). Here, we have investigated the influence of Ca2+ on receptor-triggered PLC activity in individual insulin-secreting β-cells. Evanescent wave microscopy was used to record PLC activity using green fluorescent protein (GFP)-tagged PIP2/IP3-binding pleckstrin homology domain from PLCδ1, and the cytoplasmic Ca2+ concentration ([Ca2+]i) was simultaneously measured using the indicator Fura Red. Stimulation of MIN6 β-cells with the muscarinic-receptor agonist carbachol induced rapid and sustained PLC activation. By contrast, only transient activation was observed after stimulation in the absence of extracellular Ca2+ or in the presence of the non-selective Ca2+ channel inhibitor La3+. The Ca2+-dependent sustained phase of PLC activity did not require voltage-gated Ca2+ influx, as hyperpolarization with diazoxide or direct Ca2+ channel blockade with nifedipine had no effect. Instead, the sustained PLC activity was markedly suppressed by the store-operated channel inhibitors 2-APB and SKF96365. Depletion of intracellular Ca2+ stores with the sarco(endo)plasmic reticulum Ca2+-ATPase inhibitors thapsigargin or cyclopiazonic acid abolished Ca2+ mobilization in response to carbachol, and strongly suppressed the PLC activation in Ca2+-deficient medium. Analogous suppressions were observed after loading cells with the Ca2+ chelator BAPTA. Stimulation of primary mouse pancreatic β-cells with glucagon elicited pronounced [Ca2+]i spikes, reflecting protein kinase A-mediated activation of Ca2+-induced Ca2+ release via IP3 receptors. These [Ca2+]i spikes were found to evoke rapid and transient activation of PLC. Our data indicate that receptor-triggered PLC activity is enhanced by positive feedback from Ca2+ entering the cytoplasm from intracellular stores and via store-operated channels in the plasma membrane. Such amplification of receptor signalling should be important in the regulation of insulin secretion by hormones and neurotransmitters.

Despite recent advances, the mechanisms of RNA movements and targeting within the nucleus are still mysterious. While diffusion appears to play a crucial role in nuclear dynamics and RNA transport, some data argue for a model in which diffusion is controlled, at least in part, by the organization of the nucleus in well-defined compartments. Much of the recent progress is based on imaging technologies, and this review will first present them in some detail. We will then summarize studies that analyzed nuclear movements of both polyadenylated RNA and box C/D snoRNP. Indeed, this latter model has already brought a number of interesting results. We will finally present some of our original results on box C/D snoRNA transport.

Objective. Disadvantages of the combined sentinel lymph node (SLN) procedure with radiocolloid and blue dye in vulvar cancer are the preoperative injections of radioactive tracer in the vulva, posing a painful burden on the patient. Intraoperative transcutaneous imaging of a peritumorally injected fluorescent tracer may lead to a one-step procedure, while maintaining high sensitivity. Aim of this pilot study was to investigate the applicability of intraoperative fluorescence imaging for SLN detection and transcutaneous lymphatic mapping in vulvar cancer.Methods. Ten patients with early stage squamous cell carcinoma of the vulva underwent the standard SLN procedure. Additionally, a mixture of 1 mL patent blue and 1 mL indocyanin green (ICG; 0.5 mg/mL) was injected immediately prior to surgery, with the patient under anesthesia. Color and fluorescence images and videos of lymph flow were acquired using a custom-made intraoperative fluorescence camera system. The distance between skin and femoral artery was determined on preoperative CT-scan as a measure for subcutaneous adipose tissue.Results. In 10 patients, SLNs were detected in 16 groins (4 unilateral; 6 midline tumors). Transcutaneous lymphatic mapping was possible in five patients (5 of 16 groins), and was limited to lean patients, with a maximal distance between femoral artery and skin of 24 mm, as determined on CT. In total, 29 SLNs were detected by radiocolloid, of which 26 were also detected by fluorescence and 21 were blue.Conclusions. These first clinical results indicate that intraoperative transcutaneous lymphatic mapping using fluorescence is technically feasible in a subgroup of lean vulvar cancer patients. (C) 2010 Elsevier Inc. All rights reserved.

BACKGROUND: Chromosomal abnormalities, such as t(9;22)(q34;q11) (ABL/BCR), t(12;21)(p13;q22) (TEL/AML1), and t(11q23) (MLL) are independent prognostic indicators in childhood acute lymphoblastic leukemia resulting in risk adapted therapy. Accurate and rapid detection of these abnormalities is mandatory, which is achieved by karyotyping, fluorescence in situ hybridization, and real time quantitative reverse transcriptase polymerase chain reaction (RQ-PCR). For cost-effective diagnostic approaches knowledge of diagnostic accuracy of these tests is required. Therefore, we aimed to determine the diagnostic accuracy of karyotyping, fluorescence in situ hybridization, and RQ-PCR analysis. PROCEDURE: Retrospective study conducted between January 1, 1992 and January 1, 2007 in the Emma Children Hospital in Amsterdam. All consecutive patients under 18 years with acute lymphoblastic leukaemia were included. Diagnostic tests were performed according to international standards. RESULTS: Diagnostic techniques show a high-reciprocal agreement and have a high-individual diagnostic accuracy in detecting the above-mentioned chromosomal translocations. However, the sensitivity of karyotyping for detecting the TEL-AML1 fusion gene and the sensitivity of RQ-PCR for detecting MLL-rearrangements was rather low. CONCLUSIONS: Diagnostic accuracy of tests for detecting t(9;22), t(12;21), and t(11q23) is generally high, although sensitivity is not optimal for all anomalies. Despite the high-diagnostic accuracy, all diagnostic techniques should be used complementary, because any detection of a (significant) chromosomal aberration irrespective of diagnostic mode has to be considered in therapy.

Biofilm formation is a common complication of the use of prosthetic devices. In clinical settings, biofilms can be comprised of one or more microbial species. In order to investigate the interaction between different species within a biofilm, a reproducible, reliable model system has to be utilized and an appropriate system for species identification applied. The present chapter describes the artificial throat model, a model system for growing mixed species biofilms on shunt prostheses. The model is used in conjugation with fluorescent in situ hybridization (FISH), which facilitates identification and localization of the resident microorganisms within biofilms.

The need to study molecular and functional parameters of Alzheimer's disease progression in animal models has led to the development of disease-specific fluorescent markers. However, curved optical interfaces and a highly heterogeneous internal structure make quantitative fluorescence imaging of the murine brain a particularly challenging tomographic problem. We investigated the integration of X-ray computed tomography (CT) information into a state-of-the-art fluorescence molecular tomography (FMT) scheme and establish that the dual-modality approach is essential for high fidelity reconstructions of distributed fluorescence within the murine brain, as compared to conventional fluorescence tomography. We employ this method in vivo using a fluorescent oxazine dye to quantify amyloid-beta plaque burden in transgenic APP23 mice modeling Alzheimer's disease. Multi-modal imaging allows for accurate signal localization and correlation of in vivo findings to ex vivo studies. The results point to FMT-CT as an essential tool for in vivo study of neurodegenerative disease in animal models and potentially humans.

Luciferases are widely used to monitor biological processes. Here we describe the naturally secreted Gaussia princeps luciferase (Gluc) as a highly sensitive reporter for quantitative assessment of cells in vivo by measuring its concentration in blood. The Gluc blood assay complements in vivo bioluminescence imaging, which has the ability to localize the signal and provides a multifaceted assessment of cell viability, proliferation and location in experimental disease and therapy models.