Optimized Ki-67 staining in murine cells: a tool to determine cell proliferation.

The reliable analysis of the cell cycle status has become increasingly relevant for scientific and clinical work, especially for the determination of tumor cell growth. One established method to characterize the proliferation activity of cells is the analysis of the Ki-67 protein. Ki-67 is expressed in the nucleus during the whole cell cycle except for the G0 phase. Several different protocols exist for the examination of the Ki-67 protein in tissue and cell culture, but most of them are defined for human cells. For the analysis of the Ki-67 protein in murine tissue and cell culture there is a variety of protocols existing which recommend different fixation and permeabilization reagents or special kits. In this study, we established a reliable protocol for Ki-67 staining in murine cells and tissue based on PFA fixation, which can be used not only for flow cytometry but also for immunofluorescence microscopy analysis. We tested our protocol successfully with three different Ki-67 anti-mouse antibodies in cell culture, regenerating liver tissue and mouse melanoma tumor to demonstrate the general applicability.

Immunofluorescent detection of the activation of the small GTPase Rac1 in mouse skeletal muscle fibers.

The small GTPase Rac1 acts as a molecular switch of intracellular signaling in mammals. For understanding the regulatory mechanism, it is important to identify subcellular locations in which Rac1 is activated following multiple extracellular stimuli. However, it is difficult to detect Rac1 activation in situ in animal tissues, and thus a novel method is highly desirable. Here, we report a simple method to visualize the activation of endogenous Rac1 in mouse skeletal muscle fibers. In this assay, specific interaction between activated Rac1 and a binding polypeptide is detected by immunofluorescent microscopy. This approach is readily applicable to other small GTPases.

Immunolocalization of hordein synthesis and transport in developing barley endosperm.

The spatial accumulation of hordeins in the developing endosperm of barley grains was examined by immunofluorescence microscopy (immunolight microscopy [iLM]) and immunoelectron microscopy (iEM) to establish the timing and subcellular pattern of hordein synthesis and deposition. The pattern seen for hordeins was compared to other abundant grain proteins, such as serpin Z4 and lipid transfer protein 1 (LTP1). Hordein accumulates throughout grain development, from 6 to 37 days post-anthesis (DPA). In contrast, serpin Z4 was present at 6 DPA, but the greatest synthesis and accumulation occurred during the middle of seed development, from 15 to 30 DPA. LTP1 accumulated later in seed development, from 15 to 30 DPA. Hordeins accumulated within the lumen of the endoplasmic reticulum (ER), were exocytosed from the ER membrane, and accumulated in protein bodies, which then fused either with the protein storage vacuoles or with other protein bodies, which also later fused with the protein storage vacuoles. iEM showed hordein, and LTP1 appeared not to traverse the Golgi apparatus (GA). Hordein, LTP1, and serpin Z4 colocalized to the same protein bodies and were co-transported to the protein storage vacuole in the same protein bodies. It is likely that this represents a general transport mechanism common to storage proteins in developing grains.

The potential of aptamers for the analysis of ceramic bound proteins found within pottery.

Archaeological pottery are the most numerous objects found during excavations and reflect the culinary practices of the past. However, their functionality for cooking/storing specific foods or drinks cannot be deduced solely from comparing their shapes and sizes. Analysis of protein residues bound to ceramics can reveal the protein/animal type through their amino acid sequence, thus enabling direct identification of food types. Therefore, the aim of our experimental study was to test sixteen aptamers for the analysis of proteinaceous organic residues found within the porous structure of pottery. Traditionally prepared archaeological ceramic replicas were cooked for 5 days in various food/protein suspensions, were UV aged, buried for a year, excavated, and extensively cleaned. Their shards were analysed using immunofluorescence microscopy with aptamers. Results show that eight aptamers (Clone1 and Kirby for egg residuals; seqU5 and BLG14 for milk residuals; HA for blood residuals; Gli4 for gluten residuals; Par1 for fish residuals; and D1 for collagen residuals) produced a successful/specific immunofluorescence microscopy result when they were hybridised to shards containing target protein residuals. Interestingly, on whole egg control samples, when the egg lysozyme-targeting aptamer Kirby was used, fluorescence intensity was 3.1 times greater compared to that observed with anti-ovalbumin antibodies.

Mapping the Domain Structure and Aggregation Propensity of Proteins Using a Gateway Plasmid Vector System.

Some proteins represent members of conserved families, meaning that their domain structure can be easily predicted by comparison to homologous proteins whose structures have been solved experimentally. Many other proteins, however, do not share significant detectable homology with other proteins, often as results of high amounts of coiled-coil structure and/or intrinsically unstructured regions. These proteins include many whose aggregation is linked to human disease.Here we present a refined and reliable workflow for identifying the domains of such proteins, through cloning of multiple alternative fragments, and testing whether they form soluble, folded structures when expressed as recombinant peptides in E. coli, through the use of size exclusion chromatography. By using Gateway recombination for cloning, these fragments can then be rapidly transferred to alternate vectors for testing in mammalian cells. We then specifically illustrate its use for proteins that form pathological aggregates in disease, mapping not just their basic domain structures but also the specific subdomains responsible for aggregation.

Quantitative Immunofluorescent Imaging of Immune Cells in Mucosal Tissues.

Understanding the interplay between commensals, pathogens, and immune cells in the skin and mucosal tissues is critical to improve prevention and treatment of a myriad of diseases. While high-parameter flow cytometry is the current gold standard for immune cell characterization in blood, it is less suitable for mucosal tissues, where structural and spatial information is lost during tissue disaggregation. Immunofluorescence overcomes this limitation, serving as an excellent alternative for studying immune cells in mucosal tissues. However, the use of immunofluorescent microscopy for analyzing clinical samples is hampered by a lack of high-throughput quantitative analysis techniques. In this chapter, we describe methods for sectioning, staining, and imaging whole sections of human foreskin tissue. We also describe methods to automate immune cell quantification from immunofluorescent images, including image preprocessing and methods to quantify both circular and irregularly shaped immune cells using open-source software.

Analyzing the Integrin Adhesome by In Situ Proximity Ligation Assay.

The in situ proximity ligation assay (PLA) is capable of detecting single protein events such as protein protein-interactions and posttranslational modifications (e.g., protein phosphorylation) in tissue and cell samples prepared for analysis by immunofluorescent or immunohistochemical microscopy. The targets are detected using two primary antibodies which must be from different host species. A pair of secondary antibodies (PLA probes) conjugated to complementary oligonucleotides is applied to the sample, and a signal is generated only when the two PLA probes are in close proximity by their binding to the two primary antibodies that have bound to their targets in close proximity. The signal from each pair of PLA probes is visualized as an individual fluorescent spot. These PLA signals can be quantified (counted) using image analysis software (ImageJ), and also assigned to a specific subcellular location based on microscopy image overlays. In principle, in situ PLA offers a relatively simple and sensitive technique to analyze interactions among any proteins for which suitable antibodies are available. Integrin-mediated focal adhesions (FAs) are large multiprotein complexes consisting of more than 150 proteins, also known as the integrin adhesome, which link the extracellular matrix (ECM) to the actin cytoskeleton and regulate the functioning of mechanosignaling pathways. The in situ PLA approach is well suited for examining the spatiotemporal aspects of protein posttranslational modifications and protein interactions occurring in dynamic multiprotein complexes such as integrin mediated focal adhesions.

Enumeration of Viable Chlamydia from Infected Animals Using Immunofluorescent Microscopy.

An appropriate means of quantitating infectious Chlamydia from infected animals is essential for the evaluation of vaccines. However, unlike methods involving culture, nonculture methods, including detection of antigen or DNA, are not able to differentiate between viable and nonviable organisms. As an obligate intracellular bacterium, Chlamydia replicates inside host cells by forming unique organelles called inclusions. Here, we describe the enumeration of viable C. trachomatis from infected mice by culturing vaginal swabs on McCoy cells and counting inclusions via immunofluorescent microscopy.

Isolation and Analysis of Mouse and Human Skin γδ T Cells.

Skin-resident and infiltrating γδ T lymphocytes are components of the cutaneous immune system that provide the first line of defense against pathogens and the environment. Research that employs the isolation and culture of T cells from murine and human skin can help delineate the molecular and cellular mechanisms utilized by T lymphocytes in skin-specific immunity. However, obtaining high numbers of T cells from epithelial tissue without resorting to long-term culture or transformation can be difficult. Here, specific approaches are described for the isolation and culture of γδ T lymphocytes from murine skin and human skin explant cultures. In addition, a protocol to assess the morphology and activation of epidermal γδ T cells in situ using immunofluorescent microscopy is detailed. These techniques can be used to analyze resident and infiltrating γδ T lymphocytes in the skin via flow cytometry, RNA-seq, or proteomics to further study inflammatory diseases, cancer, or autoimmunity. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Isolation, culture, and analysis of γδ T cells from murine epidermis Basic Protocol 2: Examination of γδ T cells in epidermal sheets to assess activation and morphology Basic Protocol 3: Preparation of human skin explant cultures for analysis of skin T cells Support Protocol 1: Counting live cells with hemocytometer Support Protocol 2: Preparing a Matrigel.

Immunofluorescence-based Determination of Centrosome Number in Tissue Samples.

Centrosome numerical abnormalities have been reported in a variety of tumors. Centrosome numbers in cancer cells display both inter-tumor and intra-tumor heterogeneity. The over production of centrosomes (centrosome amplification) is unique in cancer cells and is a promising target for therapy. Thus, a method to quantify centrosome numbers on a single cell level is needed. Here, we describe a protocol to quantify centrosome numbers in formalin fixed paraffin embedded (FFPE) tissue samples by multiplexing antibodies to define bona fide centrosomes and cell borders. Centrosomes in single cells are identified using high resolution immunofluorescent microscopy with Z-sectioning. This protocol is easy to perform and has been used to quantify centrosome numbers on a single cell level in a variety of human tissue samples.

Impact of gluten-friendly™ technology on wheat kernel endosperm and gluten protein structure in seeds by light and electron microscopy.

The main aim of this paper was to assess the impact of Gluten-Friendly™ (GF) technology (Italian priority patent n° 102015000084813 filed on 17th December 2015) on wheat kernel endosperm morphology and gluten protein structure, using SEM, light and immunofluorescent microscopy. Microscopy was combined with immunodetection with specific antibodies for gliadins, γ-gliadins, LMW subunits and antigenic epitopes to gain a better understanding of the technology at a molecular level. The results showed significant changes to gluten proteins after GF treatment; cross-reactivity towards the antibodies recognizing almost the entire range of gluten proteins as well as the antigenic epitopes through the sequences QQSF, QQSY, PEQPFPQGC and QQPFP was significantly reduced. The present study confirms the results from our previous work and shows, for the first time, the mechanism by which a chemical-physical treatment abolishes the antigenic capacity of gluten.

In situ detection of the activation of Rac1 and RalA small GTPases in mouse adipocytes by immunofluorescent microscopy following in vivo and ex vivo insulin stimulation.

Rac1 has been implicated in insulin-dependent glucose uptake by mechanisms involving plasma membrane translocation of the glucose transporter GLUT4 in skeletal muscle. Although the uptake of glucose is also stimulated by insulin in adipose tissue, the role for Rac1 in adipocyte insulin signaling remains controversial. As a step to reveal the role for Rac1 in adipocytes, we aimed to establish immunofluorescent microscopy to detect the intracellular distribution of activated Rac1. The epitope-tagged Rac1-binding domain of a Rac1-specific target was utilized as a probe that specifically recognizes the activated form of Rac1. Rac1 activation in response to ex vivo and in vivo insulin stimulations in primary adipocyte culture and mouse white adipose tissue, respectively, was successfully observed by immunofluorescent microscopy. These Rac1 activations were mediated by phosphoinositide 3-kinase. Another small GTPase RalA has also been implicated in insulin-stimulated glucose uptake in skeletal muscle and adipose tissue. Similarly to Rac1, immunofluorescent microscopy using an activated RalA-specific polypeptide probe allowed us to detect intracellular distribution of insulin-activated RalA in adipocytes. These novel approaches to visualize the activation status of small GTPases in adipocytes will largely contribute to the understanding of signal transduction mechanisms particularly for insulin action.

Type IV collagen is a novel DEJ biomarker that is reduced by radiotherapy.

The dental basement membrane (BM) is composed of collagen types IV, VI, VII, and XVII, fibronectin, and laminin and plays an inductive role in epithelial-mesenchymal interactions during tooth development. The BM is degraded and removed during later-stage tooth morphogenesis; however, its original position defines the location of the dentin-enamel junction (DEJ) in mature teeth. We recently demonstrated that type VII collagen is a novel component of the inner enamel organic matrix layer contiguous with the DEJ. Since it is frequently co-expressed with and forms functional complexes with type VII collagen, we hypothesized that type IV collagen should also be localized to the DEJ in mature human teeth. To identify collagen IV, we first evaluated defect-free erupted teeth from various donors. To investigate a possible stabilizing role, we also evaluated extracted teeth exposed to high-dose radiotherapy--teeth that manifest post-radiotherapy DEJ instability. We now show that type IV collagen is a component within the morphological DEJ of posterior and anterior teeth from individuals aged 18 to 80 yr. Confocal microscopy revealed that immunostained type IV collagen was restricted to the 5- to 10-µm-wide optical DEJ, while collagenase treatment or previous in vivo tooth-level exposure to > 60 Gray irradiation severely reduced immunoreactivity. This assignment was confirmed by Western blotting with whole-tooth crown and enamel extracts. Without reduction, type IV collagen contained macromolecular α-chains of 225 and 250 kDa. Compositionally, our results identify type IV collagen as the first macromolecular biomarker of the morphological DEJ of mature teeth. Given its network structure and propensity to stabilize the dermal-epidermal junction, we propose that a collagen-IV-enriched DEJ may, in part, explain its well-known fracture toughness, crack propagation resistance, and stability. In contrast, loss of type IV collagen may represent a biochemical rationale for the DEJ instability observed following oral cancer radiotherapy.

Modulation of TNF on the expression of protease activated receptors in P815 mast mells / 中华微生物学和免疫学杂志

Objective To investigate the potential influence of TNF on the expression of protease activated receptor (PAR)-1,2,3 and 4 by using P815 mast cells. Methods After being challenged with various concentrations of TNF for 2 h, 6 h and 16 h, the P815 mast cells were treated with or without Triton X-100 and the PAR expressions were detected by flow cytometry and immunofluorescent microscopy. Results Compared with the corresponding controls, TNF concentration-dependently upregulated expressions of PAR-2 and PAR-4 both in Triton X-100-treated and the untreated groups, but had no significant effect on the expression of PAR-1 and PAR-3. Moreover, no significantly different expressions of TNF-induced PAR-1, 2, 3 were observed between Triton X-100-treated and the untreated groups, whereas Triton X-100-treated PAR-4 expressions were significantly enhanced by TNF compared with the Triton X-100-untreated ones. Conclusion TNF can up-regulate PAR-2, 4 expression of P815 mast cells but has little effect on the expression of PAR-1, 3 correspondingly. And Triton X-100 treatment had no significant effect on TNF-modulated expression of PARs in P815 mast cells.