Factors to consider before choosing EV labeling method for fluorescence-based techniques.

A well-designed fluorescence-based analysis of extracellular vesicles (EV) can provide insights into the size, morphology, and biological function of EVs, which can be used in medical applications. Fluorescent nanoparticle tracking analysis with appropriate controls can provide reliable data for size and concentration measurements, while nanoscale flow cytometry is the most appropriate tool for characterizing molecular cargoes. Label selection is a crucial element in all fluorescence methods. The most comprehensive data can be obtained if several labeling approaches for a given marker are used, as they would provide complementary information about EV populations and interactions with the cells. In all EV-related experiments, the influence of lipoproteins and protein corona on the results should be considered. By reviewing and considering all the factors affecting EV labeling methods used in fluorescence-based techniques, we can assert that the data will provide as accurate as possible information about true EV biology and offer precise, clinically applicable information for future EV-based diagnostic or therapeutic applications.

Singlet oxygen detection in vivo is hindered by nonspecific SOSG staining.

Singlet oxygen is considered an important cell damaging agent due to its propensity to react with organic compounds. This drives the interest in developing methods for determination of 1O2. Simplicity of application and high sensitivity makes fluorescent probes a popular choice for in vivo 1O2 detection. Despite its proclaimed cell-impermeability, the commercially available Singlet Oxygen Sensor Green (SOSG) is widely applied to support assertions of 1O2 involvement in cell and tissue damage. Our investigation, however, demonstrate that different microbial species and cancer cells become fluorescent when exposed to SOSG under conditions which exclude generation of 1O2. Cells, permeabilized with chlorhexidine or by heat exposure under anaerobic conditions, exhibited SOSG fluorescence. Permeabilized cells could be stained with SOSG even 24 h post-permeabilization. Since SOSG is cell impermeable, the main factor that led to fluorescent staining was plasma membrane damage. Spectral analyses of different batches of SOSG revealed that SOSG endoperoxide (SOSG-EP) did not increase even after prolonged storage under the recommended conditions. The commercial preparations of SOSG, however, were not SOSG-EP free, which can produce erroneous results when SOSG staining is used as a proof of singlet oxygen production in vivo.

Design, synthesis, bioactivity and action mechanism of N-substituted N'-phenylpicolinohydrazides against phytopathogenic fungi.

N'-phenylpicolinohydrazide has been proven to be a promising lead compound for research and development of novel fungicides for agriculture in our previous study. As our continuing research, in this study, a series of N-substituted derivatives of N'-phenylpicolinohydrazide were synthesized and explored for the inhibition activity on nine phytopathogenic fungi and action mechanism. The results found that eleven of the compounds had excellent antifungal activity with more than 80% inhibition rates at 50 µg/mL on part or most of the fungi, especially A. solani and P. piricola. Compounds 5i, 5j and 5k showed EC50 values of < 8.0 µg/mL against A. solani superior to positive control carbendazim (EC50 = 36.0 µg/mL) while 5p and 5q exhibited the highest activity with EC50 values of 2.72 and 2.80 µg/mL against P. piricola superior to positive control boscalid (EC50 > 50.0 µg/mL). Furthermore, 5k also showed significant protective effect against A. solani infection on tomatoes in a concentration-dependent manner. Action mechanism research showed that 5k was able to increase the intracellular ROS level, change both MMP and permeability of cell membrane and damage mycelial morphology. Molecular docking studies showed that 5k could bind into ubiquinone-binding region of succinate dehydrogenase by hydrogen bonds, π-cation, π-π stacked, π-alkyl, and alkyl interactions. Additionally, the antibacterial activity was also investigated. Thus, N-substituted derivatives of N'-phenylpicolinohydrazide were emerged as novel and highly promising antifungal molecular skeletons to develop new fungicides for crop protection.

Methods and Protocol for Single-Cell Motility Assays under Topological Constraints.

The extracellular environment plays a crucial role in many physiological and pathological processes involving cell motility, such as metastatic invasion in cancer development, by heavily impacting the migration strategies adopted by the cells. The study of how mechanical constraints affect the dynamics of cell migration may be relevant to gain more insight into such processes, and it may prove to be a powerful tool in the hands of biologists. In this chapter, we describe the methods used to investigate the ability of neoplastic cells to migrate through narrowing, rigid microstructures upon chemoattractant stimulation.

Biological Efficacy of Ionizing Radiation Sources on 3D Organotypic Tissue Slices Assessed by Fluorescence Microscopy.

OBJECTIVE: Traditional cell-based radiobiological methods are inadequate for assessing the toxicity of ionizing radiation exposure in relation to the microstructure of the extracellular matrix. Organotypic tissue slices preserve the spatial organization observed in vivo, making the tissue easily accessible for visualization and staining. This study aims to explore the use of fluorescence microscopy of physiologically compatible 3D tissue cultures to assess the effects of ionizing radiation. METHODS: Organotypic tissue slices were obtained by vibratome, and their mechanical properties were studied. Slices were exposed by two ionizing radiation sources; electron beams (80 Gy and 4 Gy), and soft gamma irradiation (80 Gy and 4 Gy). Two tissue culture protocols were used: the standard (37°C), and hypothermic (30°C) conditions. A qualitative analysis of cell viability in organotypic tissue slices was performed using fluorescent dyes and standard laser confocal microscopy. RESULTS: Biological dosimetry is represented by differentially stained 200-µm thick organotypic tissue sections related to living and dead cells and cell metabolic activity. CONCLUSION: Our results underscore the ability of fluorescence laser scanning confocal microscopy to rapidly assess the radiobiological effects of ionizing radiation in vitro on 3D organotypic tissue slices.

The antibiofilm potential of a heteropolysaccharide produced and characterized from the isolated marine bacterium Glutamicibacter nicotianae BPM30.

Biofilms are the significant causes of 80% of chronic infections in the oral cavity, urinary tract, biliary tube, lungs, gastrointestinal tract, and so on to the general public. Treatment of pathogenic biofilm using bacterial exopolysaccharides (EPS) is an effective and promising strategy. In the present work, a marine bacterium was isolated, studied for exopolysaccharide production, and tested for its antibiofilm activity. Approximately 1.31 ± 0.07 g/L of a purified extracellular polysaccharide was produced and characterized from the isolated marine bacterium Glutamicibacter nicotianae BPM30. The hydrolyzed EPS contains multiple monosaccharides such as rhamnose, fructose, glucose, and galactose. The EPS demonstrated potential antibiofilm activity on four tested pathogens in a concentration-dependent mode. The antibiofilm activity of the purified EPS was studied by crystal violet assay and fluorescence staining method. Comparative inhibition results obtained for the tested strains are 93.25% ± 5.25 and 88.56% ± 2.25 for K. pneumoniae; 92.65% ± 7.6 and 98.33% ± 0.85 for P. aeruginosa; 90.36% ± 6.3 and 52.08% ± 7.74 for S. typhi; 84.62% ± 5.6 and 77.90% ± 5.90 for S. dysenteriae. The results of the present work demonstrated the antibiofilm potential of EPS, which could be helpful in the invention of novel curative approaches in battling bacterial biofilm-related medical complications.

Acid adaptation increased the resistance of Escherichia coli O157:H7 in bok choy (Brassica rapa subsp. chinensis) juice to high-pressure processing.

IMPORTANCE: Based on the U.S. Food and Drug Administration regulations, E. coli O157:H7 is a pertinent pathogen in high acid juices that needs to be inactivated during the pasteurization process. The results of this study suggest that the effect of acid adaptation should be considered in the selection of HPP parameters for E. coli O157:H7 inactivation to ensure that pasteurization objectives are achieved.

Double Staining with Fluorescent Tracers to Determine Myeloid Cell Migration of Leishmania-infected Cells from Mouse Skin to Lymphatic Tissues by Flow Cytometry.

Immune cell trafficking in steady-state conditions and inflammatory cell recruitment into injured tissues is crucial for the surveillance of the immune system and the maintenance of body homeostasis. Tracking the cell journey from the infection site in the skin to lymphoid tissues has been challenging, and is typically determined using fluorescent cell tracers, antibodies, or photoconvertible models. Here, we describe the detailed method to track Leishmania-infected myeloid cells migrating from the skin to lymphatic tissues by multiparametric flow cytometry. These methods involve labeling of infective Leishmania donovani parasites with fluorescent cell tracers and phenotyping of myeloid cells with fluorescent antibodies, to determine the infection status of migratory myeloid cells. We also describe the detailed protocol to trace donor monocytes transferred intradermally into recipient mice in Leishmania donovani infection. These protocols can be adapted to study skin-lymphoid tissue migration of dendritic cells, inflammatory monocytes, neutrophils, and other phagocytic myeloid cells in response to vaccine antigens and infection. Key features • Cell-tracking of cell-trace-labeled parasites and monocytes from the skin to lymphatic tissues after transference into donor mice. • Identification of migratory cells labeled with fluorescent cell tracers and antibodies by flow cytometry. • Isolation, labeling, and transference of bone marrow monocytes from donor mice into the skin of recipient mice. • Description of a double-staining technique with fluorescent cell tracers to determine cell and parasite dissemination from the skin to lymphoid tissues.

Enhancement of protein detection on cultural heritage samples after SYPRO™ Ruby staining by optical microscopy and micro-FTIR spectroscopy.

The paper investigates SYPRO™ Ruby staining in combination with external reflection micro-FTIR spectroscopy, for the detection of proteinaceous media in paint layers on cultural heritage, from unembedded micro-fragments and samples embedded in cross-sections. Combining FTIR spectroscopy with staining helped to verify that the FTIR mapping is accurate when performed by the integration of the main amide I and II bands, despite their naturally occurrent distortions due to the specular component and material absorption/surface properties. The research filled some gaps in the published literature on SYPRO™ Ruby interaction with different Cultural Heritage materials, including identifying drawbacks, e.g. swelling mechanisms in the sample after staining. The effects of the staining were investigated on different reference samples containing rabbit skin glue (proteinaceous), and samples from cultural heritage case studies undergoing technical examination as part of research projects, where identification of protein is an important aspect of understanding the sequence of complex multi-layers within a sample. Results showed that, when external reflection µ-FTIR is performed after the staining, the contribution from amide I and II, which occurs at higher wavenumbers than in transmission or attenuated total reflection, is more resolved and therefore easier to determine. When inorganic or organic compounds are present in the same layer, variation in the position of amide bands can occur. However, they can be used for chemical mapping using simple data-treatment strategies, as validated with the positive staining. This type of data processing gives a good estimation of the protein distribution in the layers, both in terms of morphology and thickness, on mock-up samples and cross-sections from real case studies.

A sample-preparation-free, point-of-care testing system for in situ detection of bovine mastitis.

We present a highly integrated point-of-care testing (POCT) device capable of immediately and accurately screening bovine mastitis infection based on somatic cell counting (SCC). The system primarily consists of a homemade cell-counting chamber and a miniature fluorescent microscope. The cell-counting chamber is pre-embedded with acridine orange (AO) in advance, which is simple and practical. And then SCC is directly identified by microscopic imaging analysis to evaluate the bovine mastitis infection. Only 4 µL of raw bovine milk is required for a simple sample testing and accurate SCC. The entire assay process from sampling to result in presentation is completed quickly within 6 min, enabling instant "sample-in and answer-out." Under laboratory conditions, we mixed bovine leukocyte suspension with whole milk and achieved a detection limit as low as 2.12 × 104 cells/mL on the system, which is capable of screening various types of clinical standards of bovine milk. The fitting degrees of the proposed POCT system with manual fluorescence microscopy were generally consistent (R2 > 0.99). As a proof of concept, four fresh milk samples were used in the test. The average accuracy of somatic cell counts was 98.0%, which was able to successfully differentiate diseased cows from healthy ones. The POCT system is user-friendly and low-cost, making it a potential tool for on-site diagnosis of bovine mastitis in resource-limited areas.

Cell Viability Assays for Candida auris.

Cell viability assays are useful for assessing the efficacy of antifungal therapeutics and disinfection strategies in vitro. In recent years these assays have been fundamental for the testing of conventional and novel therapies against the nosocomial fungal pathogen Candida auris. Here we provide detailed descriptions of methods for assessing cellular viability of Candida auris in vitro, such as metabolic assays (XTT and resazurin), colony-forming unit counting, live/dead quantitative PCR, and fluorescent staining for microscopic analyses.

Rapid quantification of intracellular polyhydroxyalkanoates via fluorescence techniques: A critical review.

Polyhydroxyalkanoates (PHA) are promising bioplastics with excellent physicochemical properties and biodegradability, whereas PHA products suffer from high manufacturing costs. To reduce costs of PHA production, experiments with mixed microbial cultures and low-cost substrates have been conducted widely, where rapid and robust PHA quantification methods are necessary. Compared with traditional gas chromatography methods, PHA fluorescence quantification (PHA-FQ) methods may be quicker, safer and more suitable for modern experiments with high throughput requirements. However, practical applications of PHA-FQ methods are still limited. Therefore, this review provides a comprehensive understanding of PHA-FQ methods. Performance of PHA-staining fluorochromes, relevant spectral properties, and important staining procedures are summarized. Current developments of PHA-FQ protocols are critically reviewed. Main considerations needed to make PHA-FQ protocol reliable are comprehensively discussed. Finally, potential improvements in various aspects of PHA-FQ methods are highlighted. This review could help researchers develop more effective PHA-FQ methods and facilitate future experiments related to PHA.

Microwave-Assisted Green Synthesis of Carbon Quantum Dots Derived from Calotropis Gigantea as a Fluorescent Probe for Bioimaging.

An eco-friendly, cost-effective, and convenient approach for synthesizing biocompatible fluorescent carbon quantum dots (CQDs) from the leaf extract of the medicinal plant Calotropis gigantea, commonly known as crown flower, has been demonstrated in this work. Fluorescence quantum yields of up to 4.24 percent were observed in as-synthesized CQDs. The size distribution of the as-synthesized CQDs varied from 2.7 to 10.4 nm, with a significant proportion of sp2 and sp3 carbon groups verified by nuclear magnetic resonance analysis. The zeta potential of as-synthesized CQDs was measured to be -13.8 mV, indicating the existence of a negatively charged surface with incipient instability in aqueous suspension. Furthermore, as an alternative to organic or synthetic dyes, the development of simple, inexpensive, and non-destructive fluorescence-based staining agents are highly desired. In this regard, as-synthesized CQDs have shown remarkable fluorescent staining capabilities in this work and might be utilised as a suitable probe for optical and bio-imaging of bacteria, fungi, and plant cells.

Analysis of the Bacterial Biocenosis of Activated Sludge Treated with Leachate from Municipal Landfills.

The influx of toxic pollutants into wastewater treatment plants can negatively affect the quality of the activated sludge (AS). One source is landfill leachate. The identification of microorganisms present in AS is very important, e.g., while improving wastewater treatment technology. Therefore, the aim of the study was to investigate the effect of raw leachate and after purification of Phragmites australis and Ceratophyllum demersum on the composition of the AS bacterial biocenosis. In addition, AS status was assessed by LIVE/DEAD BacLight ™ fluorescent staining. The obtained results showed that the leachate did not significantly affect the cell membranes of AS bacteria, and even a slight improvement was noted. The research carried out using the next-generation sequencing method shows that the origin of the samples (active and closed storage) and the method of processing do not significantly affect the composition of the AS bacterial biocenosis at higher taxonomic levels. However, at the species level, the appearance of bacteria not previously present in AS was observed, namely: Flavobacterium luticocti, Candidimonas nitroreducens and Nitrobacter hamburgensis. The obtained results suggest that the leachate may be a source of microorganisms positively influencing the condition of AS bacteria.

Bacterial Staining and Profiling for Glycan Interactions on Glycan Microarrays for t-Test Calculation.

The use of glycan microarrays to study carbohydrate interactions of bacterial cells is of great interest owing to the key roles these interactions play in bacterial colonization and infection of a host. In this chapter, the methods to fluorescently stain Gram-positive or Gram-negative bacteria and profiling them for glycan interactions using glycan microarrays are described in detail. The application of the Student's t-test to glycan microarray data using an example data set comparing glycan microarray binding of an Acinetobacter baumannii wild type and mutant strain is also described in step-by-step detail.

A new method to localise and quantify oxidative stress in live juvenile mussels.

Stress and survival of the juvenile New Zealand green-lipped mussel, Perna canaliculus, is a poorly understood bottleneck in the ecological and economic performance of a significant aquaculture crop. This species was therefore selected as a model organism for the development of a new method to quantify oxidative stress in whole individuals. An in vivo ROS-activated stain (CellROX™) was administered to anaesthetised, translucent juveniles that were subsequently formaldehyde fixed and then visualised using confocal microscopy. Subsequent application of image analysis to quantifying ROS-positive tissue areas was successfully used to detect stress differences in juvenile mussels exposed to varying levels of emersion. This integrated method can be used to localise and quantify ROS production in individual translucent bivalve life stages (larval and juvenile), while relative stability following fixation greatly expands potential practical field applications. This article has an associated First Person interview with the first and third authors of the paper.

Flow cytometric approach to evaluate the impact of hydro-technical concrete compounds' release to the freshwater microbiome.

The aim of this research was to test the potential of applying a flow cytometric procedure to evaluate the impact of concrete compounds' release to the freshwater microbiome. Cells from the collected samples were stained with a fluorogenic redox indicator dye that measures the redox potential of microbial cells. This novel approach was combined with the assessment of microorganisms' penetration into the internal structures of concrete using the Rose Bengal sodium salt staining. Rose Bengal staining revealed an intense fouling of the upper and side walls of the concrete cubes and also indicated the penetration of microorganisms inside the concrete as observed for the cubes' cross-sections. Flow cytometric cellular redox potential measurement revealed high percentages of active cells within the concrete's porous structures and in non-exposed water (32.7% and 30.2% of active cells) versus samples from exposed water and concrete's outer surfaces (6.8%, 6.1%, and 3.3% of active cells). The results demonstrated a detrimental impact of hydro-technical concrete on the vitality of microbial cells within the freshwater environment. Tested protocol by analyzing the physiology of microbial cells improved the functional description of complex communities to evaluate the fate of contaminants present in the concrete-based hydro-technical infrastructure.

Blocking Cross-Species Secondary Binding When Performing Double Immunostaining With Mouse and Rat Primary Antibodies.

Immunostaining is a powerful technique and widely used to identify molecules in tissues and cells, although critical steps are necessary to block cross-reaction. Here we focused on an overlooked cross immunoreactivity issue where a secondary antibody (secondary) cross-reacts with a primary antibody (primary) from a different species. We first confirmed the previously reported cross-species binding of goat anti-mouse secondary to rat primary. This was accomplished by staining with a rat primary against glial fibrillary acidic protein (GFAP) and visualizing with goat (or donkey) anti-mouse secondary. We then further revealed the converse cross-species binding by staining with a mouse primary against neuronal nuclear protein (NeuN) and visualizing with anti-rat secondaries. We speculate that mouse and rat primaries share antigenicity, enabling either secondary to recognize either primary. To block this cross-species binding in double staining experiments, we compared three protocols using mouse anti-NeuN and rat anti-GFAP, two primaries whose antigens have non-overlapping distributions in brain tissues. Simultaneous staining resulted in cross-species astrocytic staining (anti-mouse secondary to rat anti-GFAP primary) but no cross-species neuronal staining (anti-rat secondary to mouse anti-NeuN primary). Cross-species astrocytic staining was missing after sequential same-species staining with mouse anti-NeuN primary, followed by rat anti-GFAP. However, cross-species astrocytic staining could not be diminished after sequential same-species staining with rat anti-GFAP primary, followed by mouse anti-NeuN. We thus hypothesize that a competition exists between anti-mouse and anti-rat secondaries in their binding to both primaries. Single staining for NeuN or GFAP visualized with dual secondaries at different dilution ratio supported this hypothesis.

A simple and rapid method for imaging male meiotic cells in anthers of model and non-model plant species.

KEY MESSAGE: We describe a simple method to view meiotic cells in whole anthers from a range of plants. The method retains spatial organisation and enables simultaneous analysis of many meiotic cells. Understanding the process of male meiosis in flowering plants, and the role of genes involved in this process, offers potential for plant breeding, such as through increasing the level of genetic variation or the manipulation of ploidy levels in the gametes. A key to the characterisation of meiotic gene function and meiosis in non-model crop plants, is the analysis of cells undergoing meiosis, a task made difficult by the inaccessible nature of these cells. Here, we describe a simple and rapid method to analyse plant male meiosis in intact anthers in a range of plant species. This method allows analysis of numerous cells undergoing meiosis and, as meiotic cells stay within the anther, it retains information of the three-dimensional organisation and the location of organelles in meiotic cells. We show that the technique provides information on male meiosis by looking at the synchrony of meiotic progression between and within locules, and comparing wildtype and mutant plants through the chromosome separation stages in Arabidopsis thaliana. Additionally, we demonstrate that the protocol can be adopted to other plants with different floral morphology using Medicago truncatula as an example with small floral buds and the non-model plant kiwifruit (Actinidia chinensis) with larger buds and anthers.

Increased mRNA expression of key cytokines among suspected cases of Pneumocystis jirovecii infection.

BACKGROUND: Pneumocystis pneumonia (PCP) is a fatal infectious disease caused by Pneumocystis jirovecii (PJP). The major factor relevant to morbidity and mortality seems to be the host inflammatory reaction. The objective of this study was to evaluate the role of IL-2, IL-4, IL-10, and IL-13 cytokine mRNA expression among suspected P. jirovecii infection. METHODS: This was a cross-sectional analytical study undertaken in Aseer region, Saudi Arabia. One hundred suspected PCP cases and 100 healthy controls were included in the study. Basic clinical manifestations, radiological findings, microbiological and immunological findings were extracted from the hospital records from January 2019 to August 2019, Pneumocystis detection was done by immune-fluorescent staining (IFAT, Gomorimethanamine silver staining (GMSS), Giemsa staining, Toluidine blue O (TBO), and Pneumocystis RT-PCR. RESULTS: Increased more than 5 fold, 3 fold, 4 fold, and 7 fold of IL-2, IL-4, IL-10, and IL-13 mRNA expression were observed in PCP cases compared to controls. Higher expression of IL-2 mRNA was connected with crept, wheezing and chest X-ray findings like central perihilar infiltrate, patchy infiltrate, consolidation, hilar lymphadenopathy, pneumothorax, pleural effusion which showed higher expression compared to counterpart (p< 0.0001). Higher expression of IL-4 mRNA was found to be significantly associated with weight loss (p=0.002), dyspnea (p=0.003), crept (p=0.01), and chest X-ray findings (p< 0.0001). Significantly increased expression of IL-10 mRNA was observed to be associated with weight loss, dyspnea, night sweats, wheezing, and different findings of chest X-ray compared to their counterparts, whereas, IL-13 mRNA was observed in cases with fever. Suspected cases of PCP confirmed positive by IFTA with higher IL-2, IL-4, and IL-10 mRNA expression compared to negative cases. RT-PCR confirmed PCP cases had significantly higher expression of IL-2, IL-4, and IL-10 as well as IL-13 mRNA compared to negative cases. Positive detected cases by GMSS showed higher IL-2, IL-10 mRNA expression, while Giemsa showed only higher IL-4 mRNA expression compared to negative cases. CONCLUSION: Confirmed cases of P. jirovecii showed higher IL-2, IL-4, IL-10, and IL-13 mRNA expression comparatively to negative cases. Increased expression of cytokines may be indicative of infection severity and could help in patients' management.