Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA

The properties of six commonly used, commercially available, fluorescent dyes were compared in staining right-handed B-DNA and left-handed Z-DNA. All showed different degree of fluorescence turn-on in the presence of B-DNA, but very little in the presence of Z-DNA. The optimal range of dye-DNA ratios of DNA was determined. While these dyes do not provide a turn-on type probe for Z-DNA, staining between B- and Z-DNA using dyes such as SYBR Green I was shown to be useful in tracking the kinetics of conformational changes between these two forms of DNA. Finally, SYBR Green I showed unique circular dichroism patterns in 4 M NaCl that change in the presence of double stranded DNA, both in the visible and UV range.

Mechanism of Cell-Killing Activity of Plantaricin LD1 Against Escherichia coli ATCC 25922

Plantaricin LD1 was purified from a potential probiotic strain, Lactobacillus plantarum LD1 previously isolated from indigenous food, Dosa. In this study, we have performed a detailed mechanism of action of plantaricin LD1 against Escherichia coli ATCC 25922 considering Micrococcus luteus MTCC 106 as control. The plantaricin LD1 showed a minimum inhibitory concentration (MIC) of 34.57 µg/mL and a minimum bactericidal concentration (MBC) of 138.3 µg/mL against M. luteus MTCC 106, whereas MIC 69.15 µg/mL and MBC 276.6 µg/mL were found against E. coli ATCC 25922. The efflux of potassium ions, dissipation of membrane potential (∆ψ), and transmembrane pH gradient (∆pH) of plantaricin LD1-treated cells suggested the membrane-acting nature of plantaricin LD1. Plantaricin LD1 also caused degradation of the genomic DNA of the target strains tested. The cell killing was confirmed by staining with propidium iodide and visualized under light and electron microscopes. The bacteriocin-treated cells were found to be ruptured, swollen, and elongated. Thus, the findings indicate plantaricin LD1 kills E. coli ATCC 25922 by interacting with the cell membrane resulting in the efflux of intracellular contents and also causing degradation of nucleic acids leading to cell death.

Multiparametric Analysis of Apoptosis by Flow Cytometry

Flow cytometry remains the most widely used method for detecting and quantifying apoptosis and related forms of cell death in mammalian cells. The multiparametric nature of flow cytometry allows multiple apoptotic characteristics to be labeled and analyzed in a single sample, making it a powerful tool for analyzing the complex progression of apoptotic death. This chapter provides methods for combining assays for single apoptotic characteristics like caspase activation, annexin V binding, and cell membrane permeability into multiparametric assays that provide deeper insights into the cell death process. This approach to analyzing multiple apoptotic characteristics simultaneously yields far more information than single-parameter assays. While more informative than single-parameter assays, these multicolor methods can still be analyzed on relatively simple flow cytometers, making them widely accessible.

A Rapid and Simple Procedure for the Isolation of Embryonic Cells from Fish Eggs

Fertilized teleost fish eggs are a complex formation, in which dividing cells are located in a small point in the entire volume of eggs. Isolating embryonic cells can be considered a necessary step in the research of developmental peculiarities of fish cells at the earliest stages of embryogenesis before embryo formation. The main advantages of the offered protocol are rapid isolation, no enzymes, and overall low cost compared to other protocols. The protocol is suitable for the isolation of embryonic cells from medium-sized eggs at the stages of blastula or gastrula, for studies in a variety of applications (e.g., microscopy, flow cytometry, and other methods). Fertilized nelma eggs (Stenodus leucichthys nelma) are used in the protocol as a model. Key features • Fast and cheap isolation of cells from fish eggs at early stages (blastula or gastrula). • Applicable for most of the methods for cell study (any staining, microscopy, flow cytometry, etc.). • Can be applied to other teleost fish eggs with medium egg diameter of 3-4 mm. Graphical overview.

Practical Characterization Strategies for Comparison, Qualification, and Selection of Cell Viability Detection Methods for Cellular Therapeutic Product Development and Manufacturing

Cellular therapy development and manufacturing has focused on providing novel therapeutic cell-based products for various diseases. The International Organization for Standardization (ISO) has provided guidance on critical quality attributes (CQAs) that shall be considered when testing and releasing cellular therapeutic products. Cell count and viability measurements are two of the CQAs that are determined during development, manufacturing, testing, and product release. The ISO Cell Counting Standard Part 1 and 2 addressed the needs for improving the quality of cell counting results. However, there is currently no guidance on the qualification and selection of a fit-for-purpose cell viability detection method. In this work, we present strategies for the characterization and comparison of AO/PI and AO/DAPI staining methods using the heat-killed (HK) and low temperature/nutrient-deprived (LT/ND) cell death models to evaluate the comparability of cell viability measurements and identify potential causes of differences. We compared the AO/PI and AO/DAPI staining methods using HK and LT/ND-generated dead cells, investigated the staining time effects on cell viability measurements, and determined their viability linearity with different mixtures of live and dead cells. Furthermore, we validated AO/PI and AO/DAPI cell viability measurement with a long-term cell proliferation assay. Finally, we demonstrate a practical example of cell viability measurement comparison using AO/PI and AO/DAPI on antibiotic-selected transduced Jurkat and THP-1 cells to select a fit-for-purpose method for functional genomics screening. The proposed strategies may potentially enable scientists to properly characterize, compare, and select cell viability detection methods that are critical for cellular therapeutic product development and manufacturing.

Flow cytometry-assisted quantification of cell cycle arrest in cancer cells treated with CDK4/6 inhibitors

Cyclin-dependent kinase 4 (CDK4) and CDK6 inhibitors (i.e., palbociclib, abemaciclib, and ribociclib) are well known for their capacity to mediate cytostatic effects by promoting cell cycle arrest in the G1 phase, thus inhibiting cancer cell proliferation. Cytostatic effects induced by CDK4/6 inhibitors can be transient or lead to a permanent state of cell cycle arrest, commonly defined as cellular senescence. Induction of senescence is often associated to metabolic modifications and to the acquisition of a senescence-associated secretory phenotype (SASP) by cancer cells, which in turn can promote or limit antitumor immunity (and thus the efficacy of CDK4/6 inhibitors) depending on SASP components. Thus, although accumulating evidence suggests that anti-cancer effects of CDK4/6 inhibitors also depend on the promotion of antitumor immune responses, assessing cell cycle arrest and progression in cells treated with palbociclib remains a key approach for investigating the efficacy of CDK4/6 inhibitors. Here, we describe a method to assess cell cycle distribution simultaneously with active DNA replication by flow cytometry in cultured hormone receptor-positive breast cancer MCF7 cells.

Modified Pseudo-Schiff Propidium Iodide for Staining the Shoot Apical Meristem in Arabidopsis

Visualization of cell structure with fluorescent dye for characterizing cell size, shape, and arrangement is a common method to study tissue morphology and morphogenesis. In order to observe shoot apical meristem (SAM) in Arabidopsis thaliana by laser scanning confocal microscopy, we modified the pseudo-Schiff propidium iodide staining method by adding a series solution treatment to stain the deep cells. The advantage of this method is mainly reflected by the direct observation of the clearly bounded cell arrangement and the typical three-layer cells in SAM without the traditional tissue slicing.

Cloning, recombinant expression, purification, and functional characterization of AGAAN antibacterial peptide

A recombinant version of the AGAAN antimicrobial peptide (rAGAAN) was cloned, expressed, and purified in this study. Its antibacterial potency and stability in harsh environments were thoroughly investigated. A 15 kDa soluble rAGAAN was effectively expressed in E. coli. The purified rAGAAN exhibited a broad antibacterial spectrum and was efficacious against seven Gram-positive and Gram-negative bacteria. The minimal inhibitory concentration (MIC) of rAGAAN against the growth of M. luteus (TISTR 745) was as low as 60 µg/ml. Membrane permeation assay reveals that the integrity of the bacterial envelope is compromised. In addition, rAGAAN was resistant to temperature shock and maintained a high degree of stability throughout a reasonably extensive pH range. The bactericidal activity of rAGAAN ranged from 36.26 to 79.22% in the presence of pepsin and Bacillus proteases. Lower bile salt concentrations had no significant effect on the function of the peptide, whereas higher concentrations induced E. coli resistance. Additionally, rAGAAN exhibited minimal hemolytic activity against red blood cells. This study indicated that rAGAAN may be produced on a large scale in E. coli and that it had an excellent antibacterial activity and sufficient stability. This first work to express biologically active rAGAAN in E. coli yielded 8.01 mg/ml at 16 °C/150 rpm for 18 h in Luria Bertani (LB) medium supplemented with 1% glucose and induced with 0.5 mM IPTG. It also assesses the interfering factors that influence the activity of the peptide, demonstrating its potential for research and therapy of multidrug-resistant bacterial infections.

3D Visualization of Microtubules in Epidermal Pavement Cells

The plant cytoskeleton is instrumental in cellular processes such as cell growth, differentiation, and immune response. Microtubules, in particular, play a crucial role in morphogenesis by governing the deposition of plant cell wall polysaccharides and, in consequence, the cell wall mechanics and cell shape. Scrutinizing the microtubule dynamics is therefore integral to understanding the spatiotemporal regulation of cellular activities. In this chapter, we outline steps to acquire 3D images of microtubules in epidermal pavement cells of Arabidopsis thaliana cotyledons using a confocal microscope. We introduce the steps to assess the microtubule distribution and organization using image processing software Bitplane Imaris and ImageJ. We also demonstrate how the interpretation of image material can be facilitated by post-processing with general-purpose image enhancement software using methods trained by artificial intelligence-based algorithms.

Multiscale reconstruction of bronchus and cancer cells in human lung adenocarcinoma

BACKGROUND

While previous studies primarily focused on the structure of the normal whole mouse lung, the whole bronchus and cytoarchitectural details of the mouse intact lung lobe have been discovered at single-cell resolution. Revealing the sophisticated lung adenocarcinoma structure at three-dimensional (3D) and single-cell level remains a fundamental and critical challenge for the pathological mechanism research of lung adenocarcinoma (LA).

METHODS

Fluorescence micro-optical Sectioning Tomography (fMOST) combined with PI staining were used to obtain the 3D imaging of the human LA tissue at single-cell resolution.

RESULTS

With a spatial resolution of 0.32 × 0.32 × 1.0 μm³, the dataset of human LA with single-cell precision consists of two channels, each of which contains information about the bronchi and the cytoarchitecture. The bronchial wall is thicker and the lumen is smaller in the cancer tissue, in which its original normal structure is vanished. More solid components, more clustered cancer cells with larger nucleoli, and more significant atypia are found in cancer tissue. In paracancerous tissue, the bronchial wall cells have a monolayer or bilayer structure, cluster along the wall, and are relatively dispersed. Few fibrous structures and occasional dissemination of spread through air spaces (STAS) are observed.

CONCLUSIONS

Based on the human LA tissue dataset obtained by fMOST and PI staining, the bronchi and cells were reconstructed and visualized. This work provides a technical roadmap for studying the bronchus and cytoarchitectural structure and their spatial relationship in LA tissue, which may help with the understanding of the main histological structure of LA among pathologists.

The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants

Flow cytometry has emerged as a uniquely flexible, accurate, and widely applicable technology for the analysis of plant cells. One of its most important applications centers on the measurement of nuclear DNA contents. This chapter describes the essential features of this measurement, outlining the overall methods and strategies, but going on to provide a wealth of technical details to ensure the most accurate and reproducible results. The chapter is aimed to be equally accessible to experienced plant cytometrists as well as those newly entering the field. Besides providing a step-by-step guide for estimating genome sizes and DNA-ploidy levels from fresh tissues, special attention is paid to the use of seeds and desiccated tissues for such purposes. Methodological aspects regarding field sampling, transport, and storage of plant material are also given in detail. Finally, troubleshooting information for the most common problems that may arise during the application of these methods is provided.

Evaluation of anti-methicillin-resistant Staphylococcus aureus property of zerumbone

CONTEXT AND OBJECTIVE

Zerumbone has been reported to exert anti-microbial effects, but the mechanism by which the compound exerts its action is not known. Thus, this study aimed to investigate the mechanism of action of zerumbone against methicillin-resistance Staphylococcus aureus (MRSA), using the atomic force microscopy (AFM), scanning electron microscopy (SEM), and flow cytometry techniques.

METHODS

MRSA (NCTC 13277) cell viability was determined using the microplate AlamarBlue assay. AFM and SEM were used to determine the morphology of zerumbone-treated MRSA cells. Flow cytometric analysis was used to determine the effect of zerumbone on bacterial membrane permeability and membrane potential, using the propidium iodide (PI) staining method, membrane potential-sensitive fluorescence probe, and DiBAC4(3) dye. DCFDA dye was used to determine the generation of reactive oxygen species (ROS) by MRSA.

RESULTS

Zerumbone significantly inhibited MRSA growth with a minimum inhibitory concentration (MIC) of 125 µg/ml. The AFM analysis showed that zerumbone caused leakage of cytoplasmic content from the bacterial cells. Ultrastructure analysis showed small colonies of the bacteria with pores on the membrane surface. There were increases in zerumbone-treated MRSA PI and DiBAC4(3) fluorescence, indicating an increase in cell membrane permeability and a decrease in membrane potential that culminated in the loss of membrane structural integrity and bacterial death. Based on DCFDA dye analysis, zerumbone also reduced ROS production by MRSA.

CONCLUSIONS

Zerumbone exerts anti-MRSA effects by causing membrane depolarization, increasing membrane permeability, and finally disrupting cell membrane and bacterial killing.

In Vivo Analysis of Necrosis and Ferroptosis in Nonalcoholic Steatohepatitis (NASH)

Nonalcoholic steatohepatitis (NASH) is a metabolic liver disease that progresses from simple steatosis to the disease states such as chronic inflammation and fibrosis. In most liver diseases, immunological responses caused by tissue damages or viral infection contribute to the pathological advances, and various types of cell death have been reported to be implicated in their pathogenesis. However, the conventional detection of necrosis in vivo is not currently available, whereas the detection method for apoptosis has been relatively well-established. We recently reported a method for the in vivo detection of necrotic cells in liver disease models by an intravenous injection of Propidium Iodide (PI) into mice. We also provide standard methods for the evaluation of lipid accumulation and fibrosis characteristic of NASH. In addition, by utilizing these procedures and a murine model of steatohepatitis, we showed that ferroptosis, a type of regulated necrotic cell death, could be involved in the pathogenesis of NASH. These approaches allow us to explore the pathophysiological roles of cell death in liver diseases.

Analysis of Cell Cycle by Flow Cytometry

The cell cycle of a cell is tightly controlled by several regulators. Dysregulation of cell cycle can lead to uncontrolled cell division which is one of the main characteristics of cancer cells. DNA content of a cell is changed during the cell cycle progression and can be measured by flow cytometry. In this chapter, we aim to provide a detailed protocol on how to analyze the cell cycle using flow cytometry.

Assessment of Hepatocyte Ploidy by Flow Cytometry

Polyploidy is a common and dynamic feature of mature rodent and human hepatocytes. While polyploidization occurs naturally during growth, alterations in the distribution of diploid and polyploid cells in the liver can be indicative of tissue stress or a pathologic state. Here, we describe a method for flow cytometric quantification of ploidy distribution by staining with propidium iodide. We first outline a hepatocyte isolation procedure from mouse liver through a two-step perfusion system for analysis of cellular ploidy. In an alternative approach, we employ a nuclei isolation protocol to assess nuclear ploidy. Finally, we describe how the use of fluorescent cell markers is compatible with these methods and helps retain information on cellular position within the tissue.

Synthesis, toxicity evaluation and determination of possible mechanisms of antimicrobial effect of arabinogalactane-capped selenium nanoparticles

BACKGROUND

The elemental selenium nanoparticles (Se⁰NPs) find application in biology and medicine due to wide spectrum of their biological activity combined with low toxicity. For instance, Se⁰NPs are promising antimicrobial agents for plant treatment against the bacterial phytopathogen Clavibacter michiganensis sepedonicus (Cms). Careful characterization of possible mechanisms of antimicrobial action of Se⁰NPs as well as the assessment of their biosafety for plant and animal organisms represents urgent challenge.

METHODS

AG-stabilized Se⁰NPs (AG/Se⁰NPs) were synthesized by oxidation of selenide-anions by molecular oxygen dissolved in the reaction medium in the presence of AG macromolecules. The antimicrobial activity of AG/Se⁰NPs against Cms was investigated both by observing the change in optical density of bacterial suspension and directly evaluating the cell death using fluorescent microscopy with propidium iodide staining. The effect of AG/Se⁰NPs on the dehydrogenase activity was studied by determination of Cms enzymes ability to reduce colorless TTC to formazan. The effect of AG/Se⁰NPs nanocomposite on the respiration rate of Cms cells was examined by polarographic method. For qualitative visualization of the potential on the inner membrane of Cms mesosomes, the potential-dependent TMRM dye and fluorescence microscopy were used. The toxicity of the AG/Se⁰NPs was investigated on white mice by the Litchfield-Wilcoxon method. The effect of AG/Se⁰NPs on plant organisms (potato plants) was studied on healthy and Cms-infected plants by determining the level of chlorophyll and lipid peroxidation products (LPO) in their leaves when treated with nanoparticles.

RESULTS

Spherical Se° nanoparticles with an average size of 94 nm were obtained using the stabilizing potential of AG. It was found that these nanoparticles exhibited the pronounced (up to 60 %) bacteriostatic action (in 6.25 μg/mL concentration) against the bacterial phytopathogen Cms. It was shown and experimentally confirmed for the first time that the probable causes of the bacteriostatic action of AG/Se°NPs against Cms are non-reversible inhibition of Cms cell respiration, a decrease of the transmembrane potential with a change in the cell wall permeability for H⁺ protons and a decrease in their dehydrogenase activity. It was revealed that the treatment of healthy and Cms-infected potato plants with an aqueous solution of AG/Se°NPs involved no significant changes in the content of LPO and negative effect on the chlorophyll content, thus contributing to the saving of these values at the level of control intact plants.

CONCLUSION

Using a complex of complementary methods, we have found that antimicrobial activity of AG/Se⁰NPs is apparently due to their ability to inhibit the dehydrogenase activity of Cms cells, as well as to disrupt the integrity of the cell membrane, resulting in a decrease of transmembrane potential and reduction of cellular respiration. The antimicrobial and antibiofilm activity of AG/Se⁰NPs, together with their nontoxicity and safety for plant and animal organisms, determine the prospects for design of AG/Se⁰NPs-based drugs for the rehabilitation of plants from the Cms.

Bacteriocin isolated from the natural inhabitant of Allium cepa against Staphylococcus aureus

Extensive usage of antibiotics has led to the emergence of drug-resistant strains of pathogens and hence, there is an urgent need for alternative antimicrobial agents. Antimicrobial Peptides (AMPs) of bacterial origin have shown the potential to replace some conventional antibiotics. In the present study, an AMP was isolated from Bacillus subtilis subsp. spizizenii strain Ba49 present on the Allium cepa, the common onion and named as peptide-Ba49. The isolated AMP was purified and characterized. The purified peptide-Ba49, having a molecular weight of ~ 3.3 kDa as determined using mass spectroscopy, was stable up to 121 °C and in the pH range of 5-10. Its interaction with protein degrading enzymes confirmed the peptide nature of the molecule. The peptide exhibited low minimum inhibitory concentration (MIC) against Staphylococcus aureus and its (Methicillin-resistant Staphylococcus aureus) MRSA strains (MIC, 2-16 µM/mL). Further, time kill kinetic assay was performed and analysis of the results of membrane depolarization and permeabilization assays (TEM, DiBAC₄ (3) and PI) suggested peptide-Ba49 to be acting through the change in membrane potential leading to disruption of S. aureus membrane. Additionally, cytotoxicity studies of peptide-Ba49, carried out using three mammalian cell lines viz. HEK 293T, RAW 264.7, and L929, showed limited cytotoxicity on these cell lines at a concentration much higher than its MIC values. All these studies suggested that the AMP isolated from strain Ba49 (peptide-Ba49) has the potential to be an alternative to antibiotics in terms of eradicating the pathogenic as well as drug-resistant microorganisms.

Assaying Cell Cycle Status Using Flow Cytometry

In this chapter, four methods are described that can be used to assess cell cycle status in flow cytometry. The first method is based on the simultaneous analysis of cellular DNA content using a fluorescent DNA dye (propidium iodide) and of a nuclear proliferation marker (Ki-67). The second is based on the differential staining of DNA and RNA using Hoechst 33342 and Pyronin Y: this method is particularly useful to distinguish quiescent cells in G0 phase from G1 cells. Finally, two methods are described based on DNA incorporation of the synthetic nucleosides BrdU and EdU.

3D-ViaFlow: A Quantitative Viability Assay for Multicellular Spheroids

Three-dimensional cell culture became an essential method in molecular and cell biology research. Accumulating results show that cells grown in 3D, display increased functionality and are capable of recapitulating physiological functions that are not observed in classical in vitro models. Spheroid-based cell culture allows the cells to establish their own extracellular matrix and intricate intercellular connections promoting a tissue-like growth environment.In this paper we present the 3D-ViaFlow method that combines an optimised dual live-dead cell staining with flow cytometry to deliver a quantitative estimation of viability of cells in multicellular spheroids. The method is optimised for monolayer cultures and multicellular spheroids created from HepG2/C3A human hepatocytes or coculture of HepG2/C3A and endothelial cell line HMEC-1. It includes protocol for spheroids disassembling, labeling of cells with fluorescein diacetate and propidium iodide and instructions for flow cytometry gating optimized for analysis of heterogeneous cell populations form spheroids.

An Annexin V-FITC-Propidium Iodide-Based Method for Detecting Apoptosis in a Non-Small Cell Lung Cancer Cell Line

Annexin V and propidium iodide staining is widely used for determining the cellular death through apoptosis. In the presence of Ca²⁺ ions, annexin V has a strong binding affinity for phosphatidylserine, a membrane phospholipid that during apoptosis is translocated from the inner side of the cell membrane to its outer side. On the other hand, propidium iodide has ability for DNA binding and it can only enter into necrotic or late apoptotic cells. This chapter describes a commonly used method for detection of apoptosis in a non-small cell lung cancer cell line using annexin V and propidium iodide dye. We describe the detection of different stages of apoptosis in the A549 lung cancer cell line treated with dihydroartemisinin (DHA). This apoptosis detection method can be used to determine the efficacy of different kinds of drugs on cultured cancer cell lines.

Anti-Toxoplasma gondii activity of 5-oxo-hexahydroquinoline derivatives: synthesis, in vitro and in vivo evaluations, and molecular docking analysis

Background and purpose

The aim of this study was to evaluate the in vitro and in vivo anti-Toxoplasma gondii (T. gondii) effect of 5-oxo-hexahydroquinoline compounds. Moreover, molecular docking study of the compounds into the active site of enoyl-acyl carrier protein reductase (ENR) as a necessary enzyme for the vitality of apicoplast was carried out.

Experimental approach

A number of 5-oxo-hexahydoquinoline derivatives (Z1-Z4) were synthesized. The T. gondii tachyzoites of RH strain were treated by different concentrations (1-64 μg/mL) of the compounds. The viability of the encountered parasites with compounds was assessed using flow cytometry and propidium iodide (PI) staining. Due to the high mortality effect of Z3 and Z4 in vitro, their chemotherapy effect was assessed by inoculation of tachyzoites to four BALB/c mice groups (n = 5), followed by the gavage of various concentrations of the compounds to the mice. Molecular docking was done to study the binding affinity of the synthesized 5-oxo-hexahydroquinolines into ENR enzyme active site byusing AutoDock Vina® software. Docking was performed by a Lamarckian Genetic Algorithm with 100 runs.

Findings / Results

Flow cytometry assay results indicated compounds Z3 and Z4 had relevant mortality effect on parasite tachyzoites. Besides, in vivo experiments were also performed and a partial increase of mice longevity between control and experiment groups was recorded. Molecular docking of Z3 and Z4 in the binding site of ENR enzyme indicated that the compounds were well accommodated within the binding site. Therefore, it could be suggested that these compounds may exert their anti-T. gondii activity through the inhibition of the ENR enzyme.

Conclusion and implications

Compounds Z3 and Z4 are good leads in order to develop better anti-T. gondii agents as they demonstrated both in vitro and in vivo inhibitory effects on tachyzoites viability and infection. Further studies on altering the route of administration along with additional pharmacokinetics evaluations are needed to improve the anti-T. gondii impacts of 5-oxo-hexahydroquinoline compounds.

Computational Evaluation and In Vitro Validation of New Epidermal Growth Factor Receptor Inhibitors

BACKGROUND

The Epidermal Growth Factor Receptor (EGFR) is a transmembrane protein that acts as a receptor of extracellular protein ligands of the epidermal growth factor (EGF/ErbB) family. It has been shown that EGFR is overexpressed by many tumours and correlates with poor prognosis. Therefore, EGFR can be considered as a very interesting therapeutic target for the treatment of a large variety of cancers such as lung, ovarian, endometrial, gastric, bladder and breast cancers, cervical adenocarcinoma, malignant melanoma and glioblastoma.

METHODS

We have followed a structure-based virtual screening (SBVS) procedure with a library composed of several commercial collections of chemicals (615,462 compounds in total) and the 3D structure of EGFR obtained from the Protein Data Bank (PDB code: 1M17). The docking results from this campaign were then ranked according to the theoretical binding affinity of these molecules to EGFR, and compared with the binding affinity of erlotinib, a well-known EGFR inhibitor. A total of 23 top-rated commercial compounds displaying potential binding affinities similar or even better than erlotinib were selected for experimental evaluation. In vitro assays in different cell lines were performed. A preliminary test was carried out with a simple and standard quick cell proliferation assay kit, and six compounds showed significant activity when compared to positive control. Then, viability and cell proliferation of these compounds were further tested using a protocol based on propidium iodide (PI) and flow cytometry in HCT116, Caco-2 and H358 cell lines.

RESULTS

The whole six compounds displayed good effects when compared with erlotinib at 30 μM. When reducing the concentration to 10μM, the activity of the 6 compounds depends on the cell line used: the six compounds showed inhibitory activity with HCT116, two compounds showed inhibition with Caco-2, and three compounds showed inhibitory effects with H358. At 2 μM, one compound showed inhibiting effects close to those from erlotinib.

CONCLUSION

Therefore, these compounds could be considered as potential primary hits, acting as promising starting points to expand the therapeutic options against a wide range of cancers.

Fluorescent Staining of Arbuscular Mycorrhizal Structures Using Wheat Germ Agglutinin (WGA) and Propidium Iodide

The colonization of a host plant root by arbuscular mycorrhizal (AM) fungi is a progressive process, characterized by asynchronous hyphal growth in intercellular and intracellular spaces, leading to the coexistence of diverse intraradical structures, such as hyphae, coils, arbuscules, and vesicles. In addition, the relative abundance of intercellular and intracellular fungal structures is highly dependent on root anatomy and the combination of plant and fungal species. Lastly, more than one fungal species may colonize the same root, adding a further level of complexity. For all these reasons, detailed imaging of a large number of samples is often necessary to fully assess the developmental processes and functionality of AM symbiosis. To this aim, the use of rapid and efficient staining methods that can be used routinely is crucial.We herein present a simple protocol to obtain high detail images of both overall intraradical fungal colonization pattern and fine morphology, in AM root sections of Lotus japonicus. The procedure is based on tissue clearing, fluorescent staining of fungal cell walls with fluorescein isothiocyanate-conjugated wheat germ agglutinin (FITC-WGA), and the combined counterstaining of plant cell walls with propidium iodide (PI). The resulting images can be acquired using traditional or confocal fluorescence microscopes and used for qualitative and quantitative analyses of fungal colonization, of particular interest for the comparison of mycorrhizal phenotypes between different experimental conditions or genetic backgrounds.

Optimization of hydroponic growth system and Na+-fluorescence measurements for tree species Pongamia pinnata (L.) pierre

Domestication and cultivation of tree species, such as Pongamia pinnata is quite important because of its biofuel properties. Seedlings grown in modified hydroponic culture were morphologically similar to that of soil grown seedlings. Further, seedlings were allowed to grow without root limitation. Comparatively, our modified hydroponic growth system can be performed with minimal resources. Prior incubated root segments with CoroNa-Green AM dye retained maximum amount of dye when compared to CoroNa-Green AM dye incubated sections. Our modified protocol provides quantitative analysis of 2D and 3D imaging process at cellular and sub-cellular level.•Our protocol is customized to study individual plant behavior.•Additionally, it is customized for growing tap rooted trees species hydroponically. Changing the nutrient solution with regular intervals provides continuous supply of nutrients to the plants.•Prior incubation of root segments with Na⁺ probe (CoroNa-Green AM) provides better resolution in imaging process. Additionally, both 2D and 3D imaging provides a means to acquire and analyze entirety of the sample.

Contemporaneous Measurement of Outer and Inner Membrane Permeability in Gram-negative Bacteria

The emergence and rapid spread of multidrug resistance in bacteria have led to the urgent need for novel antibacterial agents. Membrane permeabilization is the mechanism for many antibacterial molecules that are being developed against gram-negative bacteria. Thus, to determine the efficacy of a potential antibacterial molecule, it is important to assess the change in bacterial membrane permeability after treatment. This study describes the protocol for the assays of outer and inner membrane permeability using the fluorescent probes N-phenyl-1-naphthylamine and propidium iodide. Compared with other experiments, such as electron microscopy and the assay of minimal bactericidal concentration, this methodology provides a simpler, faster, and cost-effective way of estimating the membrane-permeabilizing effect and bactericidal efficacy of antibacterial molecules. This study presents an optimized protocol with respect to the classical protocols by incubating bacteria with antibacterial molecules in the culture condition identical to that of antibacterial assays and then detecting the signal of the fluorescent probe in the buffer without broth and antibacterial molecules. This protocol avoids the effect of nutrient deficiency on the physiological status of bacteria and the interference of antibacterial molecules towards the fluorescent probe. Thus, this method can effectively and precisely evaluate the membrane permeability and match the results obtained from other antibacterial assays, such as minimum inhibitory concentration and time-kill curve assays.

Survival Tests for Leptospira spp

Measuring viability is an important and necessary assessment in studying microorganisms. Several methods can be applied to Leptospira spp., each with advantages and inconveniencies. Here, we describe the traditional colony-forming unit method, together with two other methods based, respectively, on the reducing capacity of live cells (Alamar Blue^® Assay) and differential staining of live and dead cells (LIVE/DEAD BacLight^®). The Alamar Blue^® Assay uses the blue reagent resazurin, which can be reduced into the pink reagent resorufin by live cell oxidoreductases. Production of resorufin can be quantified by absorbance or fluorescence reading. The LIVE/DEAD BacLight^® assay uses a mixture of two nucleic acid dyes (Syto9 and propidium iodide) that differentially penetrate and stain nucleic acid of cells with decreased membrane integrity. The colony-forming unit method is labor-intensive but the most sensitive and linear method. The two other methods are not laborious and well-adapted to high-throughput studies, but the range of detection and linearity are limited.

Cancellation effect is present in high-frequency reversible and irreversible electroporation

It was recently suggested that applying high-frequency short biphasic pulses (HF-IRE) reduces pain and muscle contractions in electrochemotherapy and irreversible ablation treatments; however, higher amplitudes with HF-IRE pulses are required to achieve a similar effect as with monophasic pulses. HF-IRE pulses are in the range of a microseconds, thus, the so-called cancellation effect could be responsible for the need to apply pulses of higher amplitudes. In cancellation effect, the effect of first pulse is reduced by the second pulse of opposite polarity. We evaluated cancellation effect with high-frequency biphasic pulses on CHO-K1 in different electroporation buffers. We applied eight bursts of 1-10 µs long pulses with inter-phase delays of 0.5 µs - 10 ms and evaluated membrane permeability and cell survival. In permeability experiments, cancellation effect was not observed in low-conductivity buffer. Cancellation effect was, however, observed in treatments with high-frequency biphasic pulses looking at survival in all of the tested electroporation buffers. In general, cancellation effect depended on inter-phase delay as well as on pulse duration, i.e. longer pulses and longer interphase delay cause less pronounced cancellation effect. Cancellation effect could be partially explained by the assisted discharge and not by the hyperpolarization by the chloride channels.

Microhair on the adaxial leaf surface of salt secreting halophytic Oryza coarctata Roxb. show distinct morphotypes: Isolation for molecular and functional analysis

Halophytic Oryza coarctata is a good model system to examine mechanisms of salinity tolerance in rice. O. coarctata leaves show the presence of microhairs in adaxial leaf surface furrows that secrete salt under salinity. However, detailed molecular and physiological studies of O. coarctata microhairs are limited due to their relative inaccessibility. This work presents a detailed characterization of O. coarctata leaf features. O. coarctata has two types of microhairs on the adaxial leaf surface: longer microhairs (three morphotypes) lining epidermal furrow walls and shorter microhairs (reported first time) arising from bulliform cells. Microhair morphotypes include (i) finger-like, tubular structures, (ii) tubular hairs with bilobed and flattened heads and (iii) bi-or trifurcated hairs. The unicellular nature of microhairs was confirmed by propidium iodide (PI) staining. An efficient method for the isolation and enrichment of O. coarctata microhairs is presented (yield averaging ˜2 × 10⁵/g leaf tissue). The robustness of the microhair isolation procedure was confirmed by subsequent viability staining (PI), total RNA isolation and RT-PCR amplification of O. coarctata trichome-specific WUSCHEL-related homeobox 3B (OcWox3B) and transporter gene-specific cDNA sequences. The present microhair isolation work from O. coarctata paves the way for examining genes involved in ion secretion in this halophytic wild rice model.

Evaluation of the cytotoxicity and interaction of lead with lead resistant bacterium Acinetobacter junii Pb1

This study explores the potential of lead resistant bacterium Acinetobacter junii Pb1 for adsorption/accumulation of lead using various techniques. In the present work, growth of A. junii Pb1 was investigated in the presence of a range of Pb(II) concentrations (0, 100, 250, 500, and 1000 mg l^-1). Lead was found to have no toxic effect on the growth of A. junii Pb1 at 100 and 250 mg l^-1 concentrations. However, further increase in Pb(II) concentration (500 mg l^-1) showed increase in lag phase, though growth remained unaffected and significant growth inhibition was observed when concentration was increased to 1000 mg l^-1. Same was confirmed by the observations of flow cytometry. Further, the effect of Pb(II) on A. junii Pb1 was evaluated by using fluorescence microscopy, spectrofluorimetry, and flow cytometry. The spectrofluorimetry and fluorescence microscopy results revealed the accumulation of Pb(II) inside the bacterial cells as evident by green fluorescence due to lead binding fluorescent probe, Leadmium Green AM dye. Flow cytometry observations indicate an increase in cell size and granularity of exposure to lead. Thus, present work provides a new understanding of Pb(II) tolerance in A. junii Pb1 and its potential use in remediation of lead from contaminated soil.

Measuring Cell Ploidy Level in Arabidopsis thaliana by Flow Cytometry

Cell ploidy levels are regulated by developmental and environmental factors and they also impact the outcome of plant microbe interactions. Here we describe a simple and quick procedure to measure cell ploidy levels in Arabidopsis thaliana leaves by flow cytometry. Cell nuclei are isolated by filtering tissue homogenates from chopped plant tissues. DNA in the nuclei is stained by propidium iodide and the fluorescence emitted from the DNA of each nucleus is read by using a flow cytometer. Distribution of ploidy levels within the plant tissues can be calculated based on the distribution of fluorescence signals. Multiple samples can be prepared and analyzed within the same day.

Changes in hemocytes of Biomphalaria glabrata infected with Echinostoma paraensei and exposed to glyphosate-based herbicide

The immune system of snails is highly sensitive to pollutants, which can suppress its immune response. We investigated the effects of exposure to the glyphosate-based herbicide Roundup® Original on the snail Biomphalaria glabrata infected by the platyhelminth Echinostoma paraensei by evaluating changes in the snail's internal defense system. Four cohorts were studied: control group, infected snails, snails treated with Roundup®, and snails infected and treated with Roundup®. The hemocyte viability was assessed, morphological differentiation of cells was observed and flow cytometry was performed to determine the morphology, viability and the lectin expression profiles. The frequencies of dead hemocytes were lower in the infected group and higher in both pesticide treated groups. Three cell types were identified: blast-like cells, hyalinocytes and granulocytes. The highest number of all types of hemocytes, as well as the highest number of dead cells, were observed in the infected, pesticide-treated group. The association between infection and herbicide exposure greatly increased the frequency of dead hemocytes, suggesting that this condition impairs the internal defense system of B. glabrata making the snails more vulnerable to parasitic infections.

Receptor- and store-operated mechanisms of calcium entry during the nanosecond electric pulse-induced cellular response

Nanosecond electric pulses have been shown to open nanopores in the cell plasma membrane by fluorescent imaging of calcium uptake and fluorescent dyes, including propidium (Pr) iodide and YO-PRO-1 (YP₁). Recently, we demonstrated that nsEPs also induce the phosphoinositide intracellular signaling cascade by phosphatidylinositol-4,5-bisphosphate (PIP₂) depletion resulting in physiological responses similar to those observed following stimulation of G_q11-coupled receptors. In this paper, we explore the role of receptor- and store-operated calcium entry (ROCE/SOCE) mechanisms in the observed response of cells to nsEP. We show that addition of the ROCE/SOCE and transient receptor potential channel (TRPC) blocker gadolinium (Gd³⁺, 300 μM) slows PIP2 depletion following 1 and 20 nsEP exposures. Lipid rafts, regions of the plasma membrane rich in PIP₂ and TRPC, are also disrupted by nsEP exposure suggesting that ROCE/SOCE mechanisms are likely impacted. Reducing the expression of stromal interaction molecule 1 (STIM1) protein, a key protein in ROCE and SOCE, in cells exposure to nsEP resulted in a reduction in induced intracellular calcium rise. Additionally, after exposure to 1 and 20 nsEPs (16.2 kV/cm, 5 Hz), intracellular calcium rises were significantly reduced by the addition of GD³⁺ and SKF-96365 (1-[2-(4-methoxyphenyl)-2-[3-(4-methoxyphenyl) propoxy] ethyl-1H-imidazole hydrochloride, 100 μM), a blocker of STIM1 interaction. However, using similar nsEP exposure parameters, SKF-96365 was less effective at reducing YP₁ uptake compared to Gd³⁺. Thus, it is possible that SKF-96365 could block STIM1 interactions within the cell, while Gd³⁺ could acts on TRPC/nanopores from outside of the cell. Our results present evidence of nsEP induces ROCE and SOCE mechanisms and demonstrate that YP₁ and Ca²⁺ cannot be used solely as markers of nsEP-induced nanoporation.

Comparison of different staining methods for determination of viability on Mesocestoides vogae tetrathyridia

Mesocestoides vogae is widely employed as a model for studying the biology, differentiation, and experimental chemotherapy of cestodes. Currently, there are few techniques to measure the viability of M. vogae metacestodes during pharmacological experiments. The aim of the present work was to evaluate and compare different staining techniques to determine objectively the viability of M. vogae tetrathyridia. Eosin (0.05% w/v), methylene blue (0.01% w/v), propidium iodide (PI, 2 μg/ml), and fluorescein diacetate (FDA, 0.5 μg/ml) solutions were tested against live, heat-killed (cultivated at 65 °C for 2 h) and thymol-treated tetrathyridia (50 and 250 μg/ml). Parasites were counted under a dissecting microscope or a fluorescence compound microscope, as appropriate. Studies by scanning electron microscope were performed to compare the ultrastructural damage with the viability of parasites. After comparing the performance of different dyes, we chose the eosin staining technique because its simplicity, rapidity, sensitivity, low cost and fidelity.

Codium fragile F2 sensitize colorectal cancer cells to TRAIL-induced apoptosis via c-FLIP ubiquitination

This study demonstrates that combined treatment with subtoxic doses of Codium extracts (CE), a flavonoid found in many fruits and vegetables, and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), induces apoptosis in TRAIL-resistant colorectal cancer (CRC) cells. Effective induction of apoptosis by combined treatment with CE and TRAIL was not blocked by Bcl-xL overexpression, which is known to confer resistance to various chemotherapeutic agents. While TRAIL-mediated proteolytic processing of procaspase-3 was partially blocked in various CRC cells treated with TRAIL alone, co-treatment with CE efficiently recovered TRAIL-induced caspase activation. We observed that CE treatment of CRC cells did not change the expression of anti-apoptotic proteins and pro-apoptotic proteins, including death receptors (DR4 and DR5). However, CE treatment markedly reduced the protein level of the short form of the cellular FLICE-inhibitory protein (c-FLIPS), an inhibitor of caspase-8, via proteasome-mediated degradation. Collectively, these observations show that CE recovers TRAIL sensitivity in various CRC cells via down-regulation of c-FLIPS.

A protocol combining multiphoton microscopy and propidium iodide for deep 3D root meristem imaging in rice: application for the screening and identification of tissue-specific enhancer trap lines

BACKGROUND

The clear visualization of 3D organization at the cellular level in plant tissues is needed to fully understand plant development processes. Imaging tools allow the visualization of the main fluorophores and in vivo growth monitoring. Confocal microscopy coupled with the use of propidium iodide (PI) counter-staining is one of the most popular tools used to characterize the structure of root meristems in A. thaliana. However, such an approach is relatively ineffective in species with more complex and thicker root systems.

RESULTS

We adapted a PI counter-staining protocol to visualize the internal 3D architecture of rice root meristems using multiphoton microscopy. This protocol is simple and compatible with the main fluorophores (CFP, GFP and mCherry). The efficiency and applicability of this protocol were demonstrated by screening a population of 57 enhancer trap lines. We successfully characterized GFP expression in all of the lines and identified 5 lines with tissue-specific expression.

CONCLUSIONS

All of these resources are now available for the rice community and represent critical tools for future studies of root development.

Increasing the Membrane Permeability of a Fern with DMSO

Cell membrane prevents the entrance of extra molecules (e.g., transcription and translation inhibitors) into the cell. For studying the physiological effects of transcription and translation inhibitors on Hymenophyllum caudiculatum fronds, we incubate fronds with 0.1% DMSO to test if this increases cell membrane permeability relative to incubation with ultrapure water. The study showed that DMSO could significantly improve the cell membrane permeability of filmy fronds.

An Image-based Assay for High-throughput Analysis of Cell Proliferation and Cell Death of Adherent Cells

In this protocol, we describe a method to monitor cell proliferation and death by live-cell imaging of propidium iodide (PI)-stained adherent mammalian cells. PI is widely used to assess cell death. However, it is usually used in end-point assays. Recently, we implemented the use of PI for real-time cell death assessment by automated imaging. Cells are seeded in a 96-well format, and after attachment, the treatments are added directly to the wells together with PI. Thereafter, cells are subjected to automated time-lapse imaging and quantification by computer software. Combined analyses of phase-contrast and fluorescence images allow assessment of treatment effects on cell proliferation as well as the extent and kinetics of cell death.

A fluorescence in situ staining method for investigating spores and vegetative cells of Clostridia by confocal laser scanning microscopy and structured illuminated microscopy

Non-pathogenic spore-forming Clostridia are of increasing interest due to their application in biogas production and their capability to spoil different food products. The life cycle for Clostridium includes a spore stage that can assist in survival under environmentally stressful conditions, such as extremes of temperature or pH. Due to their size, spores can be investigated by a range of microscopic techniques, many of which involve sample pre-treatment. We have developed a quick, simple and non-destructive fluorescent staining procedure that allows a clear differentiation between spores and vegetative cells and effectively stains spores, allowing recovery and tracking in subsequent experiments. Hoechst 34580, Propidium iodide and wheat germ agglutinin WGA 488 were used in combination to stain four strains of Clostridia at different life cycle stages. Staining was conducted without drying the sample, preventing changes induced by dehydration and cells observed by confocal laser scanner microscopy or using a super-resolution microscope equipped with a 3D-structured illumination module. Dual staining with Hoechst/Propidium iodide differentiated spores from vegetative cells, provided information on the viability of cells and was successfully applied to follow spore production induced by heating. Super-resolution microscopy of spores probed by Hoechst 34580 also allowed chromatin to be visualised. Direct staining of a cheese specimen using Nile Red and Fast Green allowed in situ observation of spores within the cheese and their position within the cheese matrix. The proposed staining method has broad applicability and can potentially be applied to follow Clostridium spore behaviour in a range of different environments.

Anti-apoptotic potential of several antidiabetic medicinal plants of the eastern James Bay Cree pharmacopeia in cultured kidney cells

Background

Our team has identified 17 Boreal forest species from the traditional pharmacopeia of the Eastern James Bay Cree that presented promising in vitro and in vivo biological activities in the context of type 2 diabetes (T2D).

We now screened the 17 plants extracts for potential anti-apoptotic activity in cultured kidney cells and investigated the underlying mechanisms.

Methods

MDCK (Madin-Darnby Canine Kidney) cell damage was induced by hypertonic medium (700 mOsm/L) in the presence or absence of maximal nontoxic concentrations of each of the 17 plant extracts. After 18 h’ treatment, cells were stained with Annexin V (AnnV) and Propidium iodide (PI) and subjected to flow cytometry to assess the cytoprotective (AnnV⁻/PI⁻) and anti-apoptotic (AnnV⁺/PI⁻) potential of the 17 plant extracts. We then selected a representative subset of species (most cytoprotective, moderately so or neutral) to measure the activity of caspases 3, 8 and 9.

Results

Gaultheria hispidula and Abies balsamea are amongst the most powerful cytoprotective and anti-apoptotic plants and appear to exert their modulatory effect primarily by inhibiting caspase 9 in the mitochondrial apoptotic signaling pathway.

Conclusion

We conclude that several Cree antidiabetic plants exert anti-apoptotic activity that may be relevant in the context of diabetic nephropathy (DN) that affects a significant proportion of Cree diabetics.

Quantification of Starch in Guard Cells of Arabidopsis thaliana

In this protocol, we describe how to quantify starch in guard cells of Arabidopsis thaliana using the fluorophore propidium iodide and confocal laser scanning microscopy. This simple method enables monitoring, with unprecedented resolution, the dynamics of starch in guard cells.

Multiparametric Analysis of Apoptosis by Flow Cytometry

Flow cytometry is the most widely used method for detecting and quantifying apoptosis in mammalian cells. The multiparametric nature of flow cytometry allows several apoptotic characteristics to be combined in a single sample, making it a powerful tool for analyzing the complex progression of apoptotic death. This chapter provides guidelines for combining single-apoptosis assays such as fluorogenic caspase substrates, annexin V binding, DNA dye exclusion, and covalent viability probes into informative multiparametric assays. This multiparametric approach to analyzing apoptosis provides much more information than single-parameter assays that provide only a percentage apoptotic result, given that multiple early, intermediate, and late apoptotic stages can be observed and quantified simultaneously. While much more informative than single-color assays, these multicolor methods can still be analyzed on relatively simple flow cytometers, making them accessible to many laboratories.

Appropriate vacuolar acidification in Saccharomyces cerevisiae is associated with efficient high sugar fermentation

Vacuolar acidification serves as a homeostatic mechanism to regulate intracellular pH, ion and chemical balance, as well as trafficking and recycling of proteins and nutrients, critical for normal cellular function. This study reports on the importance of vacuole acidification during wine-like fermentation. Ninety-three mutants (homozygous deletions in lab yeast strain, BY4743), which result in protracted fermentation when grown in a chemically defined grape juice with 200 g L^-1 sugar (pH 3.5), were examined to determine whether fermentation protraction was in part due to a dysfunction in vacuolar acidification (VA) during the early stages of fermentation, and whether VA was responsive to the initial sugar concentration in the medium. Cells after 24 h growth were dual-labelled with propidium iodide and vacuolar specific probe 6-carboxyfluorescein diacetate (6-CFDA) and examined with a FACS analyser for viability and impaired VA, respectively. Twenty mutants showed a greater than two-fold increase in fluorescence intensity; the experimental indicator for vacuolar dysfunction; 10 of which have not been previously annotated to this process. With the exception of Δhog1, Δpbs2 and Δvph1 mutants, where dysfunction was directly related to osmolality; the remainder exhibited increased CF-fluorescence, independent of sugar concentration at 20 g L^-1 or 200 g L^-1. These findings offer insight to the importance of VA to cell growth in high sugar media.

Honey is cytotoxic towards prostate cancer cells but interacts with the MTT reagent: Considerations for the choice of cell viability assay

Honey is a complex biological substance, consisting mainly of sugars, phenolic compounds and enzymes. Using five quick and accessible assays for measuring honey's cytotoxicity in vitro, we found honey is cytotoxic towards prostate cancer cells PC3 and DU145. However, the level of cell death varied with assay. The MTT assay was confounded by the reduction of the MTT reagent by honey's reducing sugars and phenolic compounds, and the lactate dehydrogenase assay was invalidated by honey oxidising the enzyme cofactor NADH. The sulforhodamine B assay gave valid results, but measures only protein content, providing no information about cell death in the remaining cells. The trypan blue assay and a microscope-based propidium iodide/Hoechst staining assay assess only late stage membrane permeability. However, the propidium iodide/Hoechst assay gives morphological information about cell death mechanism. A combination of the sulforhodamine B and propidium iodide/Hoechst assays would provide the most accurate quantification of honey cytotoxicity.

Characterization of the flow cytometric assay for ex vivo monitoring of cytotoxicity mediated by antigen-specific cytotoxic T lymphocytes

Several non-radioactive methods have widely been utilized to detect antigen-specific cytotoxic T lymphocyte (CTL) responses instead of the classical ⁵¹Cr-release assay. These methods include intracellular cytokine staining, major histocompatibility complex-class I tetramers, and the CD107a mobilization assay. However, they do not directly measure target-cell death. In contrast, several attempts have been made to develop the flow cytometric CTL (FC-CTL) assay for evaluation of cytotoxicity. However, further improvement is necessary for it to become standardized. Here, we evaluated the characteristics of the FC-CTL assay based on the uptake of propidium iodide (PI) using target cell lines expressing the green fluorescent protein (GFP). The FC-CTL assay was found to be sensitive enough to detect primary CTL responses. The usage of a pre-established GFP-expressing target cell line facilitated the procedure of the assay, and enabled a clear discrimination between target and effector cells. Time-course analyses demonstrated that PI-stained target cells were detected as early as surface CD107a expression after antigenic stimulation. Thus, the PI/GFP-based FC-CTL assay is sufficiently sensitive to practically detect the early stages of target-cell death, and may have a great potential for becoming a standard tool to measure CTL activity.

Assessment of Anti-Tumor Cytotoxic Activity of Naturally Occurring Antibodies in Human Serum or Plasma

A small percentage of the Western population carries antibodies in the peripheral blood, which are able to kill human tumors such as neuroblastoma or melanoma. Several observations indicate that these antibodies, preferentially of IgM isotype, belong to the class of naturally occurring antibodies. Here, we describe two screening methods for the detection and quantification of such antibodies in human blood samples: a cellular ELISA technique and a flow cytometric assay, based on intercalation of fluorescent propidium iodide into the DNA of dying or dead cells.

Data for discriminating dead/live bacteria in homogenous cell suspensions and the effect of insoluble substrates on turbidimetric measurements

Estimation of bacterial growth by rapid traditional methods such as spectrophometric measurements at 600 nm (OD600) is not applicable for cultures containing insoluble particles in the growth media. Colony counts are the only suitable alternative but these are laborious and not high-throughput. The data presented in this article is related to the research article entitled “Two-colour fluorescence fluorimetric analysis for direct quantification of bacteria and its application in monitoring bacterial growth in cellulose degradation systems” (Duedu and French, 2017) [1]. This data article presents original primary data describing the discrimination of dead/live bacteria in homogenous cell suspensions and how the presence of insoluble substrates affect the turbidity of the suspensions.

Membrane permeabilization of mammalian cells using bursts of high magnetic field pulses

BACKGROUND

Cell membrane permeabilization by pulsed electromagnetic fields (PEMF) is a novel contactless method which results in effects similar to conventional electroporation. The non-invasiveness of the methodology, independence from the biological object homogeneity and electrical conductance introduce high flexibility and potential applicability of the PEMF in biomedicine, food processing, and biotechnology. The inferior effectiveness of the PEMF permeabilization compared to standard electroporation and the lack of clear description of the induced transmembrane transport are currently of major concern.

METHODS

The PEMF permeabilization experiments have been performed using a 5.5 T, 1.2 J pulse generator with a multilayer inductor as an applicator. We investigated the feasibility to increase membrane permeability of Chinese Hamster Ovary (CHO) cells using short microsecond (15 µs) pulse bursts (100 or 200 pulses) at low frequency (1 Hz) and high dB/dt (>10⁶ T/s). The effectiveness of the treatment was evaluated by fluorescence microscopy and flow cytometry using two different fluorescent dyes: propidium iodide (PI) and YO-PRO®-1 (YP). The results were compared to conventional electroporation (single pulse, 1.2 kV/cm, 100 µs), i.e., positive control.

RESULTS

The proposed PEMF protocols (both for 100 and 200 pulses) resulted in increased number of permeable cells (70 ± 11% for PI and 67 ± 9% for YP). Both cell permeabilization assays also showed a significant (8 ± 2% for PI and 35 ± 14% for YP) increase in fluorescence intensity indicating membrane permeabilization. The survival was not affected.

DISCUSSION

The obtained results demonstrate the potential of PEMF as a contactless treatment for achieving reversible permeabilization of biological cells. Similar to electroporation, the PEMF permeabilization efficacy is influenced by pulse parameters in a dose-dependent manner.

Membrane Permeabilization of Pathogenic Yeast in Alternating Sub-microsecond Electromagnetic Fields in Combination with Conventional Electroporation

Recently, a novel contactless treatment method based on high-power pulsed electromagnetic fields (PEMF) was proposed, which results in cell membrane permeabilization effects similar to electroporation. In this work, a new PEMF generator based on multi-stage Marx circuit topology, which is capable of delivering 3.3 T, 0.19 kV/cm sub-microsecond pulses was used to permeabilize pathogenic yeast Candida albicans separately and in combination with conventional square wave electroporation (8-17 kV/cm, 100 μs). Bursts of 10, 25, and 50 PEMF pulses were used. The yeast permeabilization rate was evaluated using flow cytometric analysis and propidium iodide (PI) assay. A statistically significant (P < 0.05) combinatorial effect of electroporation and PEMF treatment was detected. Also the PEMF treatment (3.3 T, 50 pulses) resulted in up to 21% loss of yeast viability, and a dose-dependent additive effect with pulsed electric field was observed. As expected, increase of the dB/dt and subsequently the induced electric field amplitude resulted in a detectable effect solely by PEMF, which was not achievable before for yeasts in vitro.

Two-colour fluorescence fluorimetric analysis for direct quantification of bacteria and its application in monitoring bacterial growth in cellulose degradation systems

Monitoring bacterial growth is an important technique required for many applications such as testing bacteria against compounds (e.g. drugs), evaluating bacterial composition in the environment (e.g. sewage and wastewater or food suspensions) and testing engineered bacteria for various functions (e.g. cellulose degradation). T?=1,^FigItem(1) ^ReloadFigure=Yesraditionally, rapid estimation of bacterial growth is performed using spectrophotometric measurement at 600nm (OD600) but this estimation does not differentiate live and dead cells or other debris. Colony counting enumerates live cells but the process is laborious and not suitable for large numbers of samples. Enumeration of live bacteria by flow cytometry is a more suitable rapid method with the use of dual staining with SYBR I Green nucleic acid gel stain and Propidium Iodide (SYBR-I/PI). Flow cytometry equipment and maintenance costs however are relatively high and this technique is unavailable in many laboratories that may require a rapid method for evaluating bacteria growth. We therefore sought to adapt and evaluate the SYBR-I/PI technique of enumerating live bacterial cells for a cheaper platform, a fluorimeter. The fluorimetry adapted SYBR-I/PI enumeration of bacteria in turbid growth media had direct correlations with OD600 (p>0.001). To enable comparison of fluorescence results across labs and instruments, a fluorescence intensity standard unit, the equivalent fluorescent DNA (EFD) was proposed, evaluated and found useful. The technique was further evaluated for its usefulness in enumerating bacteria in turbid media containing insoluble particles. Reproducible results were obtained which OD600 could not give. An alternative method based on the assessment of total protein using the Pierce Coomassie Plus (Bradford) Assay was also evaluated and compared. In all, the SYBR-I/PI method was found to be the quickest and most reliable. The protocol is potentially useful for high-throughput applications such as monitoring of growth of live bacterial cells in 96-well microplates and in assessing in vivo activity of cellulose degrading enzyme systems.

Xylem Characterization Using Improved Pseudo-Schiff Propidium Iodide Staining of Whole Mount Samples and Confocal Laser-Scanning Microscopy

An improved pseudo-Schiff propidium iodide staining technique well suited for, but not limited to, the visualization of xylem cell walls in whole mount samples is presented. The pseudo-Schiff reaction results in covalent binding of the fluorescent dye propidium iodide to cell walls. This stable linkage permits the use of clearing agents after staining, which is itself improved following pretreatment of the plant tissue. A subsequent acid alcohol washing step eliminates unbound propidium iodide to reduce background fluorescence. The method can be used for characterizing xylem cell structure in different organs and species without the need for tissue sectioning.