Inherent lack of CMFDA/FDA staining in certain algae and its implication for ballast water testing

The approved method for testing the efficacy of ballast water management systems with respect to killing 10-50 μm organisms uses movements of the organisms or the vital stains CMFDA/FDA. The present study demonstrates that certain freshwater coccoid chlorophytes, known or suspected to contain a highly resistant cell wall component (algaenan), stain poorly with CMFDA/FDA, resulting in false negatives. The staining rates for the most dominant species were determined and were approx. 3-70 %. The use of Crystal Violet as an indicator for the presence of algaenan gave inconclusive results. The number of the 10-50 μm organisms in a small pond was found to be 10,183 organisms/mL (Lugol's fixed sample) vs. 2335 organisms/mL (CMFDA/FDA-stained sample). Using the staining rates obtained, it was estimated that the number of false negatives could make 40-50 %. The implications for biological performance evaluation of ballast water management systems are discussed.

Efficient Protoplast Isolation and DNA Transfection for Winter Oilseed Crops, Pennycress (Thlaspi arvense ) and Camelina (Camelina sativa )

Pennycress (Thlaspi arvense) and camelina (Camelina sativa) are nonfood winter oilseed crops that have the potential to contribute to sustainable biofuel production. However, undesired agronomic traits of pennycress and camelina currently hinder broad cultivation of these plants in the field. Recently, genome editing using the CRISPR-Cas technology has been applied to improve poor agronomic traits such as the weedy phenotype of pennycress and the oxidation susceptible lipid profile of camelina. In these works, the CRISPR reagents were introduced into the plants using the Agrobacterium-mediated floral dipping method. For accelerated domestication and value improvements of these winter oilseed crops, DNA-free genome editing platform and easy evaluation method of the CRISPR-Cas reagents are highly desirable. Cell wall-free protoplasts are great material to expand the use of gene engineering tools. In this chapter, we present a step-by-step guide to the mesophyll protoplast isolation from in vitro culture-grown pennycress and soil-grown camelina. The protocol also includes procedures for DNA transfection and protoplast viability test using fluorescein diacetate. With this protocol, we can isolate an average of 6 × 10⁶ cells from pennycress and 3 × 10⁶ cells from camelina per gram of fresh leaf tissues. Using a 7.3 kb plasmid DNA carrying green and red fluorescent protein marker genes, we can achieve an average transfection rate of 40% validated by flow cytometry for both plants.

Functional Soil Biological Measurements to Support Healthy Soils

Soil microorganisms contribute significantly to terrestrial ecosystem functioning through their activities. Various methods exist to characterize soil microbial activity and functional diversity including those that focus on potential enzyme activities and the respiratory responses of microbes to different substrates. Here, we describe: (1) the fluorescein diacetate hydrolysis assay for total potential microbial enzyme activity; (2) measurement of beta-glucosidase activity using ρ-nitrophenyl (pNP); (3) multienzyme assay using 4-methylumbelliferone (MUB); and (4) MicroResp assays to measure the respiratory responses of microbes to different substrates and generate a community level physiological profile (CLPP).

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.

The role of fruit exposure in the late season decline of grape berry mesocarp cell vitality

Loss of cell vitality in the mesocarp of grape (Vitis vinifera L.) berries during late ripening is programmed and under genetic control. Environmental factors such as temperature and vine water status, however, have a strong influence on the onset and extent of cell death. Following preliminary observations made on field experiment fruit, the hypothesis that exposure (increased light interception and wind velocity) at the berry level is important to the progression of cell death was tested. Transpiration, mesocarp cell vitality and total soluble solids concentration were compared in exposed and sheltered berries within single Shiraz vines. At oenological maturity (24 °Brix), exposed berries exhibited the same extent of cell death as sheltered berries, and it was not until four weeks later that cell death was more extensive in the exposed treatment. Therefore, under the conditions of this study, increased exposure over the ripening period was not a strong predictor of the extent of cell vitality at maturity. However, the results are consistent with an increase in the importance of environmental effects (including rain and exposure) on mesocarp cell death over the course of berry development, particularly in overripe fruit.

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.

Process performance determination data in thiocyanate biodegradation systems: Use of sulphate production

This data article presents the utilization of sulphates as an indirect technique for the assessment of microbial growth, activity and SCN^- biodegradation efficiency since the TDO were observed to be unable to utilise the produced sulphates as a source of sulphur (Mekuto e al., 2017) [1] The TDO demonstrated complete SCN^- biodegradation while also utilizing the produced ammonium. The production of SO₄^2- from SCN^- biodegradation had a good correlation in comparison to the traditional methods of assessing microbial growth and activity i.e. direct cell counts (DCC), heterotrophic counts (CFU) and fluorescein production from fluorescein diacetate (FDA). The concentration of the produced SO₄^2- demonstrated a similar logarithmic trend with the FDA, DCC and CFU techniques, thus confirming that the production of SO₄^2- from SCN^- biodegradation systems can be utilised as an indirect technique for the assessment of microbial growth, activity and SCN^- biodegradation performance.

Vacuole Dynamics in Rice Cells Invaded by the Blast Fungus Magnaporthe oryzae

We describe a fluorescence imaging method to visualize the dynamics of the central vacuole in rice cells during invasion by the blast fungus Magnaporthe oryzae. This method utilizes the combination of confocal microscopy, rice sheath cells (optically transparent), fluorescently tagged M. oryzae (red fluorescence), and fluorescein diacetate staining (green fluorescence; visualizing vacuole dynamics). Using this method, we demonstrate that the vacuole undergoes progressive shrinkage and collapse during M. oryzae infection.

Optimisation for assay of fluorescein diacetate hydrolytic activity as a sensitive tool to evaluate impacts of pollutants and nutrients on microbial activity in coastal sediments

Fluorescein diacetate (FDA) assay has been widely applied in coastal research to quantify microbial activity in sediments. However, the present FDA assay procedures embodied in sediment studies potentially include operational errors since the protocol was established for studies of terrestrial soil. In the present study, we optimised the procedure of FDA assay using sandy and cohesive sediments to improve experiential sensitivity and reproducibility. The optimised method describes quantitative measurement of the fluorescein produced when 1.0g of fresh sediment is incubated with 50mM phosphate buffer solution (pH: 7.3) and glass beads (2g) at 35°C for 1h under a rotation of 50rpm. The covariation coefficient of the optimised method ranged from 1.9% to 3.8% and the method sensitivity ranged from 0.25 to 1.57. The improved protocol provides a more reliable measurement of the FDA hydrolysis rate over a wide range of sediments compared to the original method.

Effect of fly ash amendment on metolachlor and atrazine degradation and microbial activity in two soils

The study reports the effect of Inderprastha (IP) and Badarpur (BP) fly ashes on degradation of metolachlor and atrazine in Inceptisol and Alfisol soils. Metolachlor dissipated at faster rate in Alfisol (t1/2 8.2-8.6 days) than in Inceptisol (t1/2 13.2-14.3 days). The fly ashes enhanced the persistence of metolachlor in both the soils; however, the extent of effect was more in Inceptisol (t1/2 16.6-33.8 days) than Alfisol (t1/2 8.4-12 days) and effect increased with fly ash dose. 2-Ethyl-6-methylacetanilide was detected as the only metabolite of metolachlor. Atrazine was more persistent in flooded soils (t1/2 10.8-20.3 days) than nonflooded soils (t1/2 3.7-12.6 days) and fly ash increased its persistence, but effect was more pronounced in the flooded Inceptisol (t1/2 23.7-31 days) and nonflooded Alfisol (t1/2 6.3-10.1 days). Increased herbicide sorption in the fly ash-amended soils might have contributed to the increased pesticide persistence. The IP fly ash inhibited microbial biomass carbon at 5 % amendment levels in both the soils, while BP fly ash slightly increased microbial biomass carbon (MBC) content. Dehydrogenase activity was inhibited by both fly ashes in both the soils with maximum inhibition observed in the IP fly ash-amended Alfisol. No significant effect of fly ash amendment was observed on the fluorescein diacetate activity.

Live-cell fluorescence imaging to investigate the dynamics of plant cell death during infection by the rice blast fungus Magnaporthe oryzae

BACKGROUND

Plant cell death plays important roles during plant-pathogen interactions. To study pathogen-induced cell death, there is a need for cytological tools that allow determining not only host cell viability, but also cellular events leading to cell death with visualization of pathogen development. Here we describe a live cell imaging method to provide insights into the dynamics of cell death in rice (Oryza sativa). This method uses live-cell confocal microscopy of rice sheath cells mechanically damaged or invaded by fluorescently-tagged Magnaporthe oryzae together with fluorescent dyes fluorescein diacetate (FDA) and propidium iodide (PI). FDA stains the cytoplasm of live cells exclusively, thus also visualizing the vacuole, whereas PI stains nuclei of dead cells.

RESULTS

We first demonstrated that confocal microscopy of rice leaf sheaths stained with FDA and PI discriminated between live cells and mechanically-killed cells. FDA-derived fluorescein was confined to the cytoplasm of live cells, indicating the intact vacuolar and plasma membranes. We also observed previously unreported fluorescein patterns in mechanically damaged cells. These patterns include: (1) homogeneous distribution of fluorescein in the increased area of the cytoplasm due to the shrunken vacuole; (2) the increase of the fluorescein intensity; and (3) containment of the brighter fluorescein signal only in affected cells likely due to closure of plasmodesmata. We refer to these as novel fluorescein patterns in this study. Simultaneous imaging of fluorescently-tagged M. oryzae (red) and FDA staining (green) in rice cells revealed characteristic features of the hemibiotrophic interaction. That is, newly invaded cells are alive but subsequently become dead when the fungus spreads into neighbor cells, and biotrophic interfacial complexes are associated with the host cytoplasm. This also revealed novel fluorescein patterns in invaded cells. Time-lapse imaging suggested that the FDA staining pattern in the infected host cell progressed from typical cytoplasmic localization (live cell with the intact vacuole), to novel patterns (dying cell with closed plasmodesmata with the shrunken or ruptured vacuole), to lack of fluorescence (dead cell).

CONCLUSION

We have developed a method to visualize cellular events leading to host cell death during rice blast disease. This method can be used to compare and contrast host cell death associated with disease resistance and susceptibility in rice-M. oryzae and other host-pathogen interactions.

Evaluation of wild herbivore faeces from South Africa as a potential source of hydrolytically active microorganisms

This study assessed faecal matter from three indigenous South African herbivores-zebra, giraffe and impala-as a potential source for hydrolytically active aerobic and facultatively anaerobic bacteria. Herbivore droppings were collected freshly in a local nature reserve in Pietermaritzburg, South Africa. Soil samples adjacent to faecal collection sites and faeces from a domestic herbivore, the Nguni cow, were included as controls. Hydrolase and dehydrogenase activity in faecal matter and soil samples were measured by the fluorescein diacetate and the triphenyltetrazolium chloride assay. Viable counts and counts for amylase, cellulase, esterase and protease producers were established using plate count agar and solid media containing cellulose, skim milk, starch and Tween 80. Zebra droppings produced the highest hydrolase and dehydrogenase activity. Faecal matter of the three indigenous herbivores generally produced higher hydrolytic activity than Nguni cow faeces and soil controls, thereby confirming that these materials are potential targets for hydrolytic enzyme mining.

High Sensitivity Bacillus thuringiensis Cry1Ac Protein Detections Using Fluorescein Diacetate Nanoparticles

A highly sensitive transgenic protein analysis method was proposed here based on fluorescein diacetate (FDA). First, FDA was prepared by the ball mill to harvest the nano-sized organic particles. Further examines showed that the FDA size can be controlled by the speed of centrifugation which can obtain FDA in well-distributed size. Cy3 antibody immobilization tests showed that the proteins can attach onto the FDA particles while keep bioactivities. FDA and Cry1Ac antibody immunoassay tests showed that when the FDA particle was in 150 nm, the linear range was 0.01 ng/L-30 μg/mL. And it has the lower detection limitation of 0.01 ng/L, which is 100 times more sensitive than the ELISA methods. These results indicate that the FDA related immunoassays are the promising approach in the transgenic analysis.

Development of an automated ballast water treatment verification system utilizing fluorescein diacetate hydrolysis as a measure of treatment efficacy

Methods for verifying ballast water treatments in foreign vessels are needed to protect the Great Lakes from the discharge of live non-native organisms or pathogens. A prototype automated viability test system using fluorescein diacetate (FDA), a membrane permeable fluorogen, to differentiate live from dead bacteria and algae is described. The automated fluorescence intensity detection device (AFIDD) captures cultured algae or organisms in Detroit River water (simulated ballast water) on 0.2 μm filters, backwashes them from the filter into a cuvette with buffer and FDA for subsequent fluorescence intensity measurements, and washes the filters with sterile water for serial automated reuse. Preliminary manual versions of these procedures were also tested. Tests of various buffers determined N,N-Bis(2-hydroxyethyl)-2-aminoethanesulfonic acid, N,N-Bis(2-hydroxyethyl)taurine (BES) and 3-(N-morpholino)propanesulfonic acid (MOPS) at pH 7.0 to be the best buffers, causing the least spontaneous FDA breakdown without inhibiting enzymatic activity. Fluorescence in the presence of live organisms increased linearly over time, and the rate of increase was dependent on the sample concentration. Following simulated ballast water treatments with heat or chlorine, the fluorescence produced by Detroit River samples decreased to near control (sterile water) levels. Automated measurements of FDA hydrolysis with a reusable filter backwash system should be applicable to near real-time remote-controlled monitoring of live organisms in ballast water.

Two-dimensional fluorescence spectroscopy - a new tool for the determination of plant cell viability

 Two-dimensional fluorescence spectroscopy (2D-FS) has been used as a new method for determining the viability of tobacco cells (Nicotiana tabacum L.). Both horizontal beam geometry and a vertical set-up achieved with bifurcated fibres were tested. The latter arrangement enabled us to avoid the negative effect of cell sedimentation. Incubation of a tobacco BY-2 cell suspension with dimethylsulfoxide (DMSO) (0-10% v/v) resulted in cell samples differing in their viability - from fully viable (0-2% DMSO) to totally non-viable (8-10%DMSO). The validity of determining viability by means of measuring cell esterase activity by 2D-FS using fluorescein diacetate as a fluorogenic substrate was verified by comparison with microscopic evaluation of fluorescein fluorescence as well as with the routinely adopted trypan blue exclusion test.