Toxicity, mutagenicity and transport inSaccharomyces cerevisiaeof three popular DNA intercalating fluorescent dyes

Comprehensive assessment of 12 commercial DNA-binding dyes as alternatives to ethidium bromide for agarose gel electrophoresis

Staining and visualization of the nucleic acid bands on agarose gels using ethidium bromide (EB) has been a widely used technique in molecular biology. Although it is an efficient dye for this purpose, EB is known to be mutagenic and genotoxic in humans. This led to the emergence of various alternative dyes, which were claimed to be safer and more efficient than EB. However, these dyes portray varied sensitivity and interference with the electrophoretic mobility of nucleic acids. This work aimed at assessing ten nucleic acid-binding dyes and two prestained dyes for these properties by three staining techniques, such as precasting, preloading, and poststaining. Of these, preloading was not suitable for any of the dye while poststaining worked optimal for most of them. Precasting was suitable for only four dyes viz. DNA Stain G, SYBR™ safe, EZ-Vision® in-gel, and LabSafe™. Poststaining was, in general, a costlier method than precasting. The work gives a comprehensive understanding of the performance of nucleic acid-binding dyes for routine molecular biology experiments.

Study of nitrogen heterocycles as DNA/HSA binder, topoisomerase inhibitors and toxicological safety

Four new nitrogen-containing heterocyclic derivatives (acridine, quinoline, indole, pyridine) were synthesized and their biological properties were evaluated. The compounds showed affinity for DNA and HSA, with CAIC and CAAC displaying higher binding constants (Kb) of 9.54 × 104 and 1.06 × 106, respectively. The fluorescence quenching assay (Ksv) revealed suppression values ranging from 0.34 to 0.64 × 103 M-1 for ethidium bromide (EB) and 0.1 to 0.34 × 103 M-1 for acridine orange (AO). Molecular docking confirmed the competition of the derivatives with intercalation probes at the same binding site. At 10 μM concentrations, the derivatives inhibited topoisomerase IIα activity. In the antiproliferative assays, the compounds demonstrated activity against MCF-7 and T47-D tumor cells and nonhemolytic profile. Regarding toxicity, no acute effects were observed in the embryos. However, some compounds caused enzymatic and cardiac changes, particularly the CAIC, which increased SOD activity and altered heart rate compared to the control. These findings suggest potential antitumor action of the derivatives and indicate that substituting the acridine core with different cores does not interfere with their interaction and topoisomerase inhibition. Further investigations are required to assess possible toxicological effects, including reactive oxygen species generation.

Versatile open-source fluorescence documentation system

Fluorescence has long been the best method for detecting bio-molecules at high sensitivity and with the possibility of easy data analysis and is routine for gel electrophoresis and much more. However, the systems for detecting the fluorophores remain expensive and thus inaccessible to many. Most commercial systems are often only optimized for one specific application, making reuse difficult. This paper demonstrates, characterizes and evaluates an inexpensive and versatile system for the detection of fluorophores with two wavelengths using high power LEDs. The LEDs are arranged in two banks angled downward at a tray in a way that allows for bright and uniform illumination while preventing direct reflections into the camera. The emitted light is filtered through an exchangeable filter frame and can be detected using the camera of a smartphone or similar device. By using filters both in front of the LEDs and the camera, very low background and using sufficient exposure times, very high sensitivity can be achieved. The two wavelengths of excitation light and the exchangeable filters allow for optimization for the specific fluorophore used and thus highest brightness.

Sustainable Methodologies for Efficient Gel Electrophoresis and Streamlined Screening of Difficult Plasmids

We describe a workflow for efficient, environmentally attentive, and sustainable practices related to routine agarose gel electrophoresis. The methods reduce plastic waste and improve efficiency, especially for the exhaustive screening of difficult-to-obtain plasmids. Sustainability is increased when agarose is used ten times over by virtue of a thorough recycling regimen. The workflow optimizes workspaces and standardizes lab practices for handling potentially hazardous waste, minimizing environmental harm. Safety, efficiency, and sustainability improve laboratory productivity, help minimize environmental contamination, and increase cost-effectiveness.

Probing cell membrane integrity using a histone-targeting protein nanocage displaying precisely positioned fluorophores

Cell membrane integrity is fundamental to the normal activities of cells and is involved in both acute and chronic pathologies. Here, we report a probe for analyzing cell membrane integrity developed from a 9 nm-sized protein nanocage named Dps via fluorophore conjugation with high spatial precision to avoid self-quenching. The probe cannot enter normal live cells but can accumulate in dead or live cells with damaged membranes, which, interestingly, leads to weak cytoplasmic and strong nuclear staining. This differential staining is found attributed to the high affinity of Dps for histones rather than DNA, providing a staining mechanism different from those of known membrane exclusion probes (MEPs). Moreover, the Dps nanoprobe is larger in size and thus applies a more stringent criterion for identifying severe membrane damage than currently available MEPs. This study shows the potential of Dps as a new bioimaging platform for biological and medical analyses.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (Figs. S1-S12 including distance information between neighboring fluorophores on Dps, TEM images, MALDI-TOF analysis, fluorescence spectra, confocal images, gel retardation analysis, tissue staining, and additional data) is available in the online version of this article at 10.1007/s12274-022-4785-5.

Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review

As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.

Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae

The production of metabolic energy in form of ATP by oxidative phosphorylation depends on the coordinated action of hundreds of nuclear-encoded mitochondrial proteins and a handful of proteins encoded by the mitochondrial genome (mtDNA). We used the yeast Saccharomyces cerevisiae as a model system to systematically identify the genes contributing to this process. Integration of genome-wide high-throughput growth assays with previously published large data sets allowed us to define with high confidence a set of 254 nuclear genes that are indispensable for respiratory growth. Next, we induced loss of mtDNA in the yeast deletion collection by growth on ethidium bromide-containing medium and identified twelve genes that are essential for viability in the absence of mtDNA (i.e. petite-negative). Replenishment of mtDNA by cytoduction showed that respiratory-deficient phenotypes are highly variable in many yeast mutants. Using a mitochondrial genome carrying a selectable marker, ARG8^m, we screened for mutants that are specifically defective in maintenance of mtDNA and mitochondrial protein synthesis. We found that up to 176 nuclear genes are required for expression of mitochondria-encoded proteins during fermentative growth. Taken together, our data provide a comprehensive picture of the molecular processes that are required for respiratory metabolism in a simple eukaryotic cell.

Phycoremediation potential of microalgae species for ethidium bromide removal from aqueous media

Ethidium Bromide (EtBr) is an organic compound used in molecular biology investigations. EtBr ability of intercalating in the DNA molecule makes it a toxic substance. The objective was to evaluate the phycoremediation potentials of Chlorella vulgaris, Desmodesmus subspicatus and Raphidocelis subcapitata tested separately and in a mixture (Mix) for EtBr removal from the aqueous medium. Experiments were conducted using an initial algae biomass of 10⁶ cell/mL, exposed to 500 µg/L of EtBr. The removal efficiency (µg EtBr L^-1) after 3 h in each treatment were: Mix (72.8 µg.L^-1) >D. subspicatus (48.4 µg.L^-1) >R. subcapitata (24.6 µg.L^-1) >C. vulgaris (19.9 µg.L^-1). However, when EtBr mass reduction per microalgae density is considered (ng.algae^-1), the efficiency ranking changes to: D. subspicatus (1.9 × 10^-5ng.algae^-1) >C. vulgaris (1.4 × 10^-5ng.algae^-1) >Mix (9.8 × 10^-6ng.algae^-1) >R. subcapitata (2.8 × 10^-6ng.algae^-1). The results suggest that initial algal population density is a determinant factor for efficient EtBr removal by microalgae species in short term treatments. In order to obtain 100% of EtBr removal, it should be necessary 10¹⁰, 10¹⁰ and 10¹¹ algae.mL^-1 of C. vulgaris, D. subspicatus and R. subcapitata, respectively. The results strongly suggest phycoremediation can be explored as an alternative method for EtBr removal.

A Nucleus-Targeting DNA Aptamer for Dead Cell Indication

Dead cells always accompany with live cells in vivo and in cell culture. It is important to distinguish dead cells from live cells in various biological studies. Currently, the probes for dead cells are mainly nucleic acid-intercalators, most of which have low affinity and potential toxicity to live cells. In this work, we report a novel aptameric probe (Ch4-1) for the first time, which binds cell nuclei with high affinity (apparent K_d = 6.65 ± 3.40 nM). Ch4-1 was generated by Cell-SELEX process, it was identified to target nucleoproteins in cell nuclei. As an oligonucleotide, Ch4-1 cannot penetrate the integrated cell membrane; therefore, it only binds to dead cells rather than live cells. Compared with traditional DNA-targeting nuclear dyes, Ch4-1 possesses a high affinity to the nucleus, no toxicity to live cells, and can be easily labeled with different fluorescent dyes. It was demonstrated to serve as a probe for distinguishing dead cells from live cells in apoptosis assay, as well as for the nuclear staining of tissue sections.

The individual components of commercial isometamidium do not possess stronger trypanocidal activity than the mixture, nor bypass isometamidium resistance

The four components present in the trypanocidal treatment Samorin, the commercially available formulation of isometamidium, were separated and purified by column chromatography. These compounds as well as the Samorin mixture and the other phenanthridine trypanocide, homidium, were tested on Trypanosoma congolense and wild type, diamidine- and isometamidium-resistant Trypanosoma brucei brucei strains using an Alamar blue drug sensitivity assay. EC₅₀ values obtained suggest that M&B4180A (2) was the most active of the components, followed by M&B38897 (1) in all the strains tested, whereas M&B4596 (4) was inactive. Samorin was found to be significantly more active than any of the individual components alone, against T. congolense and all three T. b, brucei strains. Samorin and all its active constituents displayed reduced activity against the previously characterised isometamidium-resistant strain ISMR1.

Nucleo-mitochondrial interaction of yeast in response to cadmium sulfide quantum dot exposure

Cell sensitivity to quantum dots (QDs) has been attributed to a cascade triggered by oxidative stress leading to apoptosis. The role and function of mitochondria in animal cells are well understood but little information is available on the complex genetic networks that regulate nucleo-mitochondrial interaction. The effect of CdS QD exposure in yeast Saccharomyces cerevisiae was assessed under conditions of limited lethality (<10%), using cell physiological and morphological endpoints. Whole-genomic array analysis and the screening of a deletion mutant library were also carried out. The results showed that QDs: increased the level of reactive oxygen species (ROS) and decreased the level of reduced vs oxidized glutathione (GSH/GSSG); reduced oxygen consumption and the abundance of respiratory cytochromes; disrupted mitochondrial membrane potentials and affected mitochondrial morphology. Exposure affected the capacity of cells to grow on galactose, which requires nucleo-mitochondrial involvement. However, QDs exposure did not materially induce respiratory deficient (RD) mutants but only RD phenocopies. All of these cellular changes were correlated with several key nuclear genes, including TOM5 and FKS1, involved in the maintenance of mitochondrial organization and function. The consequences of these cellular effects are discussed in terms of dysregulation of cell function in response to these "pathological mitochondria".