The present study is focused on application of a natural compound, 3, 5-dihydroxy 4\', 7-dimethoxyflavone (DHDM) from a medicinal plant Alpinia nigra for nucleic acid detection and differential cell staining. DHDM was found to interact with nucleic acid and forms complex, which was investigated for various applications. It was successfully utilized to visualize plasmid, genomic, and ds-linear DNA in agarose gel electrophoresis without affecting the DNA mobility in the gel. Fluorescence of DHDM increased several fold upon binding to dsDNA. Photostability of the compound was assessed and showed photobleaching effect that decreased gradually over time. Application of the compound was further extended to differential cell staining. When observed in fluorescence microscope, DHDM stained the dead cells and differentiated them from live cells in the case of bacterial, yeast, and mammalian cells. Higher concentration of the compound was found to be less cytotoxic to cancerous cells. Nucleic acid staining dyes like Ethidium bromide (EtBr), Propidium iodide (PI), etc. are carcinogens and environmental pollutants and therefore DHDM a natural compound, is a major benefit and thus can serve as an alternative to the current dyes.

Fluorescent dyes are used in biological systems, because they are highly sensitive and selective. In this work, we investigated the fluorescent probe properties of 2-(5-(pyridin-2-yl)-1H-pyrazol-3-yl) phenol (PYDP) in two media [sodium dodecyl sulfate (SDS) and human serum albumin (HSA)]. Energy transfer parameters, photophysical and thermodynamic parameters of probe were determined. We investigated cytotoxicity of PYDP against colorectal adenocarcinoma cell lines (HT-29), breast cancer cell lines (MCF-7) and 3T3-L1 adipocytes (3T3 L1) cells. The cell staining property of PYDP was monitored using a confocal microscope. The results showed that PYDP binds to HSA, bindings are due to electrostatic/ionic interactions, and the binding process is spontaneous. PYDP was found to exhibit negligible cytotoxicity at high concentrations, and confocal microscope images showed that PYDP stained the cytoplasm of MCF-7 cells.

Active learning has been shown to improve student outcomes across a range of science, technology, engineering, and math (STEM) disciplines. In addition, active learning with an interdisciplinary focus in the classroom is beneficial for students to pursue health and allied health careers. Case studies have also been shown to enhance student learning. In this study, we utilized a novel learning approach combining a case study with interdisciplinary focus and an active learning exercise that introduced the chemistry of stains and how this relates to staining various organelles and components in a cell. This case study along with active learning exercise (e.g., a card game, group PowerPoint presentations, or coloring organelles or structures in a eukaryotic cell upon staining with a biochemical stain) resulted in improved student performance as well as long-term retention. This activity can be implemented in introductory biology, microbiology, cell biology, and related STEM disciplines (e.g., chemistry, biochemistry).

1,3,4-Oxadiazole pharmacophore is still considered a viable biologically active scaffold for the synthesis of more effectual and broad-spectrum antimicrobial agents. Therefore, the present study is based on five 1,3,4-oxadiazole target structures, viz., CAROT, CAROP, CARON (D-A-D-A systems) and NOPON and BOPOB (D-A-D-A-D systems) bearing various bioactive heterocyclic moieties relevant to potential biological activities. Three of the compounds, CARON, NOPON and BOPOB were assessed in-vitro for their efficacy as antimicrobial agents against gram positive (Staphylococcus aureus and Bacillus cereus) and gram negative (Escherichia coli and Klebsiella pneumonia) bacteria; and two fungi, Aspergillus niger and Candida albicans; also, as an anti-tuberculosis agent against Mycobacterium tuberculosis. Most of the tested compounds displayed promising antimicrobial activity, especially CARON which was then analyzed for the minimum inhibitory concentration (MIC) studies. Similarly, NOPON portrayed the highest anti-TB activity among the studied compounds. Consequently, to justify the detected anti-TB activity of these compounds and to recognize the binding mode and important interactions between the compounds and the ligand binding site of the potential target, these compounds were docked into the active binding site of cytochrome P450 CYP121 enzyme of Mycobacterium tuberculosis, 3G5H. The docking results were in good agreement with the result of in-vitro studies. In addition, all the five compounds were tested for their cell viability and have been investigated for cell labeling applications. To conclude, one of the target compounds, CAROT was used for the selective recognition of cyanide ion by \'turn-off\' fluorescent sensing technique. The entire sensing activity was examined by spectrofluorometric method and MALDI spectral studies. The limit of detection obtained was 0.14 µM.

Simple staining of cells is a widely used method in basic medical diagnostics, education, and research laboratories. The stains are low-cost, but the extensive consumption results in excessive toxic waste generation. Thus, to decrease the amount of toxic waste resulting from the cell staining procedure is a need. In this study, we developed a magnetically driven and compartmentalized passive microfluidic chip to perform simple staining of human eukaryotic cells, K562 cells, and lymphocyte cells derived from patients. We demonstrated simple staining on cells with trypan blue, methylene blue, crystal violet, and safranin for high, medium, and low cell densities. The stained cells were imaged using a bright field optical microscope and a cell phone to count cells on the focal plane. The staining improved the color signal of the cell by 25-135-pixel intensity changes for the microscopic images. The validity of the protocol was determined using Jurkat and MDA-MB-231 cell lines as negative controls. In order to demonstrate the practicality of the system, lymphocyte cells derived from human blood samples were stained with trypan blue. The color intensity changes in the first and last compartments were analyzed to evaluate the performance of the chip. The developed method is ultra-low cost, significantly reduces the waste generated, and can be integrated with mobile imaging devices in terms of portability. By combining microfabrication technology with cell staining, this study reported a novel contribution to the field of microfluidic biosensors. In the future, we expect to demonstrate the detection of pathogens using this method.

A novel chalcone derivative (4-(5-(pyridin-2-yl)-4,5-dihydro-1H-pyrazol-3-yl) phenol (PDP) was synthesized, characterized and investigated for its potential as a fluorescent probe. The structure of the synthesized molecule was determined by FTIR, 1H NMR, 13C NMR and LC-MS/MS. The interactions of PDP with fluorescent dyes in aqueous SDS environment and HSA were studied by using fluorescence resonance energy transfer (FRET) technique and steady-state and time-resolved fluorescence spectroscopy techniques. In addition, the cytotoxic effects of PDP against various cell lines (MCF -7, HT -29, and 3 T3-L1) as well as their corresponding healthy cell lines were tested by MTT assay and visualization of FRET efficiency of PDP in vitro was monitored by confocal microscopy. MTT assay showed that PDP has no significant cytotoxic effect on HT -29 cancer cells and moderate cytotoxicity on MCF -7 and 3 T3-L1 cells even at a concentration of 250 μM. Combining confocal microscopes with the FRET technique showed that PDP significantly stained the cytoplasm of MCF -7 cell lines. These results suggest that PDP could be used in fluorescence microscopy for cell staining.

An important aspect of understanding cancer biology is to connect the diverse repertoire of genotype-to-phenotype displays in individual specimens and ultimately resolve disease course outcome through informative datasets. A focus of cancer genomics has strived to provide predictive capabilities using genomic information to further inform therapeutic strategies. The advent of single-cell sequencing and analysis now provides a route to decipher high-resolution genomic diversity in individual samples and facilitate detailed understanding of clonal evolution in clinical research settings. In addition to generating high-throughput single-cell genomic SNV and CNV data, this protocol describes a new analytical ability that adds a second dimension which provides for interrogation of surface protein marker expression. The first immediate application of this technology is quite suitable to heme cancer cell studies. This multimodal approach allows for correlation of diverse genomic signatures to key phenotypic biomarkers such as immunophenotypes in leukemic diseases.

In this study a new probe (2\'-(1H-phenanthro[9,10-d]imidazol-2-yl)-phenyl-4-carboxylic acid N-hydroxysuccinimide ester, PB1-1) was synthesized and presented, containing the ester group as reactive group for medical imaging applications. The tests included a comparison to the PB1 probe with the aldehyde group described earlier. Also, the photophysics of PB1 and PB1-1 when conjugated to albumin (HSA) and concanavalin A (Con A) was studied. The fluorescence anisotropy measurements and the method of fluorescence quenching of protein were used to examine these interactions. The results showed that both dyes are highly bound to the studied proteins, especially PB1-1. In the present study we also compared the stability of prepared conjugates. The in vitro study have shown that all tested compounds presented to be usable in the case of fixated cell staining. PB1-1-ConA and PB1-1-HSA were characterized with the lowest cytotoxicity during the MTT assay, and thus should be more suitable for live imaging applications than PB1-ConA and PB1-HSA. The results obtained in this work confirmed the theses presented in in silico studies as to the correctness of the choice of ester group as actively binding to the protein. At the same time, we have experimentally demonstrated the significant influence of a probe-protein linker on the spectral properties of conjugates used in medical imaging. We have clearly indicated that a detailed analysis of derivatives with different reactive group allows for proper probe selection. We also pointed out that based on the geometric skeleton of one dye, a whole range of fluorescent probes with different absorption and fluorescence spectra can be obtained for in vitro tests in medical imaging.

Solvent molecules significantly affect the supramolecular self-assembly, for example, in forming solvent-bridged hydrogen bonding networks. Even small changes in solvent composition can have dramatic impact on supramolecular assembly. Herein, we demonstrate the use of trace solvents (as low as 0.04%) to tune the morphology and consequent functions of supramolecular nanostructures based on an aromatic peptide bola-amphiphile. Specifically, perylene bisimide-(di)glycine-tyrosine (PBI-[GY]2) bola-amphiphile was shown to give rise to red-emitting nanofibers when assembled in water, while exposure to trace organic solvents such as tetrahydrofuran (THF) and others via solvent-evaporation followed by aqueous assembly gave rise to white-light-emitting nanospheres. Differential hydrogen bonding between water (donor and acceptor) and THF (acceptor only) impacts supramolecular organization, which was verified using a density functional theory (DFT) simulation. The tunable consequent surface hydrophobicity was utilized in staining the cytoplasm and membrane of cells, respectively. The trace-solvent effect achieved through evaporation-dissolution provides a methodology to mediate the morphologies and consequent functions for supramolecular biomaterials controlled by the self-assembly pathway.

Fluorescent materials are widely used in biological and material applications as probes for imaging or sensing; however, their customization is usually complicated without the support of an organic chemistry laboratory. Here, we present a straightforward method for the customization of BODIPY cores, which are among the most commonly used fluorescent probes. The method is based on the formation of a new C-C bond through Friedel-Crafts electrophilic aromatic substitution carried out at room temperature. The method presented can be used to obtain completely customized fluorescent materials in one or two steps from commercially available compounds. Examples of the preparation of fluorescent materials for cell staining and functionalization of silica colloids are also presented.