Crystal violet stains proteins in SDS-PAGE gels and zymograms

Human Milk-Derived Enterococcus faecalis HM20: A Potential Alternative Agent of Antimicrobial Effect against Methicillin-Resistant Staphylococcus aureus (MRSA)

The increasing global impact of skin diseases, fueled by methicillin-resistant Staphylococcus aureus (MRSA), emphasizes the necessity for alternative therapies with lower toxicity, such as lactic acid bacteria (LAB). This study aims to isolate potential LAB from human milk and evaluate their efficacy against MRSA using various methods, including well diffusion, microdilution, crystal violet assay, enzymatic characterization, SDS-PAGE, and scanning electron microscopy (SEM). Among the 26 LAB screened, the human milk-derived strain HM20 exhibited significant antimicrobial activity against S. aureus CCARM 3089 (MRSA), which is a highly resistant skin pathogen. Through 16S rRNA sequencing, strain HM20 was identified as closely related to Enterococcus faecalis ATCC 19433T, which was subsequently designated as Enterococcus faecalis HM20. The minimum inhibitory concentration (MIC) of the cell-free supernatant (CFS) of HM20 against S. aureus KCTC 3881 and S. aureus CCARM 3089 was determined to be 6.25% and 12.5%, respectively. Furthermore, the effective inhibition of biofilm formation in S. aureus KCTC 3881 and S. aureus CCARM 3089 was observed at concentrations of 12.5% and 25% or higher, respectively. The antibacterial effect of the CFS was attributed to the presence of organic acids, hydrogen peroxide, and bacteriocins. Additionally, the antimicrobial peptides produced by HM20 were found to be stable under heat treatment and analyzed to have a size below 5 kDa. SEM image observations confirmed that the CFS of HM20 caused damage to the cell wall, forming pores and wrinkles on S. aureus KCTC 3881 and S. aureus CCARM 3089. This comprehensive investigation on strain HM20 conducted in this study provides foundational data for potential developments in functional materials aimed at addressing skin infections and antibiotic-resistant strains in the future.

Thioacetalation and Multi-Component Thiomethylative Friedel-Crafts Arylation Using BF3SMe2

Herein, a method for thioacetalation using BF₃SMe₂ is presented. The method allows for convenient and odor-free transformation of aldehydes to methyl-dithioacetals, a simple but sparsely reported structural moiety, in good yields with a diverse set of aromatic aldehydes. In addition, a thiomethylative Friedel-Crafts reaction was discovered, affording thiomethylated diarylmethanes in good to excellent yields. The resulting diarylmethane core is of interest as it is found in many biologically active compounds, and its utility is further demonstrated as a novel precursor to unsymmetrical triarylmethanes. This work also highlights the usefulness and the synthetic capabilities of the readily available reagent BF₃SMe₂ beyond its reactivity profile as a dealkylation reagent.

Protein Quantitation and Analysis of Purity

The accurate quantitation of proteins and an analysis of their purity is essential in numerous areas of scientific research and is a critical factor in many clinical applications. The large number and variety of techniques employed for this purpose is therefore not surprising. The selection of a suitable assay is dependent on such factors as the level of sensitivity required, the presence of interfering agents, and the composition of the protein itself. In this chapter, protocols for the most commonly used protein determination methodologies are outlined, including an overview of the highly sensitive real-time quantitative immuno-polymerase chain reaction assay. In addition, an approach to validate the UV protein absorption assay is outlined, which can be applied to any procedure for method validation.

Multiplex immunochromatographic platform based on crystal violet tag for simultaneous detection of streptomycin and chloramphenicol

Antibiotic abuse has caused serious health risks for human beings for long. To address the problem, novel and facile detection techniques are highly desired. Here, an effective multiplex immunochromatographic platform (MICP) with synthesis-free and cost-effective merits is established for simultaneous detection of antibiotics on a single immunochromatographic assay (ICA) strip. Adopting crystal violet (CV) as a signal tag for multiplex ICA allows for direct coupling with multiple antibodies in several minutes. By combining CV and ICA perfectly, this convenient strategy offers improvements in convenience, speed, flexibility, and portability, eventually ensuring the optimized effectiveness of this approach. As a result, the established platform is successfully used to detect streptomycin (STR) and chloramphenicol (CAP) with visual detection mode, and the obtained total recoveries of milk and honey real samples changed from 83.82 to 113.38% with total RSD values of 0.48 to 4.15%.

Crystal violet staining is a reliable alternative to bicinchoninic acid assay-based normalization

Experimental data with cells often require normalization. The frequently used bicinchoninic acid (BCA) assay, in fact, indicates protein content but is influenced by incubation time, pH etc. A simple, rapid and reliable alternative is desirable. Crystal violet stains nucleic acids and proteins and was used to reflect the cell number in 96-well plates. Calibration curves and comparison with BCA confirmed excellent goodness of fit (R²: 0.98), conformity (nonsignificant difference of BCA to crystal violet) and reliability of this staining methodology. Crystal violet staining can be used to normalize experimental data to the number of adherent cells present in cell culture plates.

Photopolymerization with EDTA and Riboflavin for Proteins Analysis in Polyacrylamide Gel Electrophoresis

A new method for photosensitized polymerization of polyacrylamide gels was proposed. Photopolymerization of acrylamide/N,N'-methylenebisacrylamide (AM/Bis) was assisted with combination of catalyst ethylenediaminetetraacetic acid disodium salt dihydrate (EDTA) and photoinitiator riboflavin (RF). The prepared cross-linked AM/Bis + EDTA/RF gels were tested in electrophoretic SDS-PAGE system at high concentration of AM (20 wt%). The efficiency of these systems for electrophoretic separation of histones of human blood lymphocytes was demonstrated. In principle, such gels with small pores in the separation zone can offer advantages for resolution of proteins. The advantages of proposed method also include simple technique and possibility of gel preparation in a timely manner (for 10-15 min). However, in microporous gel systems some limitations in electroblotting technique could occur, which is particularly crucial for hydrophobic proteins.

Quantitative Determination of Whey Protein to Casein Ratio in Infant Formula Milk Powder

This study was aimed to establish a method for quantitatively determining the ratio of whey protein in the total protein of infant formula by respectively selecting two characteristic peptides from whey protein and casein and calculating the ratio between the characteristic peptides. A nanoliter high-performance liquid chromatography tandem high-resolution mass spectrometry (Q Exactive) was used to simultaneously detect the characteristic peptides of two main whey proteins and two main caseins. The characteristic peptides were calculated, predicted, and screened using the ExPASy website, and peptide information was confirmed by database retrieval after the analysis by using a high-resolution mass spectrometer. The matrix effect was compensated by comparing the characteristic peptides in whey protein with those in casein protein, in which isotope internal standards were not required. The influence of the changes of the protein content in whey protein and casein on the detection method was eliminated by the calculation formula designed by ourselves. In this detection method, the sample was stable in the total protein concentration range of between 0.1 and 0.4 mg/ml. In the simulated industrial processing environment, with desalted whey powder, the recovery rate was 98.63–113.33% under different spiked levels with good reproducibility (RSD<8%). The RSDs of intraday and interday precisions were 2.03–9.35% and 0.61–11.02%, respectively. The different processing procedures of samples had no significant impact on the detection of whey protein (RSD% for milk samples treated by different processing techniques was 2.97%). The quantitation method of whey protein was applied to evaluate the whey protein content in different brands of commercially available milk powder. In summary, the proposed method was applicable for quantitative analysis of whey proteins in the infant formula.

Proteomes Are of Proteoforms: Embracing the Complexity

Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?

Multimodal detection and analysis of a new type of advanced Heinz body-like aggregate (AHBA) and cytoskeleton deformation in human RBCs

A new type of aggregate, formed in human red blood cells (RBCs) in response to glutaraldehyde treatment, was discovered and analyzed with the classical and advanced biomolecular imaging techniques. Advanced Heinz body-like aggregates (AHBA) formed in a single human RBC are characterized by a higher level of hemoglobin (Hb) degradation compared to typical Heinz bodies, which consist of hemichromes. The complete destruction of the porphyrin structure of Hb and the aggregation of the degraded proteins in the presence of Fe³⁺ ions are observed. The presence of such aggregated, highly degraded proteins inside RBCs, without cell membrane destruction, has been never reported before. For the first time the spatial differentiation of two kinds of protein mixtures inside a single RBC, with different phenylalanine (Phe) conformations, is visualized. The non-resonant Raman spectra of altered RBCs with AHBA are characterized by the presence of a strong band located at 1037 cm^-1, which confirms that glutaraldehyde interacts strongly with Phe. The shape-shifting of RBCs from a biconcave disk to a spherical structure and sinking of AHBA to the bottom of the cell are observed. Results reveal that the presence of AHBA should be considered when fixing RBCs and indicate the analytical potential of Raman spectroscopy, atomic force microscopy and scanning near-field optical microscopy in AHBA detection and analysis.