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Intracellular protein abundance is routinely measured in mammalian cells using population-based techniques such as western blotting which fail to capture single cell protein levels or using fluorescence microscopy which is although suitable for single cell protein detection but not for rapid analysis of large no. of cells. Flow cytometry offers rapid, high-throughput, multiparameter-based analysis of intracellular protein expression in statistically significant no. of cells at single cell resolution. In past few decades, customized assays have been developed for flow cytometric detection of specific intracellular proteins. This review discusses the scope of flow cytometry for intracellular protein detection in mammalian cells along with specific applications. Technological advancements to overcome the limitations of traditional flow cytometry for the same are also discussed.

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Owing to evidence that mitochondrial dysfunction plays a dominant role in the traumatic brain injury (TBI) pathophysiology, the Western blot (WB) based immunoblotting method is widely employed to identify changes in the mitochondrial protein expressions after neurotrauma. In WB method, the housekeeping proteins (HKPs) expression is routinely used as an internal control for sample normalization. However, the traditionally employed HKPs can be susceptible to complex cascades of TBI pathogenesis, leading to their inconsistent expression. Remarkably, our data illustrated here that mitochondrial HKPs, including Voltage-dependent anion channels (VDAC), Complex-IV, Cytochrome C and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) yielded altered expressions following penetrating TBI (PTBI) as compared to Sham. Therefore, our goal was to identify more precise normalization procedure in WB. Adult male Sprague Dawley rats (N = 6 rats/group) were used to perform PTBI, and the novel REVERT Total Protein (RTP) method was used to quantify mitochondrial protein load consistency between samples at 6 h and 24 h post-injury. Notably, the RTP method displayed superior protein normalization compared to HKPs method with higher sensitivity at both time-points between experimental groups. Our data favors application of RTP based normalization to accurately quantify protein expression where inconsistent HKPs may be evident in neuroscience research.

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The last decades have illustrated the importance of microRNAs (miRNAs) in various biological and pathological processes. The combined visualization of miRNAs using fluorescent in situ hybridization (FISH) and proteins using immunofluorescence (IF) can reveal their spatiotemporal distribution in relation to the cell and tissue morphology and can provide interesting insights into miRNA-protein interactions. However, standardized protocols for co-localization of miRNAs and proteins are currently lacking, and substantial technical obstacles still need to be addressed. In particular, the incompatibility of protein IF protocols with steps required for miRNA FISH, such as proteolytic pretreatments and ethylcarbodiimide post-fixation, as well as hurdles related to low signal intensity of low-copy miRNAs, remains challenging. Our technique may considerably enhance miRNA-based research, as current detection techniques lack the ability to elucidate cellular and subcellular localization. Here, we describe an optimized 2-day protocol for combined detection of low-abundant miRNAs and proteins in cryosections of cardiac tissue, without the need for protease-dependent pretreatment or post-fixation treatment. We successfully demonstrate endothelial-specific localization of low-abundant miR-181c-5p in cardiac tissue. © 2023 Wiley Periodicals LLC. Basic Protocol: Fluorescent in situ hybridization for miRNA combined with staining of proteins.

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Knowledge on the spectral properties of the tautomers of milrinone (MLR) in solvents and solid-state, as well as under light conditions is of critical importance from both theoretical and practical points of view. Herein, we investigated the spectral properties of MLR in different conditions using UV-Vis and fluorescence spectroscopies. The experimental results demonstrated that MLR can undergo the tautomerization reaction induced by solvent polarity, light and pH, eliciting four tautomeric structures (enol, keto, anion, and cation forms). The interesting multi-functional groups in MLR enable it to coordinate with metal ions or to recognize gust molecules by H-bonding. In the use of MLR as an excited-state intermolecular proton transfer (inter-ESPT) fluorescent probe, a highly sensitive and selective analysis of Fe3+ was developed, which offered a sensitive detection of Fe3+ with the detection limit of 3.5 nM. More importantly, MLR exhibited the ability of anchoring proteins and led to the recognition-driven turn-on inter-ESPT process, highlighting the potential for the probe to image proteins in electrophoresis gels. The spectral experimental results revealed the possible degradation mechanism, so that we can better understand the side effects of oral preparations. The use of the available drug as an inter-ESPT fluorescent probe is simple and accurate, providing a good method for Fe3+ ion sensing and protein staining.

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Increased knowledge of virus assembly-generated particles is needed for understanding both virus assembly and host responses to virus infection. Here, we use a phage T3 model and perform electron microscopy (EM) of thin sections (EM-TS) of gel-supported T3 plaques formed at 30 °C. After uranyl acetate/lead staining, we observe intracellular black particles, some with a difficult-to-see capsid. Some black particles (called LBPs) are larger than phage particles. The LBP frequency is increased by including proflavine, a DNA packaging inhibitor, in the growth medium and increasing plaque-forming temperature to 37 °C. Acidic phosphotungstate-precipitate (A-PTA) staining causes LBP substitution by black rings (BRs) that have the size and shape expected of hyper-expanded capsid containers for LBP DNA. BRs are less frequent in liquid cultures, suggesting that hyper-expanded capsids evolved primarily for in-gel (e.g., in-biofilm) propagation. BR-specific A-PTA staining and other observations are explained by α-sheet intense structure of the major subunit of hyper-expanded capsids. We hypothesize that herpes virus triggering of neurodegenerative disease occurs via in-gel propagation-promoted (1) generation of α-sheet intense viral capsids and, in response, (2) host production of α-sheet intense, capsid-interactive, innate immunity amyloid protein that becomes toxic. We propose developing viruses that are therapeutic via detoxifying interaction with this innate immunity protein.

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The Human Protein Atlas is a website of protein expression in human tissues. It is an excellent resource of tissue and cell type protein localization, but only allows the query of a single protein at a time. We introduce HPAStainR as a new Shiny app and Bioconductor/R package used to query the scored staining patterns in the Human Protein Atlas with multiple proteins/genes of interest. This allows the user to determine if an experimentally-generated protein/gene list associates with a particular cell type. We validated the tool using the Panglao Database cell type specific marker genes and a Genotype Expression (GTEx) tissue deconvolution dataset.  HPAStainR identified 92% of the Panglao cell types in the top quartile of confidence scores limited to tissue type of origin results. It also appropriately identified the correct cell types from the GTEx dataset. HPAStainR fills a gap in available bioinformatics tools to identify cell type protein expression patterns and can assist in establishing ground truths and exploratory analysis. HPAStainR is available from: https://32tim32.shinyapps.io/HPAStainR/.

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Normalization of Western blotting data is a critical step that is needed to reduce errors caused by unequal sample loading across lanes in a gel, inconsistent sample preparation, and variations due to experimental errors. Several papers have suggested that total protein normalization may be better than housekeeping protein normalization for Western blotting normalization. Ponceau S is the most commonly used stain for total protein normalization. A review of the literature and commercial websites suggest a multitude of Ponceau S staining protocols for total protein staining of blots. In this study, we explored which Ponceau S staining protocol would result in the highest sensitivity of protein band detection. Unexpectedly, we found that irrespective of the Ponceau S concentration (between 0.001 and 2% (w/v)), acid concentration, and acid type (acetic acid, trichloroacetic acid and/or sulfosalicylic acid), the sensitivity of protein detection remained constant. The most commonly used concentration of Ponceau S is 0.1%, while 0.001% (100-fold less) Ponceau S resulted in the same sensitivity of protein band detection. We suggest the use of the relatively inexpensive 0.01% Ponceau S in 1% acetic acid stain for total protein normalization as it is as effective as all the expensive formulations that are currently used.

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Measuring the concentration of proteins is an essential part of enzyme analysis or serves to monitor protein yields and losses during protein isolation procedures. Decisions on the usefulness of any protein isolation procedure depend on knowing the concentration of proteins before and after a procedure. Protein concentration in solution is generally measured with spectrophotometry in the UV range or in the presence of dyes or copper interacting with the protein. This review describes absorbance at 280 nm, the Lowry, Bradford (Coomassie Blue), and Smith (bicinchoninic acid) assays for measuring protein and includes suggestions for optimizing each method.

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Most traditional post-electrophoretic processes need several hours to several days to finish the whole staining process and traditional staining solutions all contain methanol, acetic acid, or phosphoric acid, which not only produce the unpleasant smell but also cause environmental pollution. Here a fixation-free, fast protein staining method in sodium dodecyl sulfate-polyacrylamide gel electrophoresis using Coomassie blue is described. The protocol includes only staining and quick washing steps, can be completed in 0.5 h. It has a sensitivity of 10 ng. In addition, the dye stain does not contain any acid or methanol.

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Rapid evolution of state-of-the-art proteomic analyses has encompassed development of high-throughput analytical instrumentation and bioinformatic tools. However, recently there has been a particular emphasis on increasing the throughput of sample preparation, which has become one of the rate-limiting steps in protein characterization workflows. Researchers have been investigating alternative methods to conventional convection oven incubations to try and reduce sample preparation time for protein characterization. Several protocols have appeared in the literature, which employ microwave irradiation as a tool for the preparation of biological samples for subsequent characterization by a variety of analytical techniques. In this chapter, techniques for microwave-assisted protein staining, destaining, and digestion are described. In general, the application of microwave-assisted technologies resulted in the drastic reduction of overall sample preparation time, though discrepancies in the reproducibility of several published digestion protocols still remain to be clarified.

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Proteins separated by SDS-polyacrylamide gel electrophoresis need to be stained with organic dyes to be visualized. Once stained the intensity of each stained protein band can be used to compare the differences in protein concentration and to measure the relative concentration of any protein band. The most popular standard protein staining is with Coomassie Blue R-250 which takes an hour to stain proteins to saturation and several hours to remove background staining. Direct Red 81 and Amido Black stain proteins within 2.5 min and staining is complete by 10 min. Here the rapid staining of proteins with Direct Red 81 and Amido Black in comparison to staining with Coomassie Blue R-250 is described.

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It is customary to dry gels (SDS-PAGE, native gels, or two-dimensional gels) after staining for record keeping purposes. This is typically carried out with gel dryers or by drying between two cellophane sheets held together by acrylic frames. Here, we report a simple method to store a variety of stained gels without any storage buffer within flexible nonsealed polyethylene bags. Gels can be stored for several months at room temperature without significant shrinking or protein diffusion. The gel stays hydrated owing to the de facto sealing achieved by the polyethylene sheets adhering air-tightly to the gel on either side. The microsaturated environment generated by the thin film of water molecules trapped between the gel and the polyethylene sheets, combined with the nonporous nature of the polyethylene sheets, apparently keeps the gel from cracking or shrinking significantly. The intensity of stained proteins increased during storage probably from the slight gel shrinkage observed. Storing gels in this manner is convenient (a) when low abundance protein spots from multiple two-dimensional electrophoresis gels have to be excised for in-gel tryptic digestion or electroelution and (b) for wet gel autoradiography. In addition to avoiding dryer contamination and saving drying time, these bags prevent the moist gel from sticking to X-ray film. Such storage could also prove useful for electrophoretic transfer of fixed and stained gels.

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BACKGROUND: Cerebral microcirculation after severe head injury is heterogeneous and temporally variable. Microcirculation is dependent upon the severity of injury, and it is unclear how histology relates to cerebral regional blood flow. OBJECTIVE: This study assesses the changes of cerebral microcirculation blood flow over time after an experimental brain injury model in sheep and contrasts these findings with the histological analysis of the same regions with the aim of mapping cerebral flow and tissue changes after injury. METHODS: Microcirculation was quantified using flow cytometry of color microspheres injected under intracardiac ultrasound to ensure systemic and homogeneous distribution. Histological analysis used amyloid precursor protein staining as a marker of axonal injury. A mapping of microcirculation and axonal staining was performed using adjacent layers of tissue from the same anatomical area, allowing flow and tissue data to be available from the same anatomical region. A mixed effect regression model assessed microcirculation during 4 h after injury, and those results were then contrasted to the amyloid staining qualitative score. RESULTS: Microcirculation values for each subject and tissue region over time, including baseline, ranged between 20 and 80 ml/100 g/min with means that did not differ statistically from baseline flows. However, microcirculation values for each subject and tissue region were reduced from baseline, although their confidence intervals crossing the horizontal ratio of 1 indicated that such reduction was not statistically significant. Histological analysis demonstrated the presence of moderate and severe score on the amyloid staining throughout both hemispheres. CONCLUSION: Microcirculation at the ipsilateral and contralateral site of a contusion and the ipsilateral thalamus and medulla showed a consistent decline over time. Our data suggest that after severe head injury, microcirculation in predefined areas of the brain is reduced from baseline with amyloid staining in those areas reflecting the early establishment of axonal injury.

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Western blotting is an analytical method widely used for detecting and (semi-)quantifying specific proteins in given samples. Western blots are continuously applied and developed by the protein community. This review article focuses on a significant, but not yet well-established, improvement concerning the internal loading control as a prerequisite to accurately quantifying Western blots. Currently, housekeeping proteins (HKPs) like actin, tubulin, or GAPDH are often used to check for equal loading or to compensate potential loading differences. However, this loading control has multiple drawbacks. Staining of the total protein on the blotting membrane has emerged as a better loading control. Total protein staining (TPS) represents the actual loading amount more accurately than HKPs due to minor technical and biological variation. Further, the broad dynamic range of TPS solves the issue of HKPs that commonly fail to show loading differences above small loading amounts of 0.5-10 µg. Although these and further significant advantages have been demonstrated over the past 10 years, only a small percentage of laboratories take advantage of it. The objective of this review article is to collect and compare information about TPS options and to invite users to reconsider their applied loading control. Nine benefits of TPS are discussed and seven different variants are critically evaluated by comparing technical details. Consequently, this review article offers an orientation in selecting the appropriate staining type. I conclude that TPS should be the preferred loading control in future Western blot approaches.

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The development of new near infrared (NIR) dyes is crucial for diverse applications and especially bioimaging, as they absorb and emit light in the "therapeutic window" (650-950 nm). We report here a new family of NIR fluorophores that has been obtained by hybridising hemicyanines with epicocconone. Emission wavelengths of these hybrid dyes is in the range 715-795 nm and is combined with large Stokes' shifts (75-95 nm). The absorption and emission wavelength can be modulated according to the hemicyanine moiety and adding sulfonic acid moieties enhances water solubility. We demonstrate their application in the sensitive detection of proteins in gel electrophoresis and the staining of specific cellular organelles in confocal microscopy. These results are particularly encouraging and bring forward a new fluorescent skeleton for chemical biology.

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Seven luminescent iridium(III) complexes were prepared to investigate the relationships between chemical structures and properties of protein staining. For the first time, the effect of the main ligand, the π conjugation effect of the ancillary ligand, and the charge effect of organometallic complexes on protein staining has been revealed. Most importantly, this study gives the first experimental evidence of the potential applications of charge-neutral organometallic complexes in protein staining, which could open an avenue of exploiting novel protein staining agents in the future.

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Here, we introduce isatoic anhydride as a sensitive and commodious fluorescent prelabel for detection of proteins in one-dimensional polyacrylamide gels. High reactivity of isatoic anhydride with nucleophiles in mild alkaline environments makes it an appropriate tag for labeling of biomolecules. In this study, we show that preelectrophoresis labeling of proteins with isatoic anhydride for few minutes at room temperature allows detection of 2-4 ng of standard proteins, BSA and lysozyme, per band. Proteins were successfully labeled in the presence of a wide range of common biological reagents and in crude cell extract. The labeled proteins have the same electrophoretic migration in comparison to unlabeled proteins; however the application of saturation labeling method results in slight band broadening. Compatibility of the method with downstream processes was assessed by tryptic digestion of labeled proteins and study of peptide mixture using gel electrophoresis which revealed partial digestion of labeled proteins due to lysine modification. The present procedure is sensitive, rapid, and inexpensive and is a promising alternative for current protein staining procedures, where downstream processes are not desired.

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Sodium polyanethol sulfonate (SPS) is an anionic detergent with a broad range of activities and applications. While studying the excretion of cytoplasmic proteins in Staphylococcus aureus SPS was used as cell lysis inhibitor. When investigating the protein pattern of culture supernatants from cells grown in the absence or presence of SPS by Coomassie blue stained polyacrylamide gel the amount of protein bands was significantly decreased in the presence of SPS, suggesting that this effect was due to inhibition of cell lysis. However, various control studies showed that the apparent decreased protein secretion was an artifact due to the interference of SPS with Coomassie blue- and silver-staining. The only alternative method that was uninfluenced by SPS was imidazole-SDS-zinc staining. This is the method of choice particularly when protein interfering compounds are present in the extracts. For protein quantification in liquid samples the bicinchoninic acid (BCA) assay appeared to be the method of choice in the presence of SPS. The assay is based on neutral peptide bonds and is therefore rather insensitive to interfering compounds. This study shows that SPS and most likely also related detergents might falsify conventional protein staining and quantification methods.

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Regenerative medicine, which aims to restore, replace or regenerate cells and tissues using novel approaches such as iPS therapy, is currently a big issue in the field of rehabilitation medicine. Neurological recovery has been proved using marmoset monkeys with spinal cord lesions and Hematoxylin-Eosin and Luxol fast blue staining were adopted to identify the increased number of neurons at the spinal cord level. In regenerative medicine, pathophysiological findings demonstrating the recovery of motor units can provide direct evidence of neuromuscular function. In the field of rehabilitation medicine, the final common pathway, e.g. intramuscular nerve fibers and neuromuscular junctions, will be the target used to identify the recovery of motor function. Present physiatric modalities such as electrical or magnetic stimulations and therapeutic exercises will serve as the strategic applications used in neuromuscular regeneration treatments. The methylene blue vital staining method is a classical technique that when combined with the recently developed functional fluorescent protein staining along with transgenic procedures and confocal endomicroscopy examinations will illuminate our investigations into the degree of regenerative success obtained. These neuromuscular pathologies at the spinal cord level as well as the lower motor neuron level will allow us to more clearly determine the efficacy of various physical modalities used in rehabilitation medicine. The regenerative medicine era will require rehab efforts not only for treating spinal cord lesions but also for treating brain damaged patients in the future.

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Western blot analysis is routinely employed for quantifying differences in protein levels between samples. To control equal loading and to arithmetically compensate loading differences, immunodetection of housekeeping proteins is commonly used. Due to potential biases, this approach has been criticized. Here, we evaluate epicocconone-based total protein staining (E-ToPS) as an alternative. We compared it with two other total protein stainings (Coomassie and Sypro Ruby) and with immunodetection of housekeeping proteins (ß-tubulin and glyceraldehyde 3-phosphate dehydrogenase). Evaluation comprised both the natural and the synthetic epicocconone compound. Both compounds produced highly congruent results and showed more sensitive (≤ 1 µg) and less variable staining properties than the other variants. The high sensitivity of E-ToPS, covering minute protein amounts, makes it a powerful loading control, especially for precious samples. Regarding biological and technical variances, E-ToPS outperformed immunostaining against ß-tubulin and glyceraldehyde 3-phosphate dehydrogenase. Furthermore, E-ToPS had no impact on subsequent immunodetection, allowing for an early control of proper loading prior to immunodetection. In contrast to earlier studies, we found logarithmic staining properties for E-ToPS, which should be considered when using it for arithmetic normalization. In conclusion, we demonstrate the superior power of E-ToPS as a loading control for Western blots.

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