Current Methods for Analysing Mesenchymal Stem Cell-Derived Extracellular Vesicles.

The use of extracellular vesicles (EVs) generated by mesenchymal stem cells (MSCs) holds great promise as a novel therapeutic approach. Although their immunomodulatory and regeneration potential has been reported to be similar to that of MSCs, the use of MSC-derived EVs in clinical settings will require several problems to be resolved. It is necessary to develop a standardised and widely accepted isolation technology and to improve methods such as the quantification and characterisation of MSC-derived EVs. In this way, EV studies can be compared, the acquired knowledge can be safely transferred to clinical platforms and the clinical results can be evaluated appropriately. There are many procedures for the collection and analysis of vesicles derived from different cells; however, this review provides an overview of methods for the determination of the total protein amount, specific proteins, particle number, non-protein markers like lipids and RNA, microscopy and other methods focusing on MSC-derived EVs.

Smart sampling as the "Spot-on" Method for LC-MS protein analysis from dried blood spots.

This perspective explores the feasibility of smart sampling with dried blood spots for the determination of proteins and peptides from human biomatrices using liquid chromatography coupled to mass spectrometry for clinical purposes. The focus is on innovative approaches to transform filter paper from a mere sample carrier to an active element in sample preparation, with the aim of reducing the need for extensive and intensive sample preparation in the conventional sense. Specifically, we discuss the use of modified cellulose to integrate sample preparation at an early stage of sample handling. The use of paper immobilized with either trypsin or monoclonal antibodies for protein digestion and affinity clean-up is discussed as a potential benefit of starting sample preparation instantly at the moment of sampling to optimize time efficiency and enable faster analysis, diagnosis, and follow-up of patients.

Quantitative analysis of protein in thermosensitive hydroxypropyl chitin for biomedical applications.

Accurate determination of residual protein content in hydroxypropyl chitin (HPCH), a temperature-sensitive chitin derivative developed recently, is of great importance for biomedical applications. Coomassie brilliant blue (Bradford) method, Lowry method and Bicinchoninic acid (BCA) method were investigated to estimate the content of residual protein in HPCH. It was found that both Bradford and Lowry methods are not suitable for the protein assay in the HPCH sample. The BCA method could be used to determine protein content in HPCH solutions at low concentrations with good accuracy and precision and reasonable limit of detection and limit of quantitation for medical applications.

A fluorometric assay of thrombin using magnetic nanoparticles and enzyme-free hybridization chain reaction.

A fluorescence method based on functionalized magnetic nanoparticles (FMNPs) and hybridization chain reaction (HCR) is developed for the enzyme-free amplified determination of thrombin. In the proposed design, aptamer against thrombin was hybridized with the capture DNA-modified magnetic nanoparticles to yield the FMNPs. In the presence of thrombin, aptamers are released due to the specific and high-affinity binding between thrombin and its aptamer. The exposed capture DNA subsequently hybridized with the partial sequence of helper DNA, and the vacant sequence of helper DNA further hybridized with HCR products which is pre-formed by the alternate hybridization of single-stranded DNAs (H1 and H2). The immobilized HCR products were then labeled with YOYO-1 for fluorescence measurement. Fluorescence signal intensity of labeled YOYO-1 was measured at an emission wavelength of 519 nm (excitation under 488 nm) and used for calibration. By taking advantage of HCR amplification, this direct assay strategy showed a linear response in the 20- to 200-pM concentration range, and the limit of detection is 9.2 pM which is about 3-orders of magnitude lower than the serum thrombin concentration (10 nM) that triggers blood clotting. This developed method can efficiently differentiate the target protein from a protein matrix, and it is verified by determination of thrombin in spiked serum samples with recoveries in the range of 94.5-103.3%. Graphical abstract A fluorometry method for thrombin detection using magnetic nanoparticles and enzyme-free hybridization chain reaction.

Determination of conjugated protein on nanoparticles by an adaptation of the Coomassie blue dye method.

A new accurate spectrophotometric method for protein determination on nanoparticles is described. The method is based on the Coomassie blue dye that binds to the basic and aromatic amino acid residues of proteins, especially arginine and lysine. A known amount of reagent dye was mixed with a variety of protein-loaded nanoparticles. Thereafter the unconjugated reagent was mixed with excess protein (bovine serum albumin) and titrated. In this method, the reacted dye on the protein coating of nanoparticle is directly determined, in opposite to the conventional method, in which the conjugated protein is determined as the difference between the non-conjugated protein found in the supernatant after centrifugation, and the total amount of protein originally used. This method is able to measure amounts of coated protein lower than 1 ppm. •Simple and accurate method especially adapted for protein-coated nanoparticles.•The amino acid residues of protein in the nanoparticle surface react with Coomassie brilliant blue dye.•The unreacted dye is titrated with an excess of a standard protein.

Simultaneous determination of proteins in microstructured optical fibers supported by chemometric tools.

A new perspective on the relevant problem-creating simple, rapid, and efficient protein sensors based on microstructured optical fibers using a simple homogeneous analysis format-was proposed. Commercially available long-period grating hollow core microstructured optical fibers (LPG HCMOF) were used to determine bovine serum albumin (BSA) and albumin from chicken eggs (OVA) in binary mixtures as well as immunoglobulin G (IgG) in the presence of BSA and OVA. LPG HCMOF transmission spectra allowed the detection of both BSA and OVA up to 10 mg/mL with LOD as low as 0.1 and 0.8 µg/mL, respectively. Partial least squares regression (PLS) was utilized for modeling of LPG HCMOF spectral data and quantitative analysis of BSA, OVA, total protein, and IgG in binary and ternary mixtures. Rather high coefficients of determination (R2) and low root mean square error for the calibration (RMSEC) (15%) and prediction (RMSEP) (20%) were obtained for all PLS models. The proposed approach was tested in the analysis of BSA in spiked horse blood hemolyzed (HBH). The results demonstrated the functionality of the proposed approach and offered the opportunity for the creation of a wide range of sensors for protein determination in complex mixtures. Graphical abstract.

A systematic evaluation of various methods for quantifying food protein hydrolysate peptides.

This work was carried out to identify accurate methods that could be recommended for the quantification of proteins in food protein hydrolysates. Following hydrolysis with 4% alcalase, the amount of protein in various hydrolysate samples was measured using seven different analytical methods. Although the data obtained using different methods varied, HPLC amino acid analysis with a Pico-Tag column indicated that the highest concentration of amino acids in the protein hydrolysates was present in the casein sample while the lowest amount of protein was found in the sample of hempseed studied. However, the amino acid analysis data was mostly positively correlated with the Dumas and Lowry methods. We conclude that where available, amino acid analysis provides the best estimate of protein content of hydrolysates but the Dumas and Lowry methods can also be recommended as alternatives.

A practical method for extending the biuret assay to protein determination of corn-based products.

A modified biuret method suitable for protein determination of corn-based products was developed by introducing a combination of an alkaline reagent with sodium dodecyl sulfate (reagent A) and heat treatments. The method was tested on seven corn-based samples. The results showed mostly good agreement (P>0.05) as compared to the Kjeldahl values. The proposed method was found to enhance the accuracy of prediction on zein content using bovine serum albumin as standard. Reagent A and sample treatment were proved to effectively improve protein solubilization for the thermally-dried corn-based products, e.g. corn gluten meal. The absorbance was stable for at least 1-h. Moreover, the whole measurement of protein content only needs 15-20min more than the traditional biuret assay, and can be performed in batches. The findings suggest that the proposed method could be a timesaving alternative for routine protein analyses in corn processing factories.

Ultrasound-based protein determination in maize seeds.

The need for a simple and accurate method for protein estimation in alcoholic extracts led to the reexamination of the optimum conditions of a colorimetric assay based on the biuret reaction. Sonication time and the other experimental parameters were optimized after kinetics study on the extraction of either zein or total proteins. Zein extraction and purity were investigated by (1)H and (13)C NMR spectroscopy, SDS-PAGE electrophoresis, and UV-visible spectrophotometry (UV-vis). A zein assay was proposed, which involves the reaction of copper ions in copper phosphate powder with zein extracted in ethanolic solutions under strong alkaline environment. Furthermore, we extended this procedure to determine total proteins in maize samples simultaneously with their ultrasonic-assisted (US) extraction with an alkaline-alcoholic solution. Proteins in both types of extracts were well characterized by UV-vis spectroscopy. However, the 545 nm absorbance of the violet-colored supernatants which is proportional to the protein content was found to be the key parameter of the improved biuret-based protein assay. Comparison of values obtained by this procedure and by Micro-Kjeldahl method was in excellent agreement. A scaled-down procedure agreed well with the standard procedure. Enhanced accuracy and repeatability was found in protein determination in maize using the modified biuret method. The optimization of reagent concentrations and incubation times were studied as well.

A composite agarose-polyacrylamide matrix as two-dimensional hard support for solid-phase protein assays.

The solid-phase protein assays using blotting membranes as hard support do not allow achieving the low background and sensitivity of protein staining in clear gels. The membrane opacity complicates imaging of results on standard lab documentation systems. We describe a low-cost transparent matrix that can be used as an alternative to polymeric membranes for solid-phase assays. Protein samples are spotted onto a dry film of composite agarose-polyacrylamide matrix covering standard glass microscopic slides. After rehydration in protein-fixing solution, matrix with protein samples can be detached from glass support and stained as conventional protein polyacrylamide gels.

A simple and cost-effective solid-phase protein nano-assay using polyacrylamide-coated glass plates.

A new solid-phase protein nano-assay is suggested for simple and sensitive estimation of protein content in sample buffers (a 1-µl sample is sufficient for analysis). The assay is different from conventional "on-filter" assays in that it uses inexpensive fully transparent polyacrylamide gel (PAAG)-coated glass plates as solid support and, thus, combines the convenience of "on-membrane" staining with the sensitivity and ease of documentation of "in-gel" staining (and, therefore, is especially suited for standard lab gel documentation systems). The PAAG plates assay is compatible with all dyes for in-gel protein staining. Depending on the sensitivity of the staining protocol, the assay can be used in macro-, micro-, and nano-assay formats. We also describe a low-cost two-component colloidal Coomassie brilliant blue G-250 (CBB G-250) staining protocol for fast quantitative visualization of proteins spotted on a PAAG plate (the detection limit is up to 2 ng of proteins even when using a Nikon CoolPix digital camera and white light transilluminator instead of a gel scanner). The suggested colloidal CBB G-250 protocol could also be used for visualizing nano-amounts of proteins in polyacrylamide gels. The PAAG plate assay could be useful for proteomic applications and, in general, for all cases where a fast, sensitive, and easily documentable cost-effective solid-phase protein assay is required.

Multicommutated flow analysis system for determination of total protein in cerebrospinal fluid.

A fully mechanized, computer-controlled, multicommutated flow analysis (MCFA) system dedicated for total protein determination in cerebrospinal fluid samples has been developed. For the protein determination the Exton method has been applied. Dedicated turbidimetric and nephelometric flow-through detectors operating according to paired-emitter detector diode principle have been fabricated by integration of two or three respective light emitting diodes. The developed MCFA system is characterized by robust, compact design and low consumption of the sample (72 µ L). The limits of detection for turbidimetric and nephelometric detection mode are 65 mg L(-1) and 9 mg L(-1), respectively. For turbidimetric measurements the range of linear response offered by the MCFA system is 72-900 mg L(-1), whereas in the case of nephelometric detection 18-500 mg L(-1) linear range is obtained. The throughput of the MCFA system is over 30 injection per hour. The analytical system was optimized with bovine serum albumin standards and successfully validated with real samples of human cerebrospinal fluid.

Fucoidan-dependent increased membrane components in HepG2 cells: effect of fucoidan is not due to gene expression.

BACKGROUND: The precise mechanism of the therapeutic effects of fucoidan (sulphated polyfucose) on cultured hepatocarcinoma HepG2 cells is as yet unclear. MATERIALS AND METHODS: Protein components between fucoidan-treated and non-treated HepG2 cells were compared through a quantitative micro-sequencing method. RESULTS: A dramatic and immediate increment of the membrane compartment and a decrement of RNA virus by fucoidan, as an effect of the Ishi-Mozuku (an edible brown seaweed Mozuku of Japan), are demonstrated. The ratio of membrane glycoproteins to total cellular proteins increases from 28.9% to 43.2% (1.5-fold), and the positive-sense single-stranded RNA viral proteins among the total cellular proteins decrease from 5.3% to 0.29% (18-fold), respectively, in response to 0.102 mg/ml fucoidan in HepG2 cells over three days' period. CONCLUSION: Fucoidan seems to retard the growth of HepG2 cells through membrane glycoprotein metabolism. Therefore, fucoidan could be expected to have a therapeutic effect on hepatocellular carcinoma.

Are accurate computations of the 13C' shielding feasible at the DFT level of theory?

The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the (13)C' shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the (13)C' shielding at the density functional level of theory (DFT), with an accuracy similar to that of the (13)C(α) shielding, is feasible with the existing computational resources. The DFT calculations, carried out for a large number of possible conformations of the tripeptide Ac-GXY-NMe, with different combinations of X and Y residues, enable us to conclude that the accurate computation of the (13)C' shielding for a given residue X depends on the: (i) (ϕ,ψ) backbone torsional angles of X; (ii) side-chain conformation of X; (iii) (ϕ,ψ) torsional angles of Y; and (iv) identity of residue Y. Consequently, DFT-based quantum mechanical calculations of the (13)C' shielding, with all these factors taken into account, are two orders of magnitude more CPU demanding than the computation, with similar accuracy, of the (13)C(α) shielding. Despite not considering the effect of the possible hydrogen bond interaction of the carbonyl oxygen, this work contributes to our general understanding of the main structural factors affecting the accurate computation of the (13)C' shielding in proteins and may spur significant progress in effort to develop new validation methods for protein structures.

A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts.

Soil extracts usually contain large quantities of dissolved humified organic material, typically reflected by high polyphenolic content. Since polyphenols seriously confound quantification of extracted protein, minimising this interference is important to ensure measurements are representative. Although the Bradford colorimetric assay is used routinely in soil science for rapid quantification protein in soil-extracts, it has several limitations. We therefore investigated an alternative colorimetric technique based on the Lowry assay (frequently used to measure protein and humic substances as distinct pools in microbial biofilms). The accuracies of both the Bradford assay and a modified Lowry microplate method were compared in factorial combination. Protein was quantified in soil-extracts (extracted with citrate), including standard additions of model protein (BSA) and polyphenol (Sigma H1675-2). Using the Lowry microplate assay described, no interfering effects of citrate were detected even with concentrations up to 5 times greater than are typically used to extract soil protein. Moreover, the Bradford assay was found to be highly susceptible to two simultaneous and confounding artefacts: 1) the colour development due to added protein was greatly inhibited by polyphenol concentration, and 2) substantial colour development was caused directly by the polyphenol addition. In contrast, the Lowry method enabled distinction between colour development from protein and non-protein origin, providing a more accurate quantitative analysis. These results suggest that the modified-Lowry method is a more suitable measure of extract protein (defined by standard equivalents) because it is less confounded by the high polyphenolic content which is so typical of soil extracts.

Is it possible to screen for milk or whey protein adulteration with melamine, urea and ammonium sulphate, combining Kjeldahl and classical spectrophotometric methods?

The Kjeldahl method and four classic spectrophotometric methods (Biuret, Lowry, Bradford and Markwell) were applied to evaluate the protein content of samples of UHT whole milk deliberately adulterated with melamine, ammonium sulphate or urea, which can be used to defraud milk protein and whey contents. Compared with the Kjeldahl method, the response of the spectrophotometric methods was unaffected by the addition of the nitrogen compounds to milk or whey. The methods of Bradford and Markwell were most robust and did not exhibit interference subject to composition. However, the simultaneous interpretation of results obtained using these methods with those obtained using the Kjeldahl method indicated the addition of nitrogen-rich compounds to milk and/or whey. Therefore, this work suggests a combination of results of Kjeldahl and spectrophotometric methods should be used to screen for milk adulteration by these compounds.

The highly abundant urinary metabolite urobilin interferes with the bicinchoninic acid assay.

Estimation of total protein concentration is an essential step in any protein- or peptide-centric analysis pipeline. This study demonstrates that urobilin, a breakdown product of heme and a major constituent of urine, interferes considerably with the bicinchoninic acid (BCA) assay. This interference is probably due to the propensity of urobilin to reduce cupric ions (Cu(2+)) to cuprous ions (Cu(1+)), thus mimicking the reduction of copper by proteins, which the assay was designed to do. In addition, it is demonstrated that the Bradford assay is more resistant to the influence of urobilin and other small molecules. As such, urobilin has a strong confounding effect on the estimate of total protein concentrations obtained by BCA assay and thus this assay should not be used for urinary protein quantification. It is recommended that the Bradford assay be used instead.

A rapid and accurate method for determining protein content in dairy products based on asynchronous-injection alternating merging zone flow-injection spectrophotometry.

An accurate and rapid method and a system to determine protein content using asynchronous-injection alternating merging zone flow-injection spectrophotometry based on reaction between coomassie brilliant blue G250 (CBBG) and protein was established. Main merit of our approach is that it can avoid interferences of other nitric-compounds in samples, such as melamine and urea. Optimized conditions are as follows: Concentrations of CBBG, polyvinyl alcohol (PVA), NaCl and HCl are 150 mg/l, 30 mg/l, 0.1 mol/l and 1.0% (v/v), respectively; volumes of the sample and reagent are 150 µl and 30 µl, respectively; length of a reaction coil is 200 cm; total flow rate is 2.65 ml/min. The linear range of the method is 0.5-15 mg/l (BSA), its detection limit is 0.05 mg/l, relative standard deviation is less than 1.87% (n=11), and analytical speed is 60 samples per hour.

Nephelometry and turbidimetry with paired emitter detector diodes and their application for determination of total urinary protein.

Two miniature and compact optoelectronic devices fabricated by means of integration of light emitting diodes have been developed for turbidimetric and nephelometric measurements. These devices are operating according to paired-emitter-detector-diode (PEDD) principle. The detectors have been characterized using bovine serum albumin and Exton protein assay as a model analyte and a model analytical method, respectively. The developed detectors have been adapted for measurements under conditions of flow injection analysis (FIA). Under optimized conditions the turbidimetric flow system offers the range of linear response up to 400 mg L(-1) with the detection limit at 20 mg L(-1). The linear range and detection limit found for optimized nephelometric FIA system are 15-500 mg L(-1) and 8 mg L(-1), respectively. The PEDD-based FIA systems with the detector operating according to both modes of measurements have been successfully applied for urinalysis offering total protein determination at physiological and pathological levels with high throughput (over 60 injections per hour).