Protein release from interpenetrating polymer network hydrogels triggered by endogenous biomarkers

A biocompatible drug delivery system with a high-sensitive stimuli-responsive behavior is reported. Calcium alginate hydrogels interpenetrated with polyvinyl alcohol–diboronate polymer network (IPN) effectively respond to the presence of hydrogen peroxide through oxidative degradation of boronate esters. The degradation of the IPN entails the reopening of the original alginate pores, resulting in a 5–9 times increase in release rates of encapsulated proteins with molecular masses ranging from 16.7 to 66 kDa. The release can be triggered by hydrogen peroxide concentrations as low as 50 μM in the bulk solution. Alternatively, hydrogen peroxide can also be generated inside the hydrogels by incorporation of oxidase enzymes in the presence of their substrates, such as lactate, glucose, or hypoxanthine, which can serve as biomarkers of certain physiological disorders.     

Electrochemical Detection of Cardiac Biomarkers Utilizing Electrospun Multiwalled Carbon Nanotubes Embedded SU‐8 Nanofibers

In this paper we demonstrate synthesis and characterization of MWCNTs embedded SU‐8 electrospun nanofibers and their application towards ultrasensitive detection of cardiac biomarkers using Electrochemical Impedance spectroscopy (EIS). The composite nanofibers have excellent electrical and transduction properties owing to the presence of MWCNTs in addition to ease of functionalization and biocompatibility, which can be attributed to the presence of SU‐8. Thus the synthesized nanofibers are ideal candidates for sensitive biosensor applications. As a proof concept, the detection of cardiac biomarkers, Myoglobin (Myo), cardiac Troponin I (cTn I) and Creatine Kinase MB (CK‐MB) is demonstrated. The synthesized nanofibers were functionalized with the antibodies of the biomarkers and the detection was carried using Electrochemical Impedance Spectroscopy, an excellent technique for understanding the adsorption kinetics. A minimum detection limit of nano‐gram/ml is demonstrated using this nanobiosensor platform.     

Determination of 12 potential nephrotoxicity biomarkers in rat serum and urine by liquid chromatography with mass spectrometry and its application to renal failure induced by Semen Strychni

In previous nephrotoxicity metabonomic studies, several potential biomarkers were found and evaluated. To investigate the relationship between the nephrotoxicity biomarkers and the therapeutic role of Radix Glycyrrhizae extract on Semen Strychni‐induced renal failure, 12 typical biomarkers are selected and a simple LC–MS method has been developed and validated. Citric acid, guanidinosuccinic acid, taurine, guanidinoacetic acid, uric acid, creatinine, hippuric acid, xanthurenic acid, kynurenic acid, 3‐indoxyl sulfate, indole‐3‐acetic acid, and phenaceturic acid were separated by a Phenomenex Luna C₁₈ column and a methanol/water (5 mM ammonium acetate) gradient program with a runtime of 20 min. The prepared calibration curves showed good linearity with regression coefficients all above 0.9913. The absolute recoveries of analytes from serum and urine were all more than 70.4%. With the developed method, analytes were successfully determined in serum and urine samples within 52 days. Results showed that guanidinosuccinic acid, guanidinoacetic acid, 3‐indoxyl sulfate, and indole‐3‐acetic acid (only in urine) were more sensitive than the conventional renal function markers in evaluating the therapeutic role of Radix Glycyrrhizae extract on Semen Strychni‐induced renal failure. The method could be further used in predicting and monitoring renal failure cause by other reasons in the following researches.     

Forensic differentiation of biogenic organic compounds from petroleum hydrocarbons in biogenic and petrogenic compounds cross-contaminated soils and sediments

“Total petroleum hydrocarbons” (TPHs) or “petroleum hydrocarbons” (PHCs) are one of the most widespread soil pollutants in Canada, North America, and worldwide. Clean-up of PHC-contaminated soils and sediments costs the Canadian economy hundreds of million of dollars annually. Much of this activity is driven by the need to meet regulated levels of PHC in soil. These PHC values are legally required to be assessed using standard methods. The method most commonly used in Canada, specified by the Canadian Council of Ministers of the Environment (CCME), measures the total hydrocarbon concentrations in a soil by carbon range (Fraction 1: C₆–C₁₀; Fraction 2: C₁₀–C₁₆, Fraction 3: C₁₆–C₃₄: and Fraction 4: C₃₄+). Using the CCME method, all of the materials extractible by a mixture of 1:1 hexane:acetone are considered to be petroleum hydrocarbon contaminants. Many hydrocarbon compounds and other extractible materials in soil, however, may originate from non-petroleum sources. Biogenic organic compounds (BOCs) is a general term used to describe a mixture of organic compounds, including alkanes, sterols and sterones, fatty acids and fatty alcohols, and waxes and wax esters, biosynthesized by living organisms. BOCs are also produced during the early stages of diagenesis in recent aquatic sediments. BOC sources could include vascular plants, algae, bacteria and animals. Plants and algae produce BOCs as protective wax coating that are released back into the sediment at the end of their life cycle. BOCs are natural components of thriving plant communities. Many solvent-extraction methods for assessing soil hydrocarbons, however, such as the CCME method, do not differentiate PHCs from BOCs. The naturally occurring organics present in soils and wet sediments can be easily misidentified and quantified as regulated PHCs during analysis using such methods. In some cases, biogenic interferences can exceed regulatory levels, resulting in remediation of petroleum impacts that are not actually present. Consequently, reliance on these methods can trigger unnecessary and costly remediation, while also wasting valuable landfill space. Therefore, it is critically important to develop new protocols to characterize and differentiate PHCs and BOCs in contaminated sediments. In this study, a new reliable gas chromatography–mass spectrometry (GC–MS) method, in combination with a derivatization technique, for characterization of various biogenic compounds (including biogenic alkanes, sterols, fatty acids and fatty alcohols) and PHCs in the same sample has been developed. A multi-criteria approach has been developed to positively identify the presence of biogenic compounds in soil and sediment samples. More than thirty sediment samples were collected from city stormwater management (SWM) ponds and wetlands across Canada. In these wet sediment samples, abundant biogenic n-alkanes, thirteen biogenic sterols, nineteen fatty carboxylic acids, and fourteen fatty alcohols in a wide carbon range have been positively identified. Both PHCs and BOCs in these samples were quantitatively determined. The quantitation data will be used for assessment of the contamination sites and toxicity risks associated with the CCME Fraction 3 hydrocarbons.     

Biotransformation of musk xylene in trout haemoglobin: dose–response and toxicokinetics of musk xylene metabolites haemoglobin adducts by gas chromatography-mass spectrometry

Musk xylene (MX) is frequently used as a fragrance in commercial toiletries. Biotransformation of MX into 4-amino-MX (4-AMX) and 2-amino-MX (2-AMX) metabolites in rainbow trout haemoglobin (Hb) has been described. The dose–response relationship and toxicokinetics of the metabolites as adducts in the Hb were determined by gas chromatography (GC)–electron capture negative chemical ionization (NCI)–mass spectrometry (MS), and GC–electron ionization (EI)–MS/MS, using selected ion monitoring (SIM). The trout were subjected to a single exposure of 0.010, 0.030, 0.10, and/or 0.30?mg?MX/g of fish. Hb samples were collected from exposed and control fish, and analysed subsequent to exposure at intervals of 24, 72, and 168?h. Alkaline hydrolysis released 4-AMX and 2-AMX metabolites from the Hb, and the solutes were extracted into n-hexane. The extracts were preconcentrated and analysed. The presence of the metabolites in the Hb extracts was confirmed based on agreement of similar mass spectral features from NCI/MS and EI-MS/MS spectra, and retention times of the metabolites with standards. The NCI/MS results were used for dose–response and toxicokinetics measurements. For dose–response, the concentrations of adducts of the metabolites increased with dosage, and a maximum adduct formation was observed at 0.10?mg?g^?1, beyond which it decreased. The average concentrations of 4-AMX and 2-AMX at a dosage of 0.10?mg?g^?1 were 700 and 7.4?ng?g^?1, respectively. For toxicokinetics, the concentration of the metabolites in the Hb reached a maximum in the 3 day sample after administration of MX. Further elimination of the metabolites exhibited kinetics with a half-life estimated to be 1–2 days, assuming first-order kinetics. Quantitations were made based on an internal standard and a calibration plot. In control samples, non-hydrolysed Hb, and reagent blank extracts, the metabolites were not detected. The limits of detection for 4-AMX and 2-AMX in the Hb were approximately 1.7 and 1.4?µg?L^?1, respectively, based on a signal-to-noise ratio of 3 with NCI/MS.     

Fractionation of the human plasma proteome for monoclonal antibody proteomics‐based biomarker discovery 2: Antigen identification by dot‐blot array screening

Immunization with complex mixtures, like the human plasma resulted in the generation of cloned mAb libraries (PlasmaScan? and QuantiPlasma? libraries, with >1000 individual mAbs) reacting with a nonredundant set of antigenic epitopes. mAb proteomics refers to quasi‐hypothesis‐free profiling of plasma samples with nascent or cloned mAb libraries for the discovery of disease‐specific biomarkers. Once mAbs with biomarker potential have been identified, the next task is the determination of cognate antigens recognized by the respective mAbs. To determine the cognate protein antigen corresponding to each individual mAbs in the cloned mAb libraries, we have separated human plasma by consecutive steps of desalting and various chromatography procedures. The process resulted in 783 fractions, which we termed “Analyte Library” (AL). The AL represents the human plasma proteome in relatively low‐protein complexity fractions. Here, to determine the utility of the AL, we selected ten plasma proteins and checked for their presence in the fractions. Among the ten cases, the distribution of four selected plasma proteins matched expectations, as these proteins were present only in a few fractions corresponding to their physical, chemical, and biochemical properties. However, in six cases, we observed “smear” ‐like distribution or complete absence of the proteins, suggesting that protein–protein interactions or protein variants may alter the observed plasma distribution profiles. Nevertheless, we conclude that the AL is an efficient, high throughput tool to complement the mAb biomarker discovery process with cognate protein antigen identification for each mAbs.     

Determination of carbofuran, carbaryl and their main metabolites in plasma samples of agricultural populations using gas chromatography–tandem mass spectrometry

A gas chromatography–tandem mass spectrometric (GC-MS/MS) method has been developed for the determination of carbofuran (2,3-dihydro-2,2-dimethylbenzofuran-7-yl methylcarbamate), carbaryl (1-naphthyl-N-methylcarbamate) and their main metabolites in human blood plasma. Optimization of the isolation of the compounds from plasma matrix included the precipitation, denaturation and digestion of plasma proteins. Derivatization was achieved by the use of trifluoroacetic acid anhydride and was optimized for temperature, time and volume of derivatization agent. In the proposed method, a mild precipitation technique was applied using β-mercaptoethanol and ascorbic acid in combination with solid-phase extraction technique using Oasis HLB (Hydrophobic Lipophilic Balance) cartridges for further clean up of samples. Carbamate linkage was not hydrolyzed to its phenol product, but both carbamate phenol and ketones were transformed into trifluoroacetyl derivatives in order to become volatile compounds and were determined using tandem mass spectrometry. The linearity of the method was shown for nine concentrations in the range of 0.50–250 ng mL⁻¹ in fortified plasma aliquots. Limits of detection (LODs) for all compounds ranged from 0.015–0.151 ng mL⁻¹. Inter-day and intra-day assays (RSD) for all compounds, at three concentration levels of 2.5, 25 and 100 ng mL⁻¹ (n=3) in fortified plasma samples were less than 18%. Accuracy (%E _r) was calculated at three concentration levels, 8, 80 and 160 ng mL⁻¹ (n=3), and ranged from −12.0 to 15.0%. Matrix effect was evaluated so mean recoveries were calculated for all compounds and ranged from 81–107%. Specificity for the use of this method to biological monitoring studies was achieved including four main metabolites of CF, 1-naphthol and 2-naphthol from the naphthalene metabolism pathways, and both the parent compound of carbofuran and carbaryl. The proposed method was applied to plasma samples of pesticide users.     

Determination of hopane biomarkers in Arabian crude oils by gas chromatography-tandem mass spectrometry

Gas chromatography-mass spectrometry with the mass spectrometer operated in the tandem mode at a constant accelerating voltage was used to analyse for triterpanes in Arabian crude oils. Specific molecular parent-daughter ion pairs were selected for quantitative measurements owing to their metastable transitions in the first field-free region. More accurate relative distribution ratios of hydrocarbon biomarkers were determined by this sequential gating technique than by the conventional diagnostic daughter ion mass fragmentogram in common GC-MS. The data and spectra obtained from MS-MS operation may serve as unique “fingerprints” for these regional crudes     

Comparative two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE) of human milk to identify dysregulated proteins in breast cancer

Breast cancer (BC) remains a major cause of mortality, and early detection is considered important for reducing BC‐associated deaths. Early detection of BC is challenging in young women, due to the limitations of mammography on the dense breast tissue of young women. We recently reported results of a pilot proteomics study, using one‐dimensional polyacrylamide gel electrophoresis (1D‐PAGE) and mass spectrometry (MS) to investigate differences in milk proteins from women with and without BC. Here, we applied two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE) and MS to compare the protein pattern in milk from the breasts of a single woman who was diagnosed with BC in one breast 24 months after donating her milk. Statistically different gel spots were picked for protein digestion followed by nanoliquid chromatography tandem MS (nanoLC‐MS/MS) analysis. The upregulated proteins in BC versus control are alpha‐amylase, gelsolin isoform a precursor, alpha‐2‐glycoprotein 1 zinc isoform CRA_b partial, apoptosis‐inducing factor 2 and vitronectin. Several proteins were downregulated in the milk of the breast later diagnosed with cancer as compared to the milk from the healthy breast, including different isoforms of albumin, cholesterol esterase, different isoforms of lactoferrin, different proteins from the casein family and different isoforms of lysozyme. Results warrant further studies to determine the usefulness of these milk proteins for assessing risk and detecting occult disease. MS data is available via ProteomeXchange with identifier PXD009860.     

Protein-bound tyrosine oxidation,nitration and chlorination by-products assessed by ultraperformance liquid chromatography coupled to tandem mass spectrometry

Background

Free radicals cause alterations in cellular protein structure and function. Oxidized, nitrated, and chlorinated modifications of aromatic amino acids including phenylalanine and tyrosine are reliable biomarkers of oxidative stress and inflammation in clinical conditions.

Objective

To develop, validate and apply a rapid method for the quantification of known hallmarks of tyrosine oxidation, nitration and chlorination in plasma and tissue proteins providing a snapshot of the oxidative stress and inflammatory status of the organism and of target organs respectively.

Material and Methods

The extraction and clean up procedure entailed protein precipitation, followed by protein re-suspension and enzymatic digestion with pronase. An Ultra Performance Liquid Chromatography–tandem Mass Spectrometry (UPLC-MS/MS) method was developed to quantify protein released ortho-tyrosine (o-Tyr), meta-tyrosine (m-Tyr), 3-nitrotyrosine (3NO₂-Tyr) and 3-chlorotyrosine (3Cl-Tyr) as well as native phenylalanine (Phe) and tyrosine (p-Tyr) in plasma and tissue from a validated hypoxic newborn piglet experimental model.

Results

In plasma there was a significant increase in the 3NO₂-Tyr/p-Tyr ratio. On the other hand m-Tyr/Phe and 3Cl-Tyr/p-Tyr ratios were significantly increased in liver of hypoxic compared with normoxic animals. Although no significant differences were found in brain tissue, a clear tendency to increased ratios was observed under hypoxic conditions.

Conclusions

UPLC-MS/MS has proven suitable for the analysis of plasma and tissue samples from newborn piglets. The analysis of biomarkers of protein oxidation, nitration and chlorination will be applied in future studies aiming to provide a deeper insight into the mechanisms of oxidation-derived protein modification caused during neonatal asphyxia and resuscitation.