Mixtures of sediment chemical contaminants at freshwater sampling sites across Europe with different contaminant burdens.

Extended chemical analyses of fluvial sediments were undertaken to establish the key pollutant pressures and mixtures present across nine European Union inland waterways. A wide range of chemical components and physical parameters were investigated including substances from the EU Priority List and Watch List. The data set was examined for key indicator compounds, however it was found that a wide range of pollution pressures were present in the different sediments including organic hydrocarbons, metal(loid)s, nutrients, polycyclic aromatic hydrocarbon (PAH), polychlorinated biphenyl (PCB) compounds, perfluoroalkyl and polyfluoroalkyl substances and pesticides, some of which exceeded regulatory guidance at different sampling points. The presence of such a wide range of compounds underpins the complex chemical composition of sediments that have acted as sinks for many decades absorbing contaminants from urban, industrial and agricultural sources. This dataset has been used to describe average overall toxicity of the sediments sampled, a calculation which was based on key components identified by Principal Component Analysis (PCA) and for those that had existing freshwater sediment regulatory values. A total of 33 components were used including PCBs, PAHs, metal(iod)s and pesticides. This analysis reflected the contamination of each site, with most indicating some level of toxicity during the sampling period. Watch List chemicals triclosan (TCS) and diclofenac (DIC) were also investigated; levels were relatively low, typically 10-100's ng L-1, however they were present at all sampling sites. The dataset is available as a resource for future chemical, and toxicological, sediment analysis comparisons.

Electrochemical quantification of d-glucose during the production of bioethanol from thermo-mechanically pre-treated wheat straw.

Mechanical pre-treatment (disc refining) of wheat straw, at both atmospheric and elevated pressure, is shown to be an efficient process to access fermentable monosaccharides, with the potential to integrate within the infrastructure of existing first-generation bioethanol plants. The mild, enzymatic degradation of this sustainable lignocellulosic biomass affords ca. 0.10-0.13 g/g (dry weight) of d-glucose quantifiable voltammetrically in real time, over a two hundred-fold range in experimental laboratory scales (25 mL to 5.0 L), with pressure disc refining of the wheat straw enabling almost twice the amount of d-glucose to be generated during the hydrolysis stage than experiments using atmospheric refining (0.06-0.09 g/g dry weight). Fermentation of the resulting hydrolysate affords 0.08-0.10 g/g (dry weight) of ethanol over similar scales, with ethanol productivity at ca. 37 mg/(L h). These results demonstrate that minimal cellulose decomposition occurs during pressure refining of wheat straw, in contrast to hemicellulose, and suggest that the development of green, mechanochemical processes for the scalable and cost-effective manufacture of second-generation bioethanol requires improved cellulose decomposition.

The inhibitory subunit of cardiac troponin (cTnI) is modified by arginine methylation in the human heart.

BACKGROUND: The inhibitory subunit of cardiac troponin (cTnI) is a gold standard cardiac biomarker and also an essential protein in cardiomyocyte excitation-contraction coupling. The interactions of cTnI with other proteins are fine-tuned by post-translational modification of cTnI. Mutations in cTnI can lead to hypertrophic cardiomyopathy. METHODS AND RESULTS: Here we report, for the first time, that cTnI is modified by arginine methylation in human myocardium. Using Western blot, we observed reduced levels of cTnI arginine methylation in human hypertrophic cardiomyopathy compared to dilated cardiomyopathy biopsies. Similarly, using a rat model of cardiac hypertrophy we observed reduced levels of cTnI arginine methylation compared to sham controls. Using mass spectrometry, we identified cTnI methylation sites at R74/R79 and R146/R148 in human cardiac samples. R146 and R148 lie at the boundary between the critical cTnI inhibitory and switch peptides; PRMT1 methylated an extended inhibitory peptide at R146 and R148 in vitro. Mutations at R145 that have been associated with hypertrophic cardiomyopathy hampered R146/R148 methylation by PRMT1 in vitro. H9c2 cardiac-like cells transfected with plasmids encoding for a methylation-deficient R146A/R148A cTnI protein developed cell hypertrophy, with a 32% increase in cell size after 72 h, compared to control cells. DISCUSSION: Our results provide evidence for a novel and significant cTnI post-translational modification. Our work opens the door to translational investigations of cTnI arginine methylation as a biomarker of disease, which can include e.g. cardiomyopathies, myocardial infarction and heart failure, and offers a novel way to investigate the effect of cTnI mutations in the inhibitory/switch peptides.

A Disposable Microfluidic Device with a Screen Printed Electrode for Mimicking Phase II Metabolism.

Human metabolism is investigated using several in vitro methods. However, the current methodologies are often expensive, tedious and complicated. Over the last decade, the combination of electrochemistry (EC) with mass spectrometry (MS) has a simpler and a cheaper alternative to mimic the human metabolism. This paper describes the development of a disposable microfluidic device with a screen-printed electrode (SPE) for monitoring phase II GSH reactions. The proposed chip has the potential to be used as a primary screening tool, thus complementing the current in vitro methods.

Preconcentration of milk proteins using octadecylated monolithic silica microchip.

Sample preparation is a bottleneck in systems for chemical analysis and it is a required step in order to remove interference and preconcentrate the target analytes. Much research in recent years has focused on porous monolithic materials since they are highly permeable to liquid flow and show high mass transfer compared with common packed beds. This study has focused on the use of a glass microchip containing an inorganic silica-based monolithic material modified with octadecyl groups for preconcentration of milk proteins from skimmed cows' milk that vary in molecular weight, hydrophobicity, and abundance. Comparison between the fabricated device and a commercial cartridge for the preconcentration of proteins in skimmed cows' milk showed the ability of the device to successfully enrich protein mixtures from the sample. The three replicate experiments showed that the RSD of the mass to charge ratio of milk proteins ranged from 0.01 to 0.46%. In addition, it was found that there were no significant differences between the observed and reported masses of the milk proteins and the relative percentage error of the molecular masses ranged between 0.03 and 0.90%. The fact that the small amounts of sample required and short sample preparation time suggest that this new microfluidic device may be a viable alternative to existing procedures for protein extraction from real samples.

Proteomic analysis of B-cell receptor signaling in chronic lymphocytic leukaemia reveals a possible role for kininogen.

CLL is an incurable disease with variable prognosis. The hyper reactivity of the B-cell receptor (BCR) to unknown antigen ligation plays a pivotal role in CLL-cell survival. We aimed to investigate the BCR signalling pathway using proteomics to identify novel proteins which may have clinical relevance in this disease. Three CLL samples were selected based upon BCR responsiveness, demonstrated by upregulation of phospho-ERK following in vitro stimulation. The differential expression of proteins, upon artificial stimulation of the BCR, was examined in these samples using two-dimensional gel electrophoresis in combination with mass spectrometry. Proteins of interest were subsequently examined using immunoblotting. Proteomic analysis revealed that kininogen, a critical protein of kinin-kallikrein system, was upregulated in all 3 clinical samples upon BCR stimulation. There are 2 forms of kininogen: HMWK and LMWK. The upregulation of LMWK upon BCR stimulation was confirmed by immunoblotting in all 3 of these samples. In a pilot series of 52 unselected CLL samples, 71% demonstrated basal LMWK expression. There was a trend towards shorter median survival in LMWK positive cases (147months versus 253months for LMWK negative cases; p=0.125). Kininogen may be a novel therapeutic target in CLL and the possible association with prognosis warrants further investigation. BIOLOGICAL SIGNIFICANCE: We have identified the upregulation of LMWK upon BCR stimulation of CLL samples. There is no previous published research to suggest a link between kininogen and normal B-cells or CLL cells. In 52 unselected CLL samples, 71% demonstrated basal LMWK expression. There was a trend towards shorter median survival in LMWK positive cases. The absence of LMWK protein expression on normal B-cells suggests that this could be a biomarker for CLL and further research should be undertaken.

Fabrication of an octadecylated silica monolith inside a glass microchip for protein enrichment.

Silica-based monolithic materials have shown great promise for use as sorbent materials due to their large surface area and bimodal pore size distribution. In this paper, a new process for the fabrication of a silica-based monolith inside a glass microchip and its modification with octadecylsilyl ligands was successfully developed for use in the microchip-based solid phase extraction of proteins. Monolithic porous silica without cracks was prepared by a sol-gel process, followed by placement of the monolithic silica disk inside the extraction chamber in the base plate of the microchip. The two plates of the glass microchip were then thermally bonded at 575 °C for 3 hours. The silica-based monolith was not affected by the thermal bonding of the two plates of the microchip. This process completely avoids the problem of shrinkage in the silica skeleton during preparation. The monolithic silica disk inside the glass microchip was subsequently modified with octadecylsilyl (C(18)) moieties for increased protein binding capacity. The performance of the microchip was evaluated using the extraction of six proteins varying in molecular weight and isoelectric point, namely insulin, cytochrome C, lysozyme, myoglobin, ß-lactoglobulin, and hemoglobin at a concentration of 60 µM. The standard protein was mixed with a double concentration of the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS). The results show that the octadecylated silica monolith was permeable, has the ability to remove impurities, and achieved a high extraction recovery of the proteins (94.8-99.7%) compared with conventional octadecylated silica particles (48.3-91.3%). The chip-to-chip reproducibility was assessed by calculating the relative standard deviations (RSDs) for the six proteins during extraction. The intra-batch and inter-batch RSDs were in the range of 2.0-4.5% and 2.9-6.4%, respectively. This new microfluidic device for protein extraction may find an application in the area of proteomic research.

Design and evaluation of synthetic silica-based monolithic materials in shrinkable tube for efficient protein extraction.

Sample pretreatment is a required step in proteomics in order to remove interferences and preconcentrate the samples. Much research in recent years has focused on porous monolithic materials since they are highly permeable to liquid flow and show high mass transport compared with more common packed beds. These features are due to the micro-structure within the monolithic silica column which contains both macropores that reduce the back pressure, and mesopores that give good interaction with analytes. The aim of this work was to fabricate a continuous porous silica monolithic rod inside a heat shrinkable tube and to compare this with the same material whose surface has been modified with a C(18) phase, in order to use them for preconcentration/extraction of proteins. The performance of the silica-based monolithic rod was evaluated using eight proteins; insulin, cytochrome C, lysozyme, myoglobin, ß-lactoglobulin, ovalbumin, hemoglobin, and bovine serum albumin at a concentration of 60 µM. The results show that recovery of the proteins was achieved by both columns with variable yields; however, the C(18) modified silica monolith gave higher recoveries (92.7 to 109.7%) than the non-modified silica monolith (25.5 to 97.9%). Both silica monoliths can be used with very low back pressure indicating a promising approach for future fabrication of the silica monolith inside a microfluidic device for the extraction of proteins from biological media.

Detection of nitric oxide in tissue samples by ESI-MS.

A novel method to determine nitric oxide (NO) in biological tissue samples with minimal interference from the cellular detritus is described. Methylpiperazinobenzenediamine, consisting of an o-phenylenediamine and a methyl piperazine group, was chosen as a probe for the detection of NO by mass spectrometry (MS) in biological tissue samples. The o-phenylenediamine group reacts with NO to form a characteristic benzotriazole. The product was identified using electrospray ionization mass spectrometry (ESI-MS) and the method validated within the range of 95-1900 nM. NO levels associated with tissue biopsies (approximately 10 mg) from rat vasculature and intestine tissue biopsies have been successfully determined. The different rates of NO generated from tissue samples under hypoxic and normoxic conditions have been studied by this simple and sensitive method.

Proteomic identification of putative biomarkers of radiotherapy resistance: a possible role for the 26S proteasome?

PURPOSE: We aimed to identify putative predictive protein biomarkers of radioresistance. EXPERIMENTAL DESIGN: Three breast cancer cell lines (MCF7, MDA-MB-231, and T47D) were used as in vitro models to study radioresistance. Inherent radiosensitivities were examined using a clonogenic survival assay. It was revealed that each cell line differed in their response to radiotherapy. These parental breast cancer cell lines were used to establish novel derivatives (MCF7RR, MDA-MB-231RR, and T47DRR) displaying significant resistance to ionizing radiation. Derivative cells were compared with parental cells to identify putative biomarkers associated with the radioresistant phenotype. To identify these biomarkers, complementary proteomic screening approaches were exploited encompassing two-dimensional gel electrophoresis in combination with mass spectrometry, liquid chromatography coupled with tandem mass spectrometry and quantitative proteomics using iTRAQ technology. RESULTS: A large number of potential biomarkers were identified, and several of these were confirmed using Western blot analysis. In particular, a decrease in the expression of the 26S proteasome was found in all radioresistant derivatives when compared with the respective parent cells. Decreased expression of this target was also found to be associated with radioresistant laryngeal tumors (P = .05) in a small pilot immunohistochemical study. CONCLUSIONS: These findings suggest that the 26S proteasome may provide a general predictive biomarker for radiotherapy outcome.

Identification, release and olfactory detection of bile salts in the intestinal fluid of the Senegalese sole (Solea senegalensis).

Olfactory sensitivity to bile salts is wide-spread in teleosts; however, which bile salts are released in sufficient quantities to be detected is unclear. The current study identified bile salts in the intestinal and bile fluids of Solea senegalensis by mass spectrometry-liquid chromatography and assessed their olfactory potency by the electro-olfactogram. The main bile salts identified in the bile were taurocholic acid (342 mM) and taurolithocholic acid (271 mM) plus a third, unidentified, bile salt of 532.3 Da. These three were also present in the intestinal fluid (taurocholic acid, 4.13 mM; taurolithocholic acid, 0.4 mM). In sole-conditioned water, only taurocholic acid (0.31 microM) was released in sufficient quantities to be measured (release rate: 24 nmol kg(-1) min(-1)). Sole had high olfactory sensitivity to taurocholic acid but not to taurolithocholic acid. Furthermore, olfactory sensitivity was higher in the upper (right) olfactory epithelium than the lower (left). These two bile acids contribute about 40% of the olfactory potency of intestinal fluid and account for the difference in potency at the two epithelia. Taurocholic acid (but not taurolithocholic acid), and possibly other types of bile acid not tested, could be used as chemical signals and the upper olfactory epithelium is specialised for their detection.

The proteomic analysis of cisplatin resistance in breast cancer cells.

Resistance to cisplatin represents a major obstacle in the effective management of many cancers, including metastatic breast cancer. We aimed to gain further understanding of the mechanisms underlying development of cisplatin resistance using an in vitro cell line model. The MCF-7 breast cancer cell line and a novel derivative displaying significant resistance to cisplatin were analyzed using two-dimensional gel electrophoresis. The protein profiles were compared and 15 differentially expressed proteins were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The downregulation of beta-tubulin type 3, cytokeratin 17, tropomyosin 1-alpha, peroxiredoxin 4, heat shock 27-kDa protein 1, glutathione-S-transferase mu 3, ribosomal protein P0, isocitrate dehydrogenase 3, and peptidyl-prolyl isomerase A isoform 1 was associated with cisplatin-resistant cells. In contrast, the expression of hydroxyprostaglandin dehydrogenase 15-(NAD), matrix metalloproteinase 9, heterogeneous nuclear ribonucleoprotein A3, proteasome beta 1 subunit, electron transfer flavoprotein beta-polypeptide isoform 1, and peptidyl-propyl isomerase B precursor was upregulated in cisplatin-resistant cells. The downregulation (at least twofold) of glutathione-S-transferase mu 3, cytokeratin 17, and peroxiredoxin 4 was confirmed by Western blotting. We have identified alterations in the expression levels of several proteins that may be associated with cisplatin resistance and are candidates for further validation in clinical samples.

Cancer proteomics and its application to discovery of therapy response markers in human cancer.

The administration of chemotherapy either alone or in combination with radiotherapy is an important factor in reducing the mortality and morbidity of cancer patients. Resistance to both chemotherapy and radiotherapy represents a major obstacle to a successful outcome. The identification of novel biomarkers that can be used to predict treatment response would allow therapy to be tailored on an individual patient basis. Although the mechanisms are unclear, it is accepted that development of therapy resistance is a multifactorial phenomenon involving alterations in several cellular pathways. Proteome analysis methods are powerful tools for identifying factors associated with resistance to anticancer therapy because they facilitate the simultaneous analysis of whole proteomes. The current review describes the plethora of existing proteomic approaches and details the studies that have identified biomarkers that may be useful in the prediction of clinical response to anticancer therapy.

Isothiocyanato boron dipyrromethenes--the first BODIPY analogues of fluorescein isothiocyanate.

Two boron complexes of 5-phenyldipyrromethenes bearing isothiocyanate groups on the phenyl ring have been synthesized for the first time. The utility of these new fluorescence probes for labeling biologically relevant proteins is demonstrated on two monoclonal antibodies that bind to antigens overexpressed on cancer cells. Spectral comparison of the two structures reveals significant photophysical differences, including bathochromically shifted excitation and emission bands, increased molar absorptivity and a large increase in fluorescence quantum yield of approximately 10 times. Differences in photophysical parameters are linked to hindered rotation of the phenyl ring in one of the probes.

Efficient protein digestion with peptide separation in a micro-device interfaced to electrospray mass spectrometry.

A highly efficient protein digestion device has been fabricated using commercially available immobilized trypsin on agarose beads, packed into a silica capillary and connected either directly to an electrospray mass spectrometer via a 'microtight T' connector, from which aqueous acetic acid (0.2%) was pumped, or via a monolithic column connected to the mass spectrometer ion source. Six proteins with molecular mass ranging from 2848 to 77703 Da were digested completely using this system. In the second set of experiments a short monolithic separation column was placed after the immobilized trypsin capillary and partial separation of the generated peptides was obtained. The detection limits were increased from the micromol to pmol range by utilization of this separation column. Gradient elution, using a binary HPLC pump and a flow splitter, was used to optimize the peptide separation. This provided significantly enhanced resolution of the tryptic peptides but increased the analysis time to 30 minutes.

Quantitative analysis of the major constituents of St John's wort with HPLC-ESI-MS.

A method was developed to profile the major constituents of St John's wort extracts using high-performance liquid chromatography-electrospray mass spectrometry (HPLC-ESI-MS). The objective was to simultaneously separate, identify and quantify hyperforin, hypericin, pseudohypericin, rutin, hyperoside, isoquercetrin, quercitrin and chlorogenic acid using HPLC-MS. Quantification was performed using an external standardisation method with reference standards. The method consisted of two protocols: one for the analysis of flavonoids and glycosides and the other for the analysis of the more lipophilic hypericins and hyperforin. Both protocols used a reverse phase Luna phenyl hexyl column. The separation of the flavonoids and glycosides was achieved within 35 min and that of the hypericins and hyperforin within 9 min. The linear response range in ESI-MS was established for each compound and all had linear regression coefficient values greater than 0.97. Both protocols proved to be very specific for the constituents analysed. MS analysis showed no other signals within the analyte peaks. The method was robust and applicable to alcoholic tinctures, tablet/capsule extracts in various solvents and herb extracts. The method was applied to evaluate the phytopharmaceutical quality of St John's wort preparations available in the UK in order to test the method and investigate if they contain at least the main constituents and at what concentrations.

Conjugated linoleic acid isomers and trans fatty acids inhibit fatty acid transport in hepatoma 7288CTC and inguinal fat pads in Buffalo rats.

Conjugated linoleic acid (CLA) and some trans fatty acids (FA) decrease tumor growth and alter tumor and host lipid uptake and storage. The goal of this study was to test the hypothesis that the acute inhibitory effects of CLA isomers and trans FAs on FA transport in tumors and white adipose tissue are mediated via an inhibitory G-protein coupled (GPC), FFA receptor (FFAR). Experiments were performed in hepatoma 7288CTC and inguinal fat pads in Buffalo rats during perfusion in situ. CLA isomers and trans FAs (0.03-0.4 mmol/L, in plasma) were added to the arterial blood, and FA uptake or release was measured by arterial minus venous difference. In hepatoma 7288CTC, the CLA isomers, t10,c12-CLA > (+/-)-9-HODE [13-(S)-hydroxyoctadecadienoic acid] > t9,t11-CLA, and the trans FAs, linolelaidic = vaccenic > elaidic, decreased cAMP content and inhibited FA uptake, 13(S)-HODE release, extracellular signal-regulated kinase p44/p42 phosphorylation, and [(3)H]thymidine incorporation. Other CLA isomers, c9,t11-CLA, 13-(S)-HODE, c9,c11-CLA, and c11,t13-CLA, had no effect. In inguinal fat pads, FA transport was inhibited by t10,c12-CLA = linolelaidic acid > trans vaccenic acid, whereas c9,t11-CLA had no effect. In both hepatoma 7288CTC and inguinal fat pad, addition of either pertussis toxin or 8-Br-cAMP to the arterial blood reversed the inhibitions of FA transport. These results support the idea that an inhibitory GPC FFAR reduces cAMP and controls FA transport by CLA isomers and trans FAs. Ligand activity is conferred by the presence of a trans double bond proximal to the carboxyl group.

The sesame seed oil constituent, sesamol, induces growth arrest and apoptosis of cancer and cardiovascular cells.

Sesamol is a potent inhibitor of fungal fatty acid biosynthesis. This effect is apparently due to inhibition of malic enzyme and the supply of NADPH that is required for this biosynthetic pathway. It is the ability of sesamol to reduce the synthesis of the coenzyme, NADPH, that makes it attractive for use in studying the effect of oxidants on tumor and vascular endothelial cells. By conducting preliminary studies on the effect of sesamol alone, it was clear that the compound demonstrated marked cytotoxicity. This paper describes the experiments performed.