Colon extended physiologically based extraction test (CE-PBET) increases bioaccessibility of soil-bound PAH

Assessment of the risk to human health posed by contaminated land may be seriously overestimated if reliant on total pollutant concentration. In vitro extraction tests, such as the physiologically based extraction test (PBET), imitate the physicochemical conditions of the human gastro-intestinal tract and offer a more practicable alternative for routine testing purposes. However, even though passage through the colon accounts for approximately 80% of the transit time through the human digestive tract and the typical contents of the colon in vivo are a carbohydrate-rich aqueous medium with the potential to promote desorption of organic pollutants, PBET comprises stomach and small intestine compartments only. Through addition of an eight-hour colon compartment to PBET and use of a carbohydrate-rich fed-state medium we demonstrated that colon-extended PBET (CE-PBET) in- creased assessments of soil-bound PAH bioaccessibility by up to 50% in laboratory soils and a factor of 4 in field soils. We attribute this increased bioaccessibility to a combination of the additional extraction time and the presence of carbohydrates in the colon compartment, both of which favor PAH desorption from soil. We propose that future assessments of the bioaccessibility of organic pollutants in soils using physiologically based extraction tests should have a colon compartment as in CE-PBET.

Evaluating the effects of tannins on the extent and rate of in vitro measured gas and methane production using the Automated Pressure Evaluation System (APES)

An in vitro study was conducted to investigate the effect of tannins on the extent and rate of gas and methane production, using an automated pressure evaluation system (APES). In this study three condensed tannins (CT; quebracho, grape seed and green tea tannins) and four hydrolysable tannins (HT; tara, valonea, myrabolan and chestnut tannins) were evaluated, with lucerne as a control substrate. CT and HT were characterised by matrix assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF-MS). Tannins were added to the substrate at an effective concentration of 100 g/kg either with or without polyethylene glycol (PEG6000), and incubated for 72 h in pooled, buffered rumen liquid from four lactating dairy cows. After inoculation, fermentation bottles were immediately connected to the APES to measure total cumulative gas production (GP). During the incubation, 11 gas samples were collected from each bottle at 0, 1, 4, 7, 11, 15, 23, 30, 46, 52 and 72 h of incubation and analysed for methane. A modified Michaelis-Menten model was fitted to the methane concentration patterns and model estimates were used to calculate the total cumulative methane production (GPCH4). GP and GPCH4 curves were fitted using a modified monophasic Michaelis-Menten model. Addition of quebracho reduced GP (P=0.002), whilst the other tannins did not affect GP. Addition of PEG increased GP for quebracho (P=0.003), valonea (P=0.058) and grape seed tannins (P=0.071), suggesting that these tannins either inhibited or tended to inhibit fermentation. Addition of quebracho and grape seed tannins also reduced (P≤0.012) the maximum rate of gas production, indicating that microbial activity was affected. Quebracho, valonea, myrabolan and grape seed decreased (P≤0.003) GPCH4 and the maximum rate (0.001≤ P≤ 0.102) of CH4 production. Addition of chestnut, green tea and tara tannins did not affect total gas nor methane production. Valonea and myrabolan tannins have most promise for reducing methane production as they had only a minor impact on gas production.

BET surface area of carbonaceous adsorbents: verification using geometric considerations and GCMC simulations on virtual porous carbon models

The applicability of BET model for calculation of surface area of activated carbons is checked by using molecular simulations. By calculation of geometric surface areas for the simple model carbon slit-like pore with the increasing width, and by comparison of the obtained values with those for the same systems from the VEGA ZZ package (adsorbate-accessible molecular surface), it is shown that the latter methods provide correct values. For the system where a monolayer inside a pore is created the ASA approach (GCMC, Ar, T = 87 K) underestimates the value of surface area for micropores (especially, where only one layer is observed and/or two layers of adsorbed Ar are formed). Therefore, we propose the modification of this method based on searching the relationship between the pore diameter and the number of layers in a pore. Finally BET; original andmodified ASA; and A, B and C-point surface areas are calculated for a series of virtual porous carbons using simulated Ar adsorption isotherms (GCMC and T = 87 K). The comparison of results shows that the BET method underestimates and not, as it was usually postulated, overestimates the surface areas of microporous carbons.

Testing isotherm models and recovering empirical relationships for adsorption in microporous carbons using virtual carbon models and grand canonical Monte Carlo simulations

Using the plausible model of activated carbon proposed by Harris and co-workers and grand canonical Monte Carlo simulations, we study the applicability of standard methods for describing adsorption data on microporous carbons widely used in adsorption science. Two carbon structures are studied, one with a small distribution of micropores in the range up to 1 nm, and the other with micropores covering a wide range of porosity. For both structures, adsorption isotherms of noble gases (from Ne to Xe), carbon tetrachloride and benzene are simulated. The data obtained are considered in terms of Dubinin-Radushkevich plots. Moreover, for benzene and carbon tetrachloride the temperature invariance of the characteristic curve is also studied. We show that using simulated data some empirical relationships obtained from experiment can be successfully recovered. Next we test the applicability of Dubinin's related models including the Dubinin-Izotova, Dubinin-Radushkevich-Stoeckli, and Jaroniec-Choma equations. The results obtained demonstrate the limits and applications of the models studied in the field of carbon porosity characterization.

Hyper-parallel tempering Monte Carlo simulations of Ar adsorption in new models of microporous non-graphitizing activated carbon: effect of microporosity

The adsorption of gases on microporous carbons is still poorly understood, partly because the structure of these carbons is not well known. Here, a model of microporous carbons based on fullerene- like fragments is used as the basis for a theoretical study of Ar adsorption on carbon. First, a simulation box was constructed, containing a plausible arrangement of carbon fragments. Next, using a new Monte Carlo simulation algorithm, two types of carbon fragments were gradually placed into the initial structure to increase its microporosity. Thirty six different microporous carbon structures were generated in this way. Using the method proposed recently by Bhattacharya and Gubbins ( BG), the micropore size distributions of the obtained carbon models and the average micropore diameters were calculated. For ten chosen structures, Ar adsorption isotherms ( 87 K) were simulated via the hyper- parallel tempering Monte Carlo simulation method. The isotherms obtained in this way were described by widely applied methods of microporous carbon characterisation, i. e. Nguyen and Do, Horvath - Kawazoe, high- resolution alpha(a)s plots, adsorption potential distributions and the Dubinin - Astakhov ( DA) equation. From simulated isotherms described by the DA equation, the average micropore diameters were calculated using empirical relationships proposed by different authors and they were compared with those from the BG method.

Purified phenolics from hydrothermal treatments of biomass: ability to protect sunflower bulk oil and model food emulsions from oxidation

The phenolic fractions released during hydrothermal treatment of selected feedstocks (corn cobs, eucalypt wood chips, almond shells, chestnut burs, and white grape pomace) were selectively recovered by extraction with ethyl acetate and washed with ethanol/water solutions. The crude extracts were purified by a relatively simple adsorption technique using a commercial polymeric, nonionic resin. Utilization of 96% ethanol as eluting agent resulted in 47.0-72.6% phenolic desorption, yielding refined products containing 49-60% w/w phenolics (corresponding to 30-58% enrichment with respect to the crude extracts). The refined extracts produced from grape pomace and from chestnut burs were suitable for protecting bulk oil and oil-in-water and water-in-oil emulsions. A synergistic action with bovine serum albumin in the emulsions was observed.

Early detection of ovarian cancer in samples pre-diagnosis using CA125 and MALDI-MS peaks

Aim: A nested case-control discovery study was undertaken 10 test whether information within the serum peptidome can improve on the utility of CA125 for early ovarian cancer detection. Materials and Methods: High-throughput matrix-assisted laser desorption ionisation mass spectrometry (MALDI-MS) was used to profile 295 serum samples from women pre-dating their ovarian cancer diagnosis and from 585 matched control samples. Classification rules incorporating CA125 and MS peak intensities were tested for discriminating ability. Results: Two peaks were found which in combination with CA125 discriminated cases from controls up to 15 and 11 months before diagnosis, respectively, and earlier than using CA125 alone. One peak was identified as connective tissue-activating peptide III (CTAPIII), whilst the other was putatively identified as platelet factor 4 (PF4). ELISA data supported the down-regulation of PF4 in early cancer cases. Conclusion: Serum peptide information with CA125 improves lead time for early detection of ovarian cancer. The candidate markers are platelet-derived chemokines, suggesting a link between platelet function and tumour development.

Mass spectrometry imaging of glucosinolates in arabidopsis flowers and siliques

Glucosinolates are multi-functional plant secondary metabolites which play a vital role in plant defence and are, as dietary compounds, important to human health and livestock well-being. Knowledge of the tissue-specific regulation of their biosynthesis and accumulation is essential for plant breeding programs. Here, we report that in Arabidopsis thaliana, glucosinolates are accumulated differentially in specific cells of reproductive organs. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), distribution patterns of three selected compounds, 4-methylsulfinylbutyl (glucoraphanin), indol-3-ylmethyl (glucobrassicin), and 4-benzoyloxybutyl glucosinolates, were mapped in the tissues of whole flower buds, sepals and siliques. The results show that tissue localization patterns of aliphatic glucosinolate glucoraphanin and 4-benzoyloxybutyl glucosinolate were similar, but indole glucosinolate glucobrassicin had different localisation, indicating a possible difference in function. The high resolution images obtained by a complementary approach, cryo-SEM Energy Dispersive X-ray analysis (cryo-SEM-EDX), confirmed increased concentration of sulphur in areas with elevated amounts of glucosinolates, and allowed identifying the cell types implicated in accumulation of glucosinolates. High concentration of sulphur was found in S-cells adjacent to the phloem in pedicels and siliques, indicating the presence of glucosinolates. Moreover, both MALDI MSI and cryo-SEM-EDX analyses indicated accumulation of glucosinolates in cells on the outer surface of the sepals, suggesting that a layer of glucosinolate-accumulating epidermal cells protects the whole of the developing flower, in addition to the S-cells, which protect the phloem. This research demonstrates the high potential of MALDI MSI for understanding the cell-specific compartmentation of plant metabolites and its regulation.

Liquid AP-UV-MALDI enables stable ion yields of multiply charged peptide and protein ions for sensitive analysis by mass spectrometry

In biological mass spectrometry (MS), two ionization techniques are predominantly employed for the analysis of larger biomolecules, such as polypeptides. These are nano-electrospray ionization [1, 2] (nanoESI) and matrix-assisted laser desorption/ionization [3, 4] (MALDI). Both techniques are considered to be “soft”, allowing the desorption and ionization of intact molecular analyte species and thus their successful mass-spectrometric analysis. One of the main differences between these two ionization techniques lies in their ability to produce multiply charged ions. MALDI typically generates singly charged peptide ions whereas nanoESI easily provides multiply charged ions, even for peptides as low as 1000 Da in mass. The production of highly charged ions is desirable as this allows the use of mass analyzers, such as ion traps (including orbitraps) and hybrid quadrupole instruments, which typically offer only a limited m/z range (< 2000–4000). It also enables more informative fragmentation spectra using techniques such as collisioninduced dissociation (CID) and electron capture/transfer dissociation (ECD/ETD) in combination with tandem MS (MS/MS). [5, 6] Thus, there is a clear advantage of using ESI in research areas where peptide sequencing, or in general, the structural elucidation of biomolecules by MS/MS is required. Nonetheless, MALDI with its higher tolerance to contaminants and additives, ease-of-operation, potential for highspeed and automated sample preparation and analysis as well as its MS imaging capabilities makes it an ionization technique that can cover bioanalytical areas for which ESI is less suitable. [7, 8] If these strengths could be combined with the analytical power of multiply charged ions, new instrumental configurations and large-scale proteomic analyses based on MALDI MS(/MS) would become feasible.

Is there sufficient 'sink' in current bioaccessibility determinations of organic pollutants in soils?

Bioaccessibility tests can be used to improve contaminated land risk assessments. For organic pollutants a ‘sink’ is required within these tests to better mimic their desorption under the physiological conditions prevailing in the intestinal tract, where a steep diffusion gradient for the removal of organic pollutants from the soil matrix would exist. This is currently ignored in most PBET systems. By combining the CEPBET bioaccessibility test with an infinite sink, the removal of PAH from spiked solutions was monitored. Less than 10% of spiked PAH remained in the stomach media after 1 h, 10% by 4 h in the small intestine compartment and c.15% after 16 h in the colon. The addition of the infinite sink increased bioaccessibility estimates for field soils by a factor of 1.2–2.8, confirming its importance for robust PBET tests. TOC or BC were not the only factors controlling desorption of the PAH from the soils.

AP-UV-MALDI mit flüssigen Matrizes: stabile Ionenausbeuten von mehrfach geladenen Peptid- und Proteinionen für die empfindliche Massenspektrometrie

In der biologischen Massenspektrometrie (MS) werden überwiegend zwei Ionisationstechniken für die Analyse von grçßeren Biomolekfürlen wie Polypeptiden eingesetzt. Dies sind die Nano-Elektrospray-Ionisation[1,2] (nanoESI) und die matrixunterstfürtzte Laserdesorption/-ionisation[3, 4] (MALDI). Beide Techniken werden als „sanft“ bezeichnet, weil sie die Desorption und Ionisation von intakten Analytmolekfürlen und damit ihre erfolgreiche massenspektrometrische Analyse erlauben. Einer der wichtigsten Unterschiede zwischen diesen beiden Ionisationstechniken liegt in ihrer F�higkeit, mehrfach geladene Ionen zu erzeugen. MALDI erzeugt typischerweise einfach geladene Peptidionen, w�hrend nano- ESI leicht mehrfach geladene Ionen produziert, sogar für Peptide mit einer Masse von weniger als 1000 Da. Die Erzeugung von hoch geladenen Ionen ist wünschenswert, da dies die Verwendung von Massenanalysatoren wie Ionenfallen (inkl. Orbitraps) und Hybrid-Quadrupolinstrumenten ermçglicht, die typischerweise nur einen begrenzten m/z- Bereich (<2000–4000) bieten. Hohe Ladungszust�nde ermçglichen auch die Aufnahme von informativeren Fragmentionenspektren, wenn Methoden wie die kollisionsinduzierte Dissoziation (CID), die Elektroneneinfang-Dissoziation (ECD) und die Elektronentransfer-Dissoziation (ETD) in Kombination mit der Tandem-MS (MS/MS) verwendet werden.

MALDI MS profiling of post-DRE urine samples highlights the potential of b-Microseminoprotein as a marker for prostatic diseases

BACKGROUND. To use spectra acquired by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) from pre- and post-digital rectal examination (DRE) urine samples to search for discriminating peaks that can adequately distinguish between benign and malignant prostate conditions, and identify the peaks’ underlying biomolecules. METHODS. Twenty-five participants with prostate cancer (PCa) and 27 participants with a variety of benign prostatic conditions as confirmed by a 10-core tissue biopsy were included. Pre- and post-DRE urine samples were prepared for MALDI MS profiling using an automated clean-up procedure. Following mass spectra collection and processing, peak mass and intensity were extracted and subjected to statistical analysis to identify peaks capable of distinguishing between benign and cancer. Logistic regression was used to combine markers to create a sensitive and specific test. RESULTS. A peak at m/z 10,760 was identified as b-microseminoprotein (b-MSMB) and found to be statistically lower in urine from PCa participants using the peak’s average areas. By combining serum prostate-specific antigen (PSA) levels with MALDI MS-measured b-MSMB levels, optimum threshold values obtained from Receiver Operator characteristics curves gave an increased sensitivity of 96% at a specificity of 26%. CONCLUSIONS. These results demonstrate that with a simple sample clean-up followed by MALDI MS profiling, significant differences of MSMB abundance were found in post-DRE urine samples. In combination with PSA serum levels, obtained from a classic clinical assay led to high classification accuracy for PCa in the studied sample set. Our results need to be validated in a larger multicenter prospective randomized clinical trial.

MALDI mass spectrometry in prostate cancer biomarker discovery

Matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry (MS) is a highly versatile and sensitive analytical technique, which is known for its soft ionisation of biomolecules such as peptides and proteins. Generally, MALDI MS analysis requires little sample preparation, and in some cases like MS profiling it can be automated through the use of robotic liquid-handling systems. For more than a decade now, MALDI MS has been extensively utilised in the search for biomarkers that could aid clinicians in diagnosis, prognosis, and treatment decision making. This review examines the various MALDI-based MS techniques like MS imaging, MS profiling and proteomics in-depth analysis where MALDI MS follows fractionation and separation methods such as gel electrophoresis, and how these have contributed to prostate cancer biomarker research. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.

Adsorption of organic molecules at the TiO2(110) surface: the effect of van der Waals interactions

Understanding the interaction of organic molecules with TiO2 surfaces is important for a wide range of technological applications. While density functional theory (DFT) calculations can provide valuable insight about these interactions, traditional DFT approaches with local exchange-correlation functionals suffer from a poor description of non-bonding van der Waals (vdW) interactions. We examine here the contribution of vdW forces to the interaction of small organic molecules (methane, methanol, formic acid and glycine) with the TiO2 (110) surface, based on DFT calculations with the optB88-vdW functional. The adsorption geometries and energies at different configurations were also obtained in the standard generalized gradient approximation (GGA-PBE) for comparison. We find that the optB88-vdW consistently gives shorter surface adsorbate-to-surface distances and slightly stronger interactions than PBE for the weak (physisorbed) modes of adsorption. In the case of strongly adsorbed (chemisorbed) molecules both functionals give similar results for the adsorption geometries, and also similar values of the relative energies between different chemisorption modes for each molecule. In particular both functionals predict that dissociative adsorption is more favourable than molecular adsorption for methanol, formic acid and glycine, in general agreement with experiment. The dissociation energies obtained from both functionals are also very similar, indicating that vdW interactions do not affect the thermodynamics of surface deprotonation. However, the optB88-vdW always predicts stronger adsorption than PBE. The comparison of the methanol adsorption energies with values obtained from a Redhead analysis of temperature programmed desorption data suggests that optB88-vdW significantly overestimates the adsorption strength, although we warn about the uncertainties involved in such comparisons.

Surface chemistry of alanine on Cu{111}: Adsorption geometry and temperature dependence

Adsorption of l-alanine on the Cu{111} single crystal surface was investigated as a model system for interactions between small chiral modifier molecules and close-packed metal surfaces. Synchrotron-based X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy are used to determine the chemical state, bond coordination and out-of-plane orientation of the molecule on the surface. Alanine adsorbs in its anionic form at room temperature, whilst at low temperature the overlayer consists of anionic and zwitterionic molecules. NEXAFS spectra exhibit a strong angular dependence of the π ⁎ resonance associated with the carboxylate group, which allows determining the tilt angle of this group with respect to the surface plane (48° ± 2°) at room temperature. Low-energy electron diffraction (LEED) shows a p(2√13x2√13)R13° superstructure with only one domain, which breaks the mirror symmetry of the substrate and, thus, induces global chirality to the surface. Temperature-programmed XPS (TP-XPS) and temperature-programmed desorption (TPD) experiments indicate that the zwitterionic form converts into the anionic species (alaninate) at 293 K. The latter desorbs/decomposes between 435 K and 445 K.