Luminescent bacteria-based sensing method for methylmercury specific determination

A bacterial biosensor method for the selective determination of a bioavailable organomercurial compound, methylmercury, is presented. A recombinant luminescent whole-cell bacterial strain responding to total mercury content in samples was used. The bacterial cells were freeze-dried and used as robust, reagent-like compounds, without batch-to-batch variations. In this bacteria-based sensing method, luciferase is used as a reporter, which requires no substrate additions, therefore allowing homogenous, real-time monitoring of the reporter gene expression. A noninducible, constitutively light-producing control bacterial strain was included in parallel for determining the overall cytotoxicity of the samples. The specificity of the total mercury sensor Escherichia coli MC1061 (pmerRBlux) bacterial resistance system toward methylmercury is due to a coexpressed specific enzyme, organomercurial lyase. This enzyme mediates the cleavage of the carbon–mercury bond of methylmercury to yield mercury ions, which induce the reporter genes and produce a self-luminescent cell. The selective analysis of methylmercury with the total mercury strain is achieved by specifically chelating the inorganic mercury species from the sample using an optimized concentration of EDTA as a chelating agent. After the treatment with the chelating agent, a cross-reactivity of 0.2% with ionic mercury was observed at nonphysiological ionic mercury concentrations (100 nM). The assay was optimized to be performed in 3 h but results can already be read after 1 h incubation. Total mercury strain E. coli MC1061 (pmerRBlux) has been shown to be highly sensitive and capable of determining methylmercury at a subnanomolar level in optimized assay conditions with a very high dynamic range of two decades. The limit of detection of 75 ng/l (300 pM) allows measurement of methylmercury even from natural samples.     

Microchip integrating magnetic nanoparticles for allergy diagnosis

We report on the development of a simple and easy to use microchip dedicated to allergy diagnosis. This microchip combines both the advantages of homogeneous immunoassays i.e. species diffusion and heterogeneous immunoassays i.e. easy separation and preconcentration steps. In vitro allergy diagnosis is based on specific Immunoglobulin E (IgE) quantitation, in that way we have developed and integrated magnetic core-shell nanoparticles (MCSNPs) as an IgE capture nanoplatform in a microdevice taking benefit from both their magnetic and colloidal properties. Integrating such immunosupport allows to perform the target analyte (IgE) capture in the colloidal phase thus increasing the analyte capture kinetics since both immunological partners are diffusing during the immune reaction. This colloidal approach improves 1000 times the analyte capture kinetics compared to conventional methods. Moreover, based on the MCSNPs' magnetic properties and on the magnetic chamber we have previously developed the MCSNPs and therefore the target can be confined and preconcentrated within the microdevice prior to the detection step. The MCSNPs preconcentration factor achieved was about 35,000 and allows to reach high sensitivity thus avoiding catalytic amplification during the detection step. The developed microchip offers many advantages: the analytical procedure was fully integrated on-chip, analyses were performed in short assay time (20 min), the sample and reagents consumption was reduced to few microlitres (5 μL) while a low limit of detection can be achieved (about 1 ng mL(-1)).     

Design of multitarget activity landscapes that capture hierarchical activity cliff distributions

An activity landscape model of a compound data set can be rationalized as a graphical representation that integrates molecular similarity and potency relationships. Activity landscape representations of different design are utilized to aid in the analysis of structure-activity relationships and the selection of informative compounds. Activity landscape models reported thus far focus on a single target (i.e., a single biological activity) or at most two targets, giving rise to selectivity landscapes. For compounds active against more than two targets, landscapes representing multitarget activities are difficult to conceptualize and have not yet been reported. Herein, we present a first activity landscape design that integrates compound potency relationships across multiple targets in a formally consistent manner. These multitarget activity landscapes are based on a general activity cliff classification scheme and are visualized in graph representations, where activity cliffs are represented as edges. Furthermore, the contributions of individual compounds to structure-activity relationship discontinuity across multiple targets are monitored. The methodology has been applied to derive multitarget activity landscapes for compound data sets active against different target families. The resulting landscapes identify single-, dual-, and triple-target activity cliffs and reveal the presence of hierarchical cliff distributions. From these multitarget activity landscapes, compounds forming complex activity cliffs can be readily selected.     

Preparation and characterization of pore-wall modification gradients generated on porous silicon photonic crystals using diazonium salts

One-dimensional photonic crystals (rugate filters) constructed from porous silicon were modified by the chemical hydrosilylation of terminal alkenes (decyl, 10-carboxydecyl, and 10-hydroxydecyl) in the presence of a concentration gradient of diazonium salt initiators. The concentration gradient was generated by vertically orienting the Si wafer containing the porous Si layer in an alkene solution and then introducing the diazonium salt at the bottom edge of the wafer. Slow diffusion of the salt led to a varying density of grafted alkene across the surface of the porous layer. The modified surfaces were end-capped with methyl groups by electrochemical grafting to impart improved stability and greater hydrophobicity. The surface modified with 10-carboxydecyl species was ionized by deprotonation of the carboxy groups to increase the hydrophilicity of this porous silicon surface. The pore-wall modification gradients were characterized using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and scanning electron microscopy (SEM) with energy-dispersive spectroscopy (EDS). The more hydrophilic portion of the gradient changes color when water infiltrates the porous nanostructure because of a shift in the stop band of the photonic crystal. The more hydrophobic portion of the gradient excludes water, although mixtures of water and ethanol will infiltrate this region, depending on the concentration of ethanol in the mixture. A simple visual sensor for small quantities of ethanol in water, capable of detecting ethanol concentrations of between 0 and 8% with a resolution of 1% is demonstrated.     

Bifunctional rhenium complexes for the catalytic transfer-hydrogenation reactions of ketones and imines

The silyloxycyclopentadienyl hydride complexes [Re(H)(NO)(PR(3))(C(5)H(4)OSiMe(2)tBu)] (R=iPr (3 a), Cy (3 b)) were obtained by the reaction of [Re(H)(Br)(NO)(PR(3))(2)] (R=iPr, Cy) with Li[C(5)H(4)OSiMe(2)tBu]. The ligand-metal bifunctional rhenium catalysts [Re(H)(NO)(PR(3))(C(5)H(4)OH)] (R=iPr (5 a), Cy (5 b)) were prepared from compounds 3 a and 3 b by silyl deprotection with TBAF and subsequent acidification of the intermediate salts [Re(H)(NO)(PR(3))(C(5)H(4)O)][NBu(4)] (R=iPr (4 a), Cy (4 b)) with NH(4)Br. In nonpolar solvents, compounds 5 a and 5 b formed an equilibrium with the isomerized trans-dihydride cyclopentadienone species [Re(H)(2)(NO)(PR(3))(C(5)H(4)O)] (6 a,b). Deuterium-labeling studies of compounds 5 a and 5 b with D(2) and D(2)O showed H/D exchange at the H(Re) and H(O) positions. Compounds 5 a and 5 b were active catalysts in the transfer hydrogenation reactions of ketones and imines with 2-propanol as both the solvent and H(2) source. The mechanism of the transfer hydrogenation and isomerization reactions was supported by DFT calculations, which suggested a secondary-coordination-sphere mechanism for the transfer hydrogenation of ketones.     

Reproducibility of serum protein profiling by systematic assessment using solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry

Protein profiling of human serum by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is potentially a new diagnostic tool for early detection of human diseases, including cancer. Sample preparation is a key issue in MALDI MS and the analysis of complex samples such as serum requires optimized, reproducible methods for handling and deposition of protein samples. Data acquisition in MALDI MS is also a critical issue, since heterogeneity of sample deposits leads to attenuation of ion signals in MALDI MS. In order to improve the robustness and reproducibility of MALDI MS for serum protein profiling we investigated a range of sample preparation techniques and developed a statistical method based on repeated analyses for evaluation of protein-profiling performance of MALDI MS. Two different solid-phase extraction (SPE) methods were investigated, namely custom-made microcolumns and commercially available magnetic beads. Using these two methods, nineteen different sample preparation methods for serum profiling by MALDI MS were systematically tested with regard to matrix selection, stationary phase, selectivity, and reproducibility. Microcolumns were tested with regard to chromatographic properties; reversed phase (C8, C18, SDB-XC), ion-exchange (anion, weak cation, mixed-phase (SDB-RPS)) and magnetic beads were tested with regard to chromatographic properties; reversed phase (C8) or affinity chromatography (Cu-IMAC). The reproducibility of each sample preparation method was determined by enumeration and analysis of protein signals that were detected in at least six out of nine spectra obtained by three triplicate analyses of one serum sample.A candidate for best overall performance as evaluated by the number of peaks generated and the reproducibility of mass spectra was found among the tested methods. Up to 418 reproducible peaks were detected in one cancer serum sample. These protein peaks can be part of a possible diagnostic profile, suggesting that this sample preparation method and data acquisition approach is suitable for large-scale analysis of serum samples for protein profiling.     

Surface immobilization methods for aptamer diagnostic applications

In this review we examine various methods for the immobilization of aptamers onto different substrates that can be utilized in a diverse array of analytical formats. In most cases, covalent linking to surfaces is preferred over physisorption, which is reflected in the bulk of the reports covered within this review. Conjugation of aptamers with appropriate linkers directly to gold films or particles is discussed first, followed by methods for conjugating aptamers to functionally modified surfaces. In many aptamer-based applications, silicates and silicon oxide surfaces provide an advantage over metallic substrates, and generally require surface modification prior to covalent attachment of the aptamers. Chemical protocols for covalent attachment of aptamers to functionalized surfaces are summarized in the review, showing common pathways employed for aptamer immobilization on different surfaces. Biocoatings, such as avidin or one of its derivatives, have been shown to be highly successful for immobilizing biotin-tethered aptamers on various surfaces (e.g., gold, silicates, polymers). There are also a few examples reported of aptamer immobilization on other novel substrates, such as quantum dots, carbon nanotubes, and carbohydrates. This review covers the literature on aptamer immobilization up to March 2007, including comparison of different linkers of varying size and chemical structure, 3′ versus 5′ attachment, and regeneration methods of aptamers on surfaces.     

Comparative analysis of the composition of the essential oil from the shoots,leaves and stems the wild Ledum palustre L. from Estonia

The aerial parts of Ledum palustre L. were collected near to Pudisoo River, Harju country, Estonia, in September 2007. The simultaneous distillation and extraction micro-method (SDE) was used to isolate the essential oil from the plant's samples. The capillary gas chromatographic (GC/FID) analysis was applied to the identification of oil components and determination of their content in the oil. The yield of oil from the leaves was 0.92%, from the stems, 0.24% and from the shoots, 0.78%. A total of 68 constituents, accounting for over 95% of the total oil yield, were identified in the oils.     

A matrix-assisted laser desorption/ionization tandem mass spectrometry method for direct screening of small molecule mixtures against an aminoglycoside kinase

Aminoglycoside phosphotransferase 3′IIIa (APH3′IIIa) is a bacterial enzyme involved in antibiotic resistance through phosphorylation of aminoglycosides, which can potentially be overcome by co-administration of an APH3′IIIa inhibitor with the antibiotic. Current assay methods for discovery of APH3′IIIa inhibitors suffer from low specificity and high false positive/negative hit rates. Here, we describe a method for screening APH3′IIIa inhibitors based on direct detection of kanamycin A phosphorylation using MALDI-MS/MS, which is more rapid than conventional assays and does not require secondary assays or sample cleanup. The MALDI-MS/MS assay operates at an ionic strength of 45 mM and co-factors can be utilized at near-physiological levels for optimal enzyme activity. Detection via MALDI-MS/MS allowed for improved reproducibility when compared to ESI-MS/MS. Furthermore, the use of MS/MS provided better signal-to-noise ratios relative to MS alone on the MALDI instrument. The assay was validated via generation of Z′-factors, with values of 0.78 and 0.56 in the absence and presence of 0.2% DMSO, respectively. The assay was used to screen a kinase directed library of >200 compounds, assayed as 21 mixtures of 10 compounds each. Five novel synthetic inhibitors were identified following mixture deconvolution. Inhibition constants were obtained for the aforementioned inhibitors using the MALDI-MS/MS assay, revealing several low to mid micromolar “hits”, and highlighting the quantitative nature of the assay.