Defining near-surface groundwater flow regimes in the semi-arid glaciated plains of North America

The dominant transport mechanisms controlling the migration of contaminants in geologic media are advection and molecular diffusion. To date, defining which transport mechanism dominates in saturated, non-lithified sediments has been difficult. Here, we illustrate the value of using detailed profiles of the conservative stable isotope values of water (δ²H and δ¹⁸O) to identify the dominant processes of contaminant transport (i.e. diffusion- or advection-dominated transport) in near-surface, non-lithified, saturated sediments of the Interior Plains of North America (IPNA). The approach presented uses detailed δ¹⁸O analyses of glacial till, glaciolacustrine clay, and fluvial sand core samples taken to depths of 11–50 m below ground at 22 sites across the IPNA to show whether transport in the fractured and oxidized sediments is dominated by advection or diffusion. Diffusion is by far the dominant transport mechanism in fine-textured lacustrine and glacial till sediments, but lateral advection dominates transport in sand-rich sediments and some oxidized, fine-textured lacustrine and glacial till sediments. The approach presented has a number of applications, including identifying dominant transport mechanisms in geomedia and potential protective barriers for underlying aquifers or surface waters, constraining groundwater transport models, and selecting optimum locations for monitoring wells. These findings should be applicable to most glaciated regions of the world that are composed of similar hydrogeologic units (i.e. low K clay till layers overlain by higher K coarse-textured aquifers or weathered clay till layers) and may also be applicable to non-glaciated regions exhibiting similar hydrogeologic characteristics.     

Floquet theory for second order linear homogeneous difference equations

In this paper we provide a version of the Floquet’s theorem to be applied to any second order difference equations with quasi-periodic coefficients. To do this we extend to second order linear difference equations with quasi-periodic coefficients, the known equivalence between the Chebyshev equations and the second order linear difference equations with constant coefficients. So, any second order linear difference equations with quasi-periodic coefficients is essentially equivalent to a Chebyshev equation, whose parameter only depends on the values of the quasi-periodic coefficients and can be determined by a non-linear recurrence. Moreover, we solve this recurrence and obtaining a closed expression for this parameter. As a by-product we also obtain a Floquet’s type result; that is, the necessary and sufficient condition for the equation has quasi-periodic solutions.     

A dinuclear ruthenium(II) complex that functions as a label-free colorimetric sensor for DNA

A dinuclear ruthenium(II) complex groove binds to DNA and this interaction results in distinctive color changes that are dependent on both DNA sequence and structure.     

MALDI-TOF mass signatures for differentiation of yeast species,strain grouping and monitoring of morphogenesis markers

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is demonstrated to be a potentially useful tool for the rapid identification of yeasts, the grouping of Candida albicans strains, and the monitoring of germ tube-specific markers. Co-crystallized with sinapinic acid as the MALDI matrix, intact yeast cells yielded a sufficient number of medium-sized ions (4–15 kDa) in MALDI mass spectra to provide “mass signatures” that were diagnostic of strain type. For most isolates, the mass signatures were affected by the growth medium, length of incubation and the cell preparation method. While the overall past success of this methodology for fungal cells has been relatively low compared to its application to bacteria, fixing the yeast cells in 50% methanol inactivated the cells, reduced cell aggregation in aqueous suspension solution, and more importantly, it significantly improved the mass signature quality. This simple but critical advance in sample treatment improved mass spectrometric signal-to-noise ratios and allowed the identification of yeasts by a mass signature approach. Under optimized conditions, Candida species (C. albicans, C. glabrata, C. krusei, C. kefyr), Aspergillus species (A. terreus, A. fumigatus, A. syndowii) and other yeast genera (Cryptococcus neoformans, Saccharomyces cerevisiae and a Rhodotorula sp.) could be distinguished. Within the C. albicans species, several common ions in the m/z 5,000–10,000 range were apparent in the mass spectra of all tested strains. In addition to shared ions, the mass spectra of individual C. albicans strains permitted grouping of the strains. Principal component analysis (PCA) was employed to confirm spectral reproducibility and C. albicans strain grouping by mass signatures. Finally, C. albicans germ tubes produced MALDI-TOF mass signatures that differed from yeast forms of this species. This is a rapid, sensitive and simple method for identifying yeasts, grouping strains and following the morphogenesis of C. albicans. Figure       

Stereoselective quantitation of a serine protease inhibitor using LC-MS/MS at elevated column temperature

A LC-MS/MS method using a LC column packed with sub-2 micron particles and elevated column temperatures was validated for the quantitation of SCH 503034 diastereomers (SCH 534128 and SCH 534129) in human plasma. The method was validated over the concentration range of 2.5 to 1250 ng/mL. Inter-assay precision, based on percent relative deviation for n = 18 replicate quality controls, was 4.5% for SCH 534128 and 4.9% for SCH 534129. Inter-assay accuracy based on n = 18 replicate quality controls was +/- 7.8% for both SCH 534128 and SCH 534129. The method involved the novel application of ion pairing reagents to increase the stereoselectivity of the separation. Temperature, types of ion pairing reagent, and concentration of ion pairing reagent were all found to play significant roles in the resolution of the SCH 534128 and SCH 534129 diastereomers on a LC column packed with sub-2 micron particles. Specifically, a sensitivity increase of five-fold was demonstrated by increasing the column temperature. Without sacrificing resolution, the run time was significantly shortened when the column temperature was elevated to 100 degrees C.     

A family of hydrogels based on ureido-linked aminopolyol-derived amphiphiles and bolaamphiphiles: synthesis, gelation under thermal and sonochemical stimuli, and mesomorphic characterization

This article describes the systematic preparation of a novel family of carbohydrate amphiphiles and bolaamphiphiles in which hydrophilic and hydrophobic units are connected via a ureido or bis(ureido) moiety. The sugar core is derived from aminopolyols such as D-glucamine (1), N-methyl-D-glucamine (2), or the sugar-like species tris(hydroxymethyl)aminomethane (3). The O-unprotected derivatives behave as self-organizing nonionic surfactants with good water gelation ability, which can be induced under thermal or ultrasound-driven stimuli. In addition, some derivatives of 1 and 2, and rarely 3 also formed lyotropic liquid crystals with lamellar or hexagonal structures that exhibit low-temperature transitions.     

The bound conformation of microtubule-stabilizing agents: NMR insights into the bioactive 3D structure of discodermolide and dictyostatin

A protocol based on a combination of NMR experimental data with molecular mechanics calculations and docking procedures has been employed to determine the microtubule-bound conformation of two microtubule-stabilizing agents, discodermolide (DDM) and dictyostatin (DCT). The data indicate that tubulin in assembled microtubules recognizes DDM through a conformational selection process, with minor changes in the molecular skeleton between the major conformer in water solution and that bound to assembled microtubules. For DCT, the deduced bound geometry presents some key conformation differences around certain torsion angles, with respect to the major conformer in solution, and still displays mobility even when bound. The bound conformer of DCT resembles that of DDM and provides very similar contacts with the receptor. Competition experiments indicate that both molecules compete with the taxane-binding site. A model of the binding mode of DDM and DCT to tubulin is proposed.     

Separation of flavins and nicotinamide cofactors in Chinese hamster ovary cells by capillary electrophoresis

Simultaneous extraction, separation and quantitation of reduced nicotinamide adenine dinucleotide (NADH), reduced nicotinamide adenine dinucleotide phosphate (NADPH), flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) in Chinese Hamster Ovary (CHO) cells were investigated. The separation of flavins and nicotinamide cofactors was performed by capillary electrophoresis with laser-induced fluorescence detection at the excitation wavelength of 325 nm. The separation protocol was established by investigating the excitation wavelength, high voltage and effects of buffer nature, pH and concentration. All endogenous fluorophores riboflavin, FAD, FMN, NADH and NADPH show wide linear range of quantitation. The limits of detection for the five compounds ranged from 4.5 to 23 nM. Extraction conditions were optimized for high-efficiency recovery of all endogenous fluorophores from CHO cells. To account for the complex matrix of cell extracts, a standard addition method was used to quantify FAD, FMN, NADH and NADPH in CHO cells. The quantitative results should be useful to reveal the metabolic status of cells. The protocols for extraction, separation and quantitation are readily adaptable to normal and cancer cell lines for the analysis of endogenous fluorophores.     

Structural, magnetic coupling and oxidation state trends in models of the CaMn4 cluster in photosystem II

Density functional theory calculations are reported on a set of isomeric structures I, II and III that share the structural formula [CaMn4C9H10N2O16]q+.(H2O)3 (q= -1, 0, 1, 2, 3). Species I has a skeletal structure, which has been previously identified as a close match to the ligated CaMn4 cluster in Photosystem II, as characterized in the most recent 3.0 angstroms crystal structure. Structures II and III are rearrangements of I, which largely retain that model's bridging ligand framework, but feature metal atom positions broadly consistent with, respectively, the earlier 3.5 and 3.2 angstroms crystal structures for the Photosystem II water-oxidising complex (WOC). Our study explores the influence of the cluster charge state (and hence S state) on several important properties of the model structures; including the relative energies of the three models, their interconversion, trends in the individual Mn oxidation states, preferred hydration sites and favoured modes of magnetic coupling between the manganese atoms. We find that, for several of the explored cluster charge states, modest differences in the bridging-ligand geometry exert a powerful influence over the individual manganese oxidation states, but throughout these states the robustness of the tetrahedron formed by the Ca and three of the Mn atoms remains a significant feature and contrasts with the positional flexibility of the fourth Mn atom. Although structure I is lowest in energy for most S states, the energy differences between structures for a given S state are not large. Overall, structure II provides a better match for the EXAFS derived metal-metal distance parameters for the earlier S states (S0 to S2), but not for S3 in which a significant structural change is observed experimentally. In this S state structure III provides a closer fit. The implications of these results, for the possible action of the WOC, are discussed.