Host-guest interactions at self-assembled monolayers of cyclodextrins on gold

We have developed synthesis routes for the introduction of short and long dialkylsulfides onto the primary side of alpha-, beta-, and gamma-cyclodextrins. Monolayers of these cyclodextrin adsorbates were characterized by electrochemistry, wettability studies, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and atomic force microscopy (AFM). The differences in thickness and polarity of the outerface of the monolayers were measured by electro-chemistry and wettability studies. On average about 70% of the sulfide moieties were used for binding to the gold, as measured by XPS. Tof-SIMS measurements showed that the cyclodextrin adsorbates adsorb without any bond breakage. AFM measurements revealed for beta-cyclodextrin monolayers a quasi-hexagonal lattice with a lattice constant of 20.6 A, which matches the geometrical size of the adsorbate. The alpha-cyclodextrin and gamma-cyclodextrin monolayers are less ordered. Interactions of the anionic guests 1-anilinonaphthalene-8-sulfonic acid (1,8-ANS) and 2-(p-toluidinyl)naphthalene-6-sulfonic acid (2,6-TNS) and the highly ordered monolayers of heptapodant beta-cyclodextrin adsorbates were studied by surface plasmon resonance (SPR) and electrochemical impedance spectroscopy. The SPR measurements clearly showed interactions between a beta-cyclodextrin monolayer and 1,8-ANS. Electrochemical impedance spectroscopy measurements gave high responses even at low guest concentrations (< or = 5 microM). The association constant for the binding of 1,8-ANS (K = 289,000 +/- 13,000M-1) is considerably higher than the corresponding value in solution. (Partial) methylation of the secondary side of the beta-cyclodextrin strongly decreases the binding.     

A signal filtering method for improved quantification and noise discrimination in fourier transform ion cyclotron resonance mass spectrometry-based metabolomics data

Direct-infusion electrospray-ionization Fourier transform ion cyclotron resonance mass spectrometry (DI ESI FT-ICR MS) is increasingly being utilized in metabolomics, including the high sensitivity selected ion monitoring (SIM)-stitching approach. Accurate signal quantification and the discrimination of real signals from noise remain major challenges for this approach, with both adversely affected by factors including ion suppression during electrospray, ion—ion interactions in the detector cell, and thermally-induced white noise. This is particularly problematic for complex mixture analysis where hundreds of metabolites are present near the noise level. Here we address relative signal quantification and noise discrimination issues in SIM-stitched DI ESI FT-ICR MS-based metabolomics. Using liver tissue, we first optimized the number of scans (n) acquired per SIM window to address the balance between quantification accuracy versus acquisition time (and thus sample throughput); a minimum of n = 5 is recommended. Secondly, we characterized and computationally-corrected an effect whereby an ion’s intensity is dependent upon its location within a SIM window, exhibiting a 3-fold higher intensity at the high m/z end. This resulted in significantly improved quantification accuracy. Finally, we thoroughly characterized a three-stage filter to discriminate noise from real signals, which comprised a signal-to-noise-ratio (SNR) hard threshold, then a “replicate” filter (retaining only peaks in r-out-of-3 replicate analyses), and then a “sample” filter (retaining only peaks in >s% of biological samples). We document the benefits of three-stage filtering versus one- and two-stage filters, and show the importance of selecting filter parameters that balance the confidence that a signal is real versus the total number of peaks detected.     

Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow

Direct infusion mass spectrometry (DIMS)-based untargeted metabolomics measures many hundreds of metabolites in a single experiment. While every effort is made to reduce within-experiment analytical variation in untargeted metabolomics, unavoidable sources of measurement error are introduced. This is particularly true for large-scale multi-batch experiments, necessitating the development of robust workflows that minimise batch-to-batch variation. Here, we conducted a purpose-designed, eight-batch DIMS metabolomics study using nanoelectrospray (nESI) Fourier transform ion cyclotron resonance mass spectrometric analyses of mammalian heart extracts. First, we characterised the intrinsic analytical variation of this approach to determine whether our existing workflows are fit for purpose when applied to a multi-batch investigation. Batch-to-batch variation was readily observed across the 7-day experiment, both in terms of its absolute measurement using quality control (QC) and biological replicate samples, as well as its adverse impact on our ability to discover significant metabolic information within the data. Subsequently, we developed and implemented a computational workflow that includes total-ion-current filtering, QC-robust spline batch correction and spectral cleaning, and provide conclusive evidence that this workflow reduces analytical variation and increases the proportion of significant peaks. We report an overall analytical precision of 15.9 %, measured as the median relative standard deviation (RSD) for the technical replicates of the biological samples, across eight batches and 7 days of measurements. When compared against the FDA guidelines for biomarker studies, which specify an RSD of <20 % as an acceptable level of precision, we conclude that our new workflows are fit for purpose for large-scale, high-throughput nESI DIMS metabolomics studies.     

A new approach to variable selection in least squares problems

The title Lasso has been suggested by Tibshirani (1996) as acolourful name for a technique of variable selection which requiresthe minimization of a sum of squares subject to an l₁ bound on the solution. This forces zero components in the minimizingsolution for small values of . Thus this bound can functionas a selection parameter. This paper makes two contributionsto computational problems associated with implementing the Lasso:(1) a compact descent method for solving the constrained problemfor a particular value of is formulated, and (2) a homotopymethod, in which the constraint bound becomes the homotopyparameter, is developed to completely describe the possibleselection regimes. Both algorithms have a finite terminationproperty. It is suggested that modified Gram-Schmidt orthogonalizationapplied to an augmented design matrix provides an effectivebasis for implementing the algorithms.     

Siderophore-Mediated Iron Uptake Promotes Yeast–Bacterial Symbiosis

In the present study, siderophore produced by the marine yeast Aureobasidium pullulans was characterized as hydroxamate by chemical and bioassays. The hydroxamate assignment was supported by the appearance of peaks at 1,647.21?C1,625.99?cm^?1 and at 1,435.04?cm^?1 in the infrared spectrum. The purified siderophore exhibited specific growth-promoting activity under iron-limited conditions for siderophore auxotrophic probiotic bacteria. Cross-utilization of siderophore indicates a symbiotic relationship between the yeast A. pullulans and the selected probiotic bacterial strains. Statistical optimization of medium components for improved siderophore production in A. pullulans was depicted by response surface methodology. The shift in UV?CVis spectroscopy indicates the photoreactive property and subsequent oxidative cleavage of purified siderophore on exposure to sunlight.     

Flux line lattice symmetries in the borocarbide superconductor LuNi2B2C

We compare the results of small angle neutron scattering on the flux line lattice (FLL) obtained in the borocarbide superconductor LuNi₂B₂C with the applied field along the c- and a-axes. For H‖c the temperature dependence of the FLL structural phase transition from square to hexagonal symmetry was investigated. Above 10 K the transition onset field. H ₂(T), rises sharply, bending away from H _c2(T) in contradiction to theoretical predictions of the two merging. For H‖a a first order FLL reorientation transition is observed at H _tr=3–3.5 kOe. Below H _tr the FLL nearest neighbor direction is parallel to the b-axis, and above H _tr to the c-axis. This transition cannot be explained using nonlocal corrections to the London model.     

Far-infrared VRT spectroscopy of two water trimer isotopomers: vibrationally averaged structures and rearrangement dynamics

We report the measurement of far-infrared vibration-rotation tunnelling parallel bands of two partially deuterated water trimer isotopomers: (D2O)2DOH and (H2O)2DOH at 97.2607 cm-1 and approximately 86 cm-1, respectively. The hydrogen bond rearrangement dynamics of the two mixed trimers can be described by the simplified molecular symmetry G8, which accounts for both the flipping and bifurcation tunnelling motions previously established for (H2O)3 and (D2O)3. The observed donor tunnelling quartet, rather than triplet, splitting indicates that the two homogeneous monomers (D2O or H2O) in each mixed trimer experience slightly different environments. Vibrationally averaged structures of (H2O)3, (D2O)3, and (D2O)2DOH were examined in a Monte Carlo simulation of the out-of-plane flipping motions of the free atoms. The simulation addresses both the symmetric top behaviour and the negative zero-point inertial defect for (H2O)3 and (D2O)3, which were insufficiently counted in all previous structure models. The average ground state O--O separations, which are correlated to other angular coordinates, were determined to be 2.84 +/- 0.01 angstroms for all three species. The simulated difference in hydrogen bond nonlinearity also supports the inequivalency of the two homogeneous monomers. The structural simulation shows that the unique H in (D2O)2DOH is free, while a torsional analysis suggests the unique D in (H2O)2DOH is bound within the cyclic ring. Both bands can be assigned to the pseudorotational transitions which correlate to those found in the pure trimers.