High-throughput, low-volume, multianalyte quantification of plasma metabolites related to one-carbon metabolism using HPLC-MS/MS

Risk of chronic diseases, like cardiovascular disease and cancer, has been associated with biomarkers related to one-carbon metabolism, which comprises a metabolic network of cross-talking pathways. To address this complexity in epidemiological studies, we have established an isotope dilution HPLC-MS/MS method for quantification of 12 biomarkers and metabolites. All sample handling is performed by a robotic workstation. The assay uses 45 μL of plasma, and sample treatment consists of protein precipitation by trichloroacetic acid. The analytes were separated on a Fortis Phenyl column using an isocratic mobile phase that contained water, methanol and acetic acid. Methionine, methionine sulfoxide, choline, betaine, dimethylglycine, arginine, asymmetric dimethylarginine, symmetric dimethylarginine, homoarginine, creatinine, cystathionine and trimethyllysine all showed limits of detection well below the 5th percentile of plasma distributions in healthy humans, coefficients of variation were in the range 2.2–12.3 %, and recoveries were 80–131 %. Simple sample processing, low-volume consumption, multiplexing and high capacity/short run time of this method make it suitable for large-scale metabolic profiling of precious biobank samples.     

Syntheses, photophysical properties, and application of through-bond energy-transfer cassettes for biotechnology

We have designed fluorescent "through-bond energy-transfer cassettes" that can harvest energy of a relatively short wavelength (e.g., 490 nm), and emit it at appreciably longer wavelengths without significant loss of intensity. Probes of this type could be particularly useful in biotechnology for multiplexing experiments in which several different outputs are to be observed from a single excitation source. Cassettes 1-4 were designed, prepared, and studied as model systems to achieve this end. They were synthesized through convergent routes that feature coupling of specially prepared fluorescein- and rhodamine-derived fragments. The four cassettes were shown to emit strongly, with highly efficient energy transfer. Their emission maxima cover a broad range of wavelengths (broader than the four dye cassettes currently used for most high-throughput DNA sequencing), and they exhibit faster energy-transfer rates than a similar through-space energy-transfer cassette. Specifically, energy-transfer rates in these cassettes is around 6-7 ps, in contrast to a similar through-space energy-transfer system shown to have a decay time of around 35 ps. Moreover, the cassettes are considerably more stable to photobleaching than fluorescein, even though they each contain fluorescein-derived donors. This was confirmed by bulk fluorescent measurements, and in single-molecule-detection studies. Modification of a commercial automated DNA-sequencing apparatus to detect the emissions of these four energy-transfer cassettes enabled single-color dye-primer sequencing.     

Development of a new protein labeling strategy, oxidation labeling. part 1: Preliminary evaluation and synthesis of tautomycin containing a metal coordinating unit

In the current work we present our preliminary evaluation of a new protein labeling strategy, namely oxidation labeling. We found that a bis(2-picolyl) amine analogue coordinating Cu⁺ was able to oxidize histidine to oxo-histedine in a small peptide by generating reactive oxygen species upon exposure to hydrogen peroxide. The bis(2-picolyl) amine unit was then incorporated into the natural product tautomycin via an oxime linker. The compound, which showed good activity toward protein phosphatase 1γ (PP1γ), will be used in oxidation labeling studies with PP1γ.     

Large eddy simulations of the turbulent flow between a rotating and a stationary disk

Large eddy simulations of the flow between a rotating and a stationary disk have been performed using a dynamic and a mixed dynamic subgrid-scale model. The simulations were compared to direct numerical simulation results. The mixed dynamic model gave better overall predictions than the dynamic model. Modifications of the near-wall structures caused by the mean flow three-dimensionality were also investigated. Conditional averages near strong stress-producing events led to the same conclusions regarding these modifications as studies of the flow generated by direct numerical simulation, namely a distinct asymmetry of the vortices producing sweeps and ejections.     

Efficient total synthesis of (+)-negamycin, a potential chemotherapeutic agent for genetic diseases

Herein, we describe an efficient strategy for the total synthesis of (+)-negamycin using commercially available achiral N-Boc-2-aminoacetaldehyde as starting material with 42% overall yield for a limited number of steps.     

Determination of Solvent‐Trapped Products Obtained by Photolysis of Aryl Azides in 2,2,2‐Trifluoroethanol

A series of nonfluorinated and fluorinated aryl azides with varied functionality patterns were irradiated in 2,2,2‐trifluoroethanol with either a high‐pressure or a low‐pressure mercury lamp. Interestingly, one of the major products in these reactions was the result of the recombination of anilino and alkyl radicals to form the corresponding hemiaminal compounds. The structure of the recombination products was assigned unambiguously after proton/deuterium exchange experiments followed by MS and MS/MS analysis.     

Covariate Selection in High-Dimensional Generalized Linear Models With Measurement Error

In many problems involving generalized linear models, the covariates are subject to measurement error. When the number of covariates p exceeds the sample size n, regularized methods like the lasso or Dantzig selector are required. Several recent papers have studied methods which correct for measurement error in the lasso or Dantzig selector for linear models in the p > n setting. We study a correction for generalized linear models, based on Rosenbaum and Tsybakov’s matrix uncertainty selector. By not requiring an estimate of the measurement error covariance matrix, this generalized matrix uncertainty selector has a great practical advantage in problems involving high-dimensional data. We further derive an alternative method based on the lasso, and develop efficient algorithms for both methods. In our simulation studies of logistic and Poisson regression with measurement error, the proposed methods outperform the standard lasso and Dantzig selector with respect to covariate selection, by reducing the number of false positives considerably. We also consider classification of patients on the basis of gene expression data with noisy measurements. Supplementary materials for this article are available online.     

Some infinite series related to Feynman diagrams

Results are presented for some infinite series appearing in Feynman diagram calculations, many of which are similar to the Euler series. These include both one-, two- and three-dimensional series. The sums of these series can be evaluated with the help of various integral representations for hypergeometric functions, and expressed in terms of ζ(2),ζ(3), the Catalan constant G and Cl₂(π/3) where Cl₂(θ) is Clausen's function.     

Probing BSA binding to citrate-coated gold nanoparticles and surfaces

The interaction of bovine serum albumin (BSA) with gold colloids and surfaces was studied using zeta-potential and quartz crystal microbalance (QCM) measurements, respectively, to determine the surface charge and coverage. The combination of these two measurements suggests that BSA binding to gold nanoparticles and gold surfaces occurs by an electrostatic mechanism when citrate is present. The binding of BSA to bare gold is nearly two times greater than the binding of BSA to a citrate-coated gold surface, suggesting that protein spreading (denaturation) on the surface may occur followed by secondary protein binding. On the other hand, binding to citrate-coated gold surfaces can be fit to a Langmuir isotherm model to obtain a maximum surface coverage of (3.7 +/- 0.2) x 10(12) molecules/cm(2) and a binding constant of 1.0 +/- 0.3 microM(-1). The zeta-potential measurements show that the stabilization of colloids by BSA has a significant contribution from a steric mechanism because the colloids are stable, even at their isoelectric point (pI approximately 4.6). To be consistent with the observed phenomena, the electrostatic interactions between BSA and citrate must consist of salt-bridges, for example, of the carboxylate-ammonium type, between the citrate and the lysine on the protein surface. The data support the role of strong electrostatic binding but do not exclude contributions from steric or hydrophobic interactions with the surface adlayer.     

Plasma Reactivity and Plasma-Surface Interactions During Treatment of Toluene by a Dielectric Barrier Discharge

Toluene removal is investigated in filamentary plasmas produced in N₂ and in N₂/O₂ mixtures by a pulse high voltage energised DBD. Influence of the oxygen percentage (lower than 10%) and of the temperature (lower than 350°C) is examined. Toluene is removed in N₂ through collisions with electrons and nitrogen excited states. The removal efficiency is a few higher in N₂/O₂. It increases when the temperature increases for N₂ and N₂/O₂. Both H- and O-atoms play an important role in toluene removal because H can readily recombine with O to form OH, which is much more reactive with toluene than O. H follows from dissociation of toluene and of hydrogenated by-products by electron collisions. Detection of cyanhidric acid, acetylene, formaldehyde, and methyl nitrate strengthens that dissociation processes, to produce H and CH₃, must be taken into account in kinetic analysis. Formation and treatment of deposits are also analysed.