Implications of partial tryptic digestion in organic-aqueous solvent systems for bottom-up proteome analysis

For bottom-up MS, the digestion step is critical and is typically performed with trypsin. Solvent-assisted digestion in 80% acetonitrile has previously been shown to improve protein sequence coverage at shorter digestion times. This has been attributed to enhanced enzyme digestion efficiency in this solvent. However, our results demonstrate that tryptic digestion in 80% acetonitrile is less efficient than that of conventional (aqueous) digestion. This is a consequence of decreased enzyme activity beyond ∼40% acetonitrile, increased enzyme autolysis and lower protein solubility in 80% acetonitrile. We observe multiple missed cleavages and reduced concentration of fully cleaved digestion products. Nonetheless we confirm, through room temperature solvent-assisted digestion, a consistent improvement in protein sequence coverage when analyzed by mass spectrometry. These results are explained through the increased number of unique digestion products available for detection. Thus, while solvent-assisted digestion has clear merits for proteome analysis, one should be aware of the inefficiency of protein digestion though this protocol, particularly with absolute protein quantitation experiments.     

Fusion of Symmetric D-Branes and Verlinde Rings

We explain how multiplicative bundle gerbes over a compact, connected and simple Lie group G lead to a certain fusion category of equivariant bundle gerbe modules given by pre-quantizable Hamiltonian LG-manifolds arising from Alekseev-Malkin-Meinrenken’s quasi-Hamiltonian G-spaces. The motivation comes from string theory namely, by generalising the notion of D-branes in G to allow subsets of G that are the image of a G-valued moment map we can define a ‘fusion of D-branes’ and a map to the Verlinde ring of the loop group of G which preserves the product structure. The idea is suggested by the theorem of Freed-Hopkins-Teleman. The case where G is not simply connected is studied carefully in terms of equivariant bundle gerbe modules for multiplicative bundle gerbes.     

A Dirac Type Operator on the Non-Commutative Disk

We study an example of the index problem for a Dirac-like operator subject to Atiyah–Patodi–Singer boundary conditions on the noncommutative unit disk.     

A spectral–finite difference solution of the Navier–Stokes equations in three dimensions

A new computational code for the numerical integration of the three-dimensional Navier–Stokes equations in their non-dimensional velocity–pressure formulation is presented. The system of non-linear partial differential equations governing the time-dependent flow of a viscous incompressible fluid in a channel is managed by means of a mixed spectral–finite difference method, in which different numerical techniques are applied: Fourier decomposition is used along the homogeneous directions, second-order Crank–Nicolson algorithms are employed for the spatial derivatives in the direction orthogonal to the solid walls and a fourth-order Runge–Kutta procedure is implemented for both the calculation of the convective term and the time advancement. The pressure problem, cast in the Helmholtz form, is solved with the use of a cyclic reduction procedure. No-slip boundary conditions are used at the walls of the channel and cyclic conditions are imposed at the other boundaries of the computing domain. Results are provided for different values of the Reynolds number at several time steps of integration and are compared with results obtained by other authors. © 1998 John Wiley & Sons, Ltd.     

Analysis of high speed non‐equilibrium chemically reacting gas flows. Part I. Physical modeling and sensitivity studies

In this part, a theoretical model for high speed flow of chemically reacting gases out of thermal and chemical equilibrium is presented. The main features of the physical model are discussed together with details for a new form of the kinetic rate coefficients for non‐equilibrium flows and presentation of a two‐layer radiation model used for a plasma torch problem. This model is implemented in a new hybrid finite volume/finite element scheme, which is developed in Part II. Results from this physical model are compared with experiments and other results in the literature for an arcjet and non‐equilibrium nozzle test case. Sensitivity studies are included for the nozzle problem to simulate the influence of the rate coefficients. Copyright © 2000 John Wiley & Sons, Ltd.     

Determination of N-Acetyl-l-cysteine Ethyl Ester (NACET) by Flow Injection Analysis and Spectrophotometric Detection Using Different Thiol-Sensitive Ligands

A new flow injection spectrophotometric method for the determination of N-acetyl-l-cysteine ethyl ester (NACET) was developed and validated. The method is based on the reduction of Cu(II)-ligand complexes to chromophoric Cu(I)-ligand complexes with the analyte. The studied ligands were neocuproine (NCN), bicinchoninic acid (BCA) and bathocuproine disulfonic acid (BCS). The absorbance of the Cu(I)-ligand complex was measured at 458, 562 and 483 nm for the reactions of NACET with NCN, BCA and BCS, respectively. The method was validated in terms of linear dynamic range, limit of detection and quantitation, accuracy, selectivity, and precision. Experimental conditions were optimized by a univariate method, yielding linear calibration curves in a concentration range from 2.0 × 10⁻⁶ mol L⁻¹ to 2.0 × 10⁻⁴ mol L⁻¹ using NCN; 2.0 × 10⁻⁶ mol L⁻¹ to 1.0 × 10⁻⁴ mol L⁻¹ using BCA and 6.0 × 10⁻⁷ mol L⁻¹ to 1.2 × 10⁻⁴ mol L⁻¹ using BCS. The achieved analytical frequency was 90 h⁻¹ for all three ligands. The method was successfully employed for NACET determination in pharmaceutical preparations, indicating that this FIA method fulfilled all the essential demands for the determination of NACET in quality control laboratories, as it combined low instrument and reagent costs with a high sampling rate.     

ChemInform Abstract: The Gallides SrRh2Ga2, SrIr2Ga2, and Sr3Ir4Ga4.

The title gallides are prepared from the elements by induction melting and subsequent annealing (Ta ampules, 800 mbar Ar, 873—1073 K, 4 d) and characterized by powder and single crystal XRD.     

Comparison of salivary sodium and potassium concentrations measured by handheld ion-selective electrode meters and an automated biochemical analyser

Ion-selective electrode pocket meters available for use with saliva could be a convenient tool to assess how diseases, drugs, exercise or nutrition affect salivary composition. This study compared salivary sodium and potassium concentrations measured by handheld LAQUAtwin meters and a fully-automated biochemical analyzer. Agreement between two methods was assessed with Passing-Bablok regression and Bland-Altman plots. LAQUAtwin meters measured lower values of both analytes and provided repeatable though not accurate results. The meters may serve as an alternative to laboratory methods to gain insight into between-group differences in electrolyte concentrations, or a concentration change induced by an experimental procedure.