Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides

The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography–electrospray ionization–tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.     

Spectral beam combining of 2 μm Tm fiber laser systems

Output beams from three independently frequency-stabilized thulium master-oscillator power-amplifier fiber laser systems were spectrally combined using a plane-ruled metal diffraction grating. Two laser channels were frequency-stabilized with guided mode resonance filters and the third was stabilized using a plane-ruled metal diffraction grating. The systems had output wavelengths between 1984 and 2015 nm, each with a spectral width of 100-450 pm and output powers between 40-120 W. The combined beam had powers up to 49 W and was 32% efficient with respect to the launched pump power.     

Variable angle NMR spectroscopy and its application to the measurement of residual chemical shift anisotropy

The successful measurement of anisotropic NMR parameters like residual dipolar couplings (RDCs), residual quadrupolar couplings (RQCs), or residual chemical shift anisotropy (RCSA) involves the partial alignment of solute molecules in an alignment medium. To avoid any influence of the change of environment from the isotropic to the anisotropic sample, the measurement of both datasets with a single sample is highly desirable. Here, we introduce the scaling of alignment for mechanically stretched polymer gels by varying the angle of the director of alignment relative to the static magnetic field, which we call variable angle NMR spectroscopy (VA-NMR). The technique is closely related to variable angle sample spinning NMR spectroscopy (VASS-NMR) of liquid crystalline samples, but due to the mechanical fixation of the director of alignment no sample spinning is necessary. Also, in contrast to VASS-NMR, VA-NMR works for the full range of sample inclinations between 0° and 90°. Isotropic spectra are obtained at the magic angle. As a demonstration of the approach we measure 13C-RCSA values for strychnine in a stretched PDMS/CDCl? gel and show their usefulness for assignment purposes. In this context special care has been taken with respect to the exact calibration of chemical shift data, for which three approaches have been derived and tested.     

Controlling ghost traps in holographic optical tweezers

Computer-generated holograms displayed by phase-modulating spatial light modulators have become a well-established tool for beam shaping purposes in holographic optical tweezers. Still, the generation of light intensity patterns with high spatial symmetry and simultaneously without interfering ghost traps is a challenge. We have implemented an iterative Fourier transform algorithm that is capable of controlling these ghost traps and demonstrate the benefit of this approach in the experiment.     

Modifications of interface chemistry of LSM-YSZ composite by ceria nanoparticles

A porous composite electrode LSM-YSZ (lanthanum strontium manganite and yttria stabilized zirconia) was impregnated with different amounts of SDC (samarium substituted ceria) nanoparticles. The materials were investigated with X-ray diffraction, scanning electron microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy to determine the microstructure, the interface chemistry and the surface chemistry of the various impregnated samples. The SDC nanoparticles cover the surface of the LSM-YSZ backbone to a large extent; they are approximately 5-20 nm in diameter and have a cubic crystal structure. Low concentrations of lanthanum and manganese originating from LSM were detected within SDC particles. It was also observed that the relative atomic concentration of strontium increased on the LSM-YSZ surface with increasing amount of SDC nanoparticles. These findings are related to the applied nanoparticle impregnation method. It is indicated that interactions between surfactant, nanoparticles, impregnation solution and the LSM-YSZ composite take place which can locally affect the surface and interface chemistry of the investigated materials.     

Analytical modelling of the in-plane compressive behaviour of pile fibres in Spacer Fabric Composites

The mechanical behaviour of Spacer Fabric Composites (SFC) is highly influenced by their pile fibres. Within this work, the in-plane compressive behaviour of pile fibres in SFC is investigated. An analytical model is developed based on rigid hinged struts. Therefore, a representative part of the continuous fibre is chosen. The bending behaviour and the interaction of the pile fibre with facesheet fibres is modelled using rotational and extension springs respectively. The system proposed is fully defined by three generalized coordinates. The total potential energy of the system is determined and used to obtain information about the deformation behaviour. (© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Application of nonlinear continuum dislocation theory to antiplane shear

We apply the nonlinear dislocation theory to the problem of antiplane constrained shear in a single crystal with one slip system. By taking dissipation into account, the relaxed energy functional has to be minimized. We show that, up to a threshold strain, no dislocations are nucleated and therefore the plastic slip is zero. Since this threshold value depends on the width of the specimen, a size effect takes place. The stress strain curve turns out to be a hysteresis loop exhibiting the work hardening due to the dislocation pile-up. It is shown that the Bauschinger effect holds true. (© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Forbidden Configurations and Product Constructions

A simple matrix is a (0,1)-matrix with no repeated columns. For a (0,1)-matrix F, we say that a (0,1)-matrix A has F as a configuration if there is a submatrix of A which is a row and column permutation of F (trace is the set system version of a configuration). Let \({\|A\|}\) denote the number of columns of A. We define \({{\rm forb}(m, F) = {\rm max}\{\|A\| \,:\, A}\) is m-rowed simple matrix and has no configuration F. We extend this to a family \({\mathcal{F} = \{F_1, F_2, \ldots , F_t\}}\) and define \({{\rm forb}(m, \mathcal{F}) = {\rm max}\{\|A\| \,:\, A}\) is m-rowed simple matrix and has no configuration \({F \in \mathcal{F}\}}\) . We consider products of matrices. Given an m ₁ × n ₁ matrix A and an m ₂ × n ₂ matrix B, we define the product A × B as the (m ₁ + m ₂) × n ₁ n ₂ matrix whose columns consist of all possible combinations obtained from placing a column of A on top of a column of B. Let I _k denote the k × k identity matrix, let \({I_k^{c}}\) denote the (0,1)-complement of I _k and let T _k denote the k × k upper triangular (0,1)-matrix with a 1 in position i, j if and only if i ≤ j. We show forb(m, {I ₂ × I ₂, T ₂ × T ₂}) is \({\Theta(m^{3/2})}\) while obtaining a linear bound when forbidding all 2-fold products of all 2 × 2 (0,1)-simple matrices. For two matrices F, P, where P is m-rowed, let \({f(F, P) = {\rm max}_{A} \{\|A\| \,:\,A}\) is m-rowed submatrix of P with no configuration F}. We establish f(I ₂ × I ₂, I _m/2 × I _m/2) is \({\Theta(m^{3/2})}\) whereas f(I ₂ × T ₂, I _m/2 × T _m/2) and f(T ₂ × T ₂, T _m/2 × T _m/2) are both \({\Theta(m)}\) . Additional results are obtained. One of the results requires extensive use of a computer program. We use the results on patterns due to Marcus and Tardos and generalizations due to Klazar and Marcus, Balogh, Bollobás and Morris.     

Correlations in financial time series: established versus emerging markets

Long-time correlations in both well-developed and emerging market indexes are studied. The Hurst exponent as well as detrended fluctuations analysis (DFA) are used as technical tools. Some features that seem to be specific for developing markets are discovered and briefly discussed. Received 17 October 2000