Identification and relative quantification of specific glycation sites in human serum albumin

Glycation (or non-enzymatic glycosylation) is a common non-enzymatic covalent modification of human proteins. Glucose, the highest concentrated monosaccharide in blood, can reversibly react with amino groups of proteins to form Schiff bases that can rearrange to form relatively stable Amadori products. These can be further oxidized to advanced glycation end products (AGEs). Here, we analyzed the glycation patterns of human serum albumin (HSA) in plasma samples obtained from five patients with type 2 diabetes mellitus. Therefore, glycated peptides from a tryptic digest of plasma were enriched with m-aminophenylboronic acid (mAPBA) affinity chromatography. The glycated peptides were then further separated in the second dimension by RP-HPLC coupled on-line to an electrospray ionization (ESI) tandem mass spectrometer (MS/MS). Altogether, 18 Amadori peptides, encompassing 40% of the HSA sequence, were identified. The majority of the peptides were detected and relatively quantified in all five samples with a high reproducibility among the replicas. Eleven Lys-residues were glycated at similar quantities in all samples, with glycation site Lys₅₄₉ (K_Am(Glc)QTALVELVK) being the most abundant. In conclusion, the established mAPBA/nanoRP-HPLC-ESI-MS/MS approach could reproducibly identify and quantify glycation sites in plasma samples, potentially useful in diagnosis and therapeutic control.     

Topographical distance matrices for porous arrays

The topographical Wiener index is calculated for two-dimensional graphs describing porous arrays, including bee honeycomb. For tiling in the plane, we model hexagonal, triangular, and square arrays and compare with topological formulas for the Wiener index derived from the distance matrix. The normalized Wiener indices of C₄, T₁₃, and O(4), for hexagonal, triangular, and square arrays are 0.993, 0.995, and 0.985, respectively, indicating that the arrays have smaller bond lengths near the center of the array, since these contribute more to the Wiener index. The normalized Perron root (the first eigenvalue, λ ₁), calculated from distance/distance matrices describes an order parameter, f = l₁/n{\phi=\lambda_1/n} , where f = 1{\phi= 1} for a linear graph and n is the order of the matrix. This parameter correlates with the convexity of the tessellations. The distributions of the normalized distances for nearest neighbor coordinates are determined from the porous arrays. The distributions range from normal to skewed to multimodal depending on the array. These results introduce some new calculations for 2D graphs of porous arrays.     

AC susceptibility of thin Pb films in intermediate and mixed state

Thin films of type I superconductors of a thickness comparable or less than a flux penetration length behave like type II superconductors in a mixed state. With decreasing film thickness normal domains carrying a magnetic flux get smaller with smaller number of flux quanta per domain and finally transform into single quantum flux lines, i.e. quantum vortices similar to those found in type II superconductors. We give an evidence of this behavior from the measurements of the nonlinear response of a total magnetic moment to an applied AC magnetic field, directly from the temperature dependence of an AC susceptibility.     

Seismic rays as Finsler geodesics

We prove that, in general, for anisotropic nonuniform continua, seismic rays are geodesics in Finsler geometry. In particular, for separable velocity functions, the geometry is Wagnerian. We provide concrete examples with theoretical discussions and introduce the seismic Finsler metric.     

Molecular structure,p<Emphasis Type="Italic">K</Emphasis>a,lipophilicity, solubility,absorption, polar surface area,and blood brain barrier penetration of some antiangiogenic agents

The methods of theoretical chemistry have been used to elucidate molecular properties of selected and novel antiangiogenic agents (semaxanib, sunitinib, N-methylsunitinib, sorafenib, motesanib, ABT-869, vatalanib, vandetanib, AEE 788, CP-547632, A-1, A-2, A-3, and A-4). The geometries and energies of these drugs have been computed using HF/6-31G(d), Becke3LYP/6-31G(d) and Becke3LYP/6-31++G(d,p) model chemistries. Wherever possible the most stable conformations of inhibitors studied are stabilized by means of intramolecular hydrogen bonds. Water has a remarkable effect on the geometry of the antiangiogenic agents studied. Computed partition coefficients (ALOGPS method) varied between 2.3 and 5. Compounds studied are described as lipophilic inhibitors. Semaxanib is inhibitor with lowest lipophilicity. The antiangiogenic agents studied are only slightly soluble in water; their computed solubility (log S) from interval between −3.4 and −5.4 is sufficient for fast absorption. Selection criteria for drug-like properties of VEGFR2 inhibitors investigated were designed. Based on these criteria, three compounds (A-2, A-3, and A-4) were selected for synthesis and biological testing for antianiogenic activity on VEGFR2 receptor.     

ToF-SIMS characterisation of diterpenoic acids after chromatographic separation

Microcolumn liquid chromatography (μHPLC) coupled on-line with time of flight secondary ion mass spectrometry (ToF-SIMS) was applied for mixture of diterpenoic acids (abietic, gibberellic and kaurenoic) analysis. Chromatographic effluent, with analytes separated, was carried out directly onto different, ToF-SIMS compatible surface substrates, for further ToF-SIMS analysis. Silica gel Si₆₀, aluminium backplate modified Si₆₀, monolithic silica gel and Raman spectroscopy chromatographic thin layers were used as the deposition substrates in this experiment. By ToF-SIMS surface imaging the deposition trace picture has been obtained. Effluent deposition surface area was scanned for diterpenoic acid fragment mass values based on mass spectrometric library. Measured ToF-SIMS dataset of fragment abundance and intensities were used for preliminary fragmentation schemes construction. The lowest substrate background activity has been established for monolithic silica gel thin layer and aluminium backplate modified Si₆₀ thin layer. In the case of Raman spectroscopy pre-treated thin layer or conventional chromatographic thin layer Si₆₀, the both, high background signal intensity and impossibility to construct negative ions surface image, were observed. Diterpenoic acids studied serve the similar mass spectrum but ToF-SIMS coupled with liquid chromatographic separation brings new impact to the positive identification of analytes studied.     

Gravitational Stability of the Interface in Water Over Steam Geothermal Reservoirs

Stability of a geothermal system is considered in a case when the water layer lies over the layer of superheated vapor in a stratum having relatively low permeability. This stratum locates between two parallel high permeable layers. Under the assumption of smallness of advective energy transfer as compared with the conductive one, the stationary distribution of the characteristics in the stratum with an interface of phase transition is obtained. The interface separates the domains occupied by water and vapor. Investigation of normal stability of the interface shows, that stable configurations in the geothermal system under consideration exist within the range of permeability values bounded by k 0.6 × 10^–15 m² from above. The most unstable configurations occur to be the quiescent states when the permeability exceeds a certain threshold. A sufficiently high value of permeability, satisfying the criterion of smallness of the advective energy transfer as compared with the conductive one makes it possible to explain the existence of a wide class of stable natural geothermal reservoirs, where the vapor layer underlies the water one.     

On a quest of reverse translation

Explaining the emergence of life is perhaps central and the most challenging question in modern science. Within this area of research, the emergence and evolution of the genetic code is supposed to be a critical transition in the evolution of modern organisms. The canonical genetic code is one of the most dominant aspects of life on this planet, and thus studying its origin is critical to understanding the evolution of life, including life’s emergence. In this sense it is possible to view the ribosome as a digital-to-analogue information converter. Why the translation apparatus evolved, is one of the enduring mysteries of molecular biology. Assuming the hypothesis that during the emergence of life evolution had to first involve autocatalytic systems, which only subsequently acquired the capacity of genetic heredity, in the present article we discuss some aspects and causes of the possible emergence of digital, discrete information arising from analogue information realized in the intra- and inter-molecular interactions throughout molecular evolution. How such reverse translation was achieved at a molecular level is still unclear. The results of such debates and investigations might shift current biological paradigms and might also have a momentous significance for modern philosophy in understanding our place in the universe.     

Propagation of Reactions in Inhomogeneous Media

Consider reaction‐diffusion equation u _t =Δ u + f (x,u ) with and general inhomogeneous ignition reaction f ≥ 0 vanishing at u = 0,1. Typical solutions 0 ≤ u ≤ 1 transition from 0 to 1 as time progresses, and we study them in the region where this transition occurs. Under fairly general qualitative hypotheses on f we show that in dimensions d ≤ 3, the Hausdorff distance of the superlevel sets {u ≥ ε } and {u ≥ 1‐ε} remains uniformly bounded in time for each ε ? (0,1). Thus, u remains uniformly in time close to the characteristic function of in the sense of Hausdorff distance of superlevel sets. We also show that each {u ≥ ε} expands with average speed (over any long enough time interval) between the two spreading speeds corresponding to any x ‐independent lower and upper bounds on f . On the other hand, these results turn out to be false in dimensions d ≥ 4, at least without further quantitative hypotheses on f . The proof for d ≤ 3 is based on showing that as the solution propagates, small values of u cannot escape far ahead of values close to 1. The proof for d ≥ 4 is via construction of a counterexample for which this fails. Such results were before known for d =1 but are new for general non‐periodic media in dimensions d ≥ 2 (some are also new for homogeneous and periodic media). They extend in a somewhat weaker sense to monostable, bistable, and mixed reaction types, as well as to transitions between general equilibria of the PDE and to solutions not necessarily satisfying . © 2016 Wiley Periodicals, Inc.