Gene expression profiling using advanced mass spectrometric approaches

In the era of systems biology, computational and high-throughput experimental biological approaches are increasingly being combined to provide global snapshots of entire genomes and proteomes under tissue- and disease-specific conditions. The aim is to identify proteins changing in concentration and/or post-translational state and/or location, and develop a better molecular level understanding of the operation of biological systems. Here we describe an approach for comparative proteomics that builds upon the combination of high-performance nano-scale separations with the high-mass measurement accuracy, mass-resolving power and sensitivity of Fourier transform ion cyclotron resonance mass spectrometry to provide broad dynamic range, comprehensive and quantitative proteome measurements.     

Pyridoxylidene aminoguanidine and its copper(II) complexes – Syntheses,structure, and DFT calculations

Two nitrate salts of the well-known, and due to its significant biological activity very important, compound pyridoxylidene aminoguanidine (PLAG) were obtained in the form of single crystals. Thus this ligand is structurally characterized for the first time. In addition, the first data on the structure of a Schiff base of aminoguanidine with the active form of vitamin B₆, i.e. pyridoxal-phosphate, of the formula PLPAG·HCl·2H₂O, are presented. Two new square-pyramidal Cu(II) complexes of PLAG were synthesized and their physicochemical and structural properties analyzed. In these complexes, PLAG is coordinated as a zwitter-ion, in a tridentate ONN manner, via the oxygen atom of the deprotonated phenolic OH-group and nitrogen atoms of the azomethine and imino group of the aminoguanidine moiety. For the first time it was possible to make a comparative analysis of the structural properties of ligand salts and the coordinated ligand, so the effects of coordination could be unequivocally pointed out. Common fragments encountered in ligand structures were compared by half-normal probability plots. Density functional theory calculations have been conducted in order to gain insight into reactive properties of the investigated molecules. Molecular electrostatic potential, average local ionization energy surfaces, and Fukui functions have been calculated in order to obtain further information on the reactive properties.     

COMMON FIXED POINT THEOREMS FOR MULTI-VALUED MAPS

We establish some results on coincidence and common fixed points for a twopair of multi-valued and single-valued maps in complete metric spaces.Presented theorems generalize recent results of Gordji et...     

On matrices with operator entries

In this paper we consider certain matrix equations in the field of Mikusiński operators, and construct a method for obtaining an approximate solution which allows working with numerical constants instead of operators. The theory of diagonally dominant matrices is applied for the analysis, existence and character of the obtained solutions. We introduce a method for determining approximate solutions of a discrete analogue for operational differential equations and give conditions for their existence. The error of the approximation is estimated.     

Statistical causality,martingale problems and local uniqueness

The paper considers a statistical concept of causality in continuous time in the filtered probability spaces which is based on the Granger’s definition of causality. The given causality concept is then applied to the solution of the martingale problem (associated with the stochastic differential equation driven with semimartingales). More precisely, we show that the given causality concept is closely connected to the concept of extremality of measures for the solutions of the martingale problem, for the stopped martingale problem and for the local martingale problem. We also show the equivalence between some models of causality and local uniqueness (for the solutions of the martingale problem).     

A quadratic programming approach to the Randić index

Let G(k, n) be the set of connected graphs without multiple edges or loops which have n vertices and the minimum degree of vertices is k. The Randi? index χ = χ(G) of a graph G   is defined by χ(G)=_∑(uv)(_δuδv)^-1/2$\chi (G)={\sum }_{(\mathit{uv})}({\delta }_u{\delta }_v{)}^{-1/2}$, where δ_u is the degree of vertex u and the summation extends over all edges (uv) of G. Caporossi et al. [G. Caporossi, I. Gutman, P. Hansen, Variable neighborhood search for extremal graphs IV: Chemical trees with extremal connectivity index, Computers and Chemistry 23 (1999) 469–477] proposed the use of linear programming as one of the tools for finding the extremal graphs. In this paper we introduce a new approach based on quadratic programming for finding the extremal graphs in G(k, n) for this index. We found the extremal graphs or gave good bounds for this index when the number n_k of vertices of degree k is between n − k and n. We also tried to find the graphs for which the Randi? index attained its minimum value with given k (k ? n/2) and n. We have solved this problem partially, that is, we have showed that the extremal graphs must have the number n_k of vertices of degree k less or equal n − k and the number of vertices of degree n − 1 less or equal k.     

Universal pion freeze-out in heavy-ion collisions

Based on an evaluation of data on pion interferometry and on particle yields at midrapidity, we propose a universal condition for thermal freeze-out of pions in heavy-ion collisions. We show that freeze-out occurs when the mean free path of pions lambda(f) reaches a value of about 1 fm, which is much smaller than the spatial extent of the system at freeze-out. This critical mean free path is independent of the centrality of the collision and beam energy from the Alternating Gradient Synchrotron to the Relativistic Heavy Ion Collider.     

Explorative data analysis of two-dimensional electrophoresis gels

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.     

Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots

Analysis of fragmentation patterns from 5654 unique doubly charged tryptic peptides is obtained. Great variability of average relative abundance of bond cleavage is found between different amino acid combinations. There exist similarities as well as differences between b and y ions. Strong enhancement or suppression of cleavage gives insight into possible chemical interactions at reactive conformations formed by preferred phi-psi angles.