Free Volatile Compounds of ssp. (Baumg.) Eb. Fisch. and Their Biological Activity.

The composition of free volatile compounds of essential oils (EO) and hydrosols (Hy) from four different localities of the species ssp. (Baumg.) Eb.

On the history of the connectivity index: from the connectivity index to the exact solution of the protein alignment problem.

We briefly review the history of the connectivity index from 1975 to date. We hope to throw some light on why this unique, by its design, graph theoretical molecular descriptor continues to be of interest in QSAR, having wide use in applications in structure-property and structure-activity studies. We will elaborate on its generalizations and the insights it offered on applications in Multiple Regression Analysis (MRA).

Morphological, genetic and phytochemical variation of the endemic Teucrium arduini L. (Lamiaceae).

Analysis of the morphological traits of leaves, genetic variability (analyzed by AFLP) and chemical composition of essential oils (analyzed by GC-MS) was conducted on eleven populations of the endemic Illyric-Balcanic species Teucrium arduini L. in Croatia, Bosnia and Herzegovina, and Montenegro. Average blade length and width ranged from 20.

Protein alignment: Exact versus approximate. An illustration.

We illustrate solving the protein alignment problem exactly using the algorithm VESPA (very efficient search for protein alignment). We have compared our result with the approximate solution obtained with BLAST (basic local alignment search tool) software, which is currently the most widely used for searching for protein alignment. We have selected human and mouse proteins having around 170 amino acids for comparison.

Antimicrobial and Antioxidant Properties of Satureja Montana L. and S. Subspicata Vis. (Lamiaceae).

Satureja montanaL. and S. subspicata Vis.

On the centrality of vertices of molecular graphs.

For acyclic systems the center of a graph has been known to be either a single vertex of two adjacent vertices, that is, an edge. It has not been quite clear how to extend the concept of graph center to polycyclic systems. Several approaches to the graph center of molecular graphs of polycyclic graphs have been proposed in the literature.

Common vertex matrix: a novel characterization of molecular graphs by counting.

We present a novel matrix representation of graphs based on the count of equal-distance common vertices to each pair of vertices in a graph. The element (i, j) of this matrix is defined as the number of vertices at the same distance from vertices (i, j). As illustrated on smaller alkanes, these novel matrices are very sensitive to molecular branching and the distribution of vertices in a graph.

Chemotaxonomic and micromorphological traits of Satureja montana L. and S. subspicata Vis. (Lamiaceae).

Satureja montana and S. subspicata are used as spice, pepper substitute, for preparing tea, juice, and as a medicine. Fourteen populations (seven per species) of Satureja montana L.

Anthraquinone profile, antioxidant and antimicrobial activity of bark extracts of Rhamnus alaternus, R. fallax, R. intermedia and R. pumila.

The quantity of phenols, as well as antioxidant and antimicrobial activities, were investigated in bark of Rhamnus alaternus L., R. fallax Boiss.

Re-investigation of the anthraquinone pool of Rhamnus spp.: madagascin from the fruits of Rhamnus cathartica and R. intermedia.

As a continuation of our ongoing studies aimed at revealing the presence of oxyprenylated anthraquinones in plants belonging to the genus Rhamnus, in this paper we describe the extraction and HPLC separation of madagascin (3-isopentenyloxyemodin) from the fruits of R. cathartica L. and R.

Very efficient search for nucleotide alignments.

We describe a very efficient search for nucleotide alignments, which is analogous to the novel very efficient search for protein alignment. Just as it has been the case with the alignment of proteins, based on 20 × 20 adjacency matrices for amino acids, obtained from a superposition of labeled amino acids adjacency matrices for the proteins considered, one can construct labeled matrices of size 4 × 4, listing adjacencies of nucleotides in DNA sequence. The matrix elements correspond to 16 pairs of adjacent nucleotides.

On graphical representation of trans-membrane proteins.

In the first part of this paper, we present a novel graphical representation of proteins, which starts with constructing a map of a protein that is obtained from a matrix, the elements of which record the adjacencies of pairs of amino acids in the primary structure of a protein. Starting with the novel protein map, one interprets its matrix elements as vertices of a graph, which are labelled in sequential order as in the protein sequence. The nearest vertices are connected to the nearest neighbour which has a smaller label.

Conjugated circuits currents in hexabenzocoronene and its derivatives formed by joining proximal carbons.

We report on calculated CC bond currents for a dozen derivatives of hexabenzocoroenene in which one or more proximal carbon atoms at the molecular periphery have been bridged. The approach that we use is graph-theoretical in nature, following our outline of this method in 2003, which is based on finding all conjugated circuits in all Kekulé valence structures of these molecules. To the π-electrons having 4n + 2 π-electrons are assigned anticlockwise π-electron currents and to conjugated circuits having 4n π-electrons are assigned π-electron currents.

Development and application of high-performance liquid chromatography for the study of two new oxyprenylated anthraquinones produced by Rhamnus species.

Rhamnus spp. is known to contain biologically active anthraquinone secondary metabolites but the presence of oxyprenylated ones is not reported. To this aim, a new simple, and accurate analytical method was developed to reveal chemical fingerprint of these analytes in plant extracts.

Very efficient search for protein alignment--VESPA.

A novel approach to the problem of protein alignments is described, which in comparison with existing approaches is visibly more efficient. This approach is based on superposition of amino acid adjacency matrices of a pair of proteins, which have been modified to record the sequential order of amino acids. As a result, one obtains simultaneously all segments of the two proteins which are shifted relative to one another by one or more positions in either directions, without need of a prior exhaustive search for an alignment that included unproductive directions and unknown displacement steps.

Applying the conjugated circuits method to Clar structures of [n]phenylenes for determining resonance energies.

We consider the aromaticity of biphenylene and structurally related linear or angular [n]phenylenes for which the direct application of the model of conjugated circuits does not offer valid expressions for resonance energy and aromaticity. We located the cause of this problem as being due to Kekulé valence structures in which neighboring benzenoid rings are connected by two CC double bonds. By restricting the selection of Kekulé valence structures to those that contribute to Clar structures of such systems, we were able to show that linear and angular [n]phenylenes have approximately similar resonance energies, with angular [n]phenylenes being slightly more stable due to second order contributions arising from disjoint conjugated circuits.

Algebraic clar formulas - numerical representation of clar structural formula.

We outline the construction of an algebraic (numerical) representation for Clar's valence formulas which in their geometrical form are illustrated with π-aromatic sextets as inscribed circles in benzenoid rings.

Study of proteome maps using partial ordering.

This paper describes numerical characterization of proteome maps based on partial ordering of protein spots with respect to the mass and the charge. The partial ordering diagram is embedded directly over the 2D map and the corresponding adjacency matrix is constructed. The adjacency matrix is augmented by including the information on the abundance of proteins in a gel as suitably scaled diagonal entries of the matrix.

Novel graph distance matrix.

We have introduced novel distance matrix for graphs, which is based on interpretation of columns of the adjacency matrix of a graph as a set of points in n-dimensional space, n being the number of vertices in the graph. Numerical values for the distances are based on the Euclidean distance between n points in n-dimensional space. In this way, we have combined the traditional representation of graphs (drawn as 2D object of no fixed geometry) with their representation in n-dimensional space, defined by a set of n-points that lead to a representation of definite geometry.

Spectral representation of reduced protein models.

We consider a spectrum-like two-dimensional graphical representation of proteins based on a reduced protein model in which 20 amino acids are grouped into five classes. This particular grouping of amino acids was suggested by Riddle and co-workers in 1997. The graphical representation is based on depicting sequentially the amino acids on five horizontal lines at equal separations.

Graphical representation of proteins as four-color maps and their numerical characterization.

We put forward a novel compact 2-D graphical representation of proteins based on the concept of virtual genetic code and a four-color map. The novel graphical representation uniquely represents proteins and allows one to easily and quickly visually observe and inspect similarity/dissimilarity between them. It also leads to a novel protein descriptor, a 10-dimensional vector derived from a novel structure matrix S associated with the map.

A new yardstick for benzenoid polycyclic aromatic hydrocarbons.

The newly introduced signature of benzenoids (a sequence of six real numbers Si with i = 6-1) shows the composition of the pi-electron partition by indicating the number of times all rings of the benzenoid are assigned 6, 5, 4, 3, 2, or 1 pi-electrons. It allows the introduction of a new ordering criterion for such polycyclic aromatic hydrocarbons by summing some of the terms in the signature. There is an almost perfect linear correlation between sums S6 + S5 and S4 + S3 for isomeric cata- or peri-fused benzenoids, so that one can sort such isomers according to ascending s 6 + S5 or to descending S4 + S3 sums (the resulting ordering does not differ much and agrees with that based on increasing numbers of Clar sextets and of Kekule structures).

Involvement of group I metabotropic glutamate receptors and glutamate transporters in the slow excitatory synaptic transmission in the spinal cord dorsal horn.

Our experiments demonstrate a novel role for group I metabotropic glutamate receptor (mGluR) subtypes 1 and 5 in generating a long-lasting synaptic excitation in the substantia gelatinosa (SG) and deep dorsal horn (DH) neurons of the rat spinal cord. In the present study we have investigated a slow excitatory postsynaptic current (EPSC), elicited by a brief high intensity (at Adelta/C fiber strength) and high frequency (20 or 100 Hz) stimulation of primary afferent fibers (PAFs) using whole-cell patch-clamp recordings from neurons located in the DH (laminae II-V) in spinal cord slices of young rats and wild-type and gene-targeted mice lacking mGluR1 subtype. The results shown here suggest that the activation of both mGluR1 and mGluR5 along with NK1 receptors, may be involved in the generation of the slow EPSC in the spinal cord DH.

On novel representation of proteins based on amino acid adjacency matrix.

A novel characterization of proteins is presented based on selected properties of recently introduced 20 x 20 amino acid adjacency matrix of proteins in which matrix elements count the occurrence of all 400 possible pair-wise adjacencies obtained by reading protein primary sequence from the left to the right. In particular we consider the characterization based on the sum and the difference of the rows and the corresponding columns, which characterize proteins by a pair of 20-component vectors. The approach is illustrated on a set of ND6 proteins of eight species.