Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals.

Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions – friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour. We used samples from hypothalamus, mesencephalic tegmentum and periaqueductum grey matter from brain areas of grey rats genetically selected by behaviour in many generations. The set of computer tools and data processing pipelines helped to find genes and gene regulation patterns related to behaviour patterns. RNA - profiling experiments revealed the lists of differentially expressed genes in the contrast samples as well as differentially spliced isoforms. The gene ontology categories of protein transport, phosphoproteins, and nucleotide binding are presented together with categories of transmission of nerve impulses and neuron development were identified. Differential alternative splicing events found in the brain areas studied are statistically significant. We discuss role of alternative splicing events for neurospecific genes in behaviour patterns as well as extension of brain transcriptomics profiling.

Experimental and computational studies of the macrocyclic effect of an auxiliary ligand on electron and proton transfers within ternary copper(II)-histidine complexes.

The dissociation of [Cu(II)(L)His](*2+) complexes [L = diethylenetriamine (dien) or 1,4,7-triazacyclononane (9-aneN(3))] bears a strong resemblance to the previously reported behavior of [Cu(II)(L)GGH](*2+) complexes. We have used low-energy collision-induced dissociation experiments and density functional theory (DFT) calculations at the B3LYP/6-31+G(d) level to study the macrocyclic effect of the auxiliary ligands on the formation of His(*+) from prototypical [Cu(II)(L)His](*2+) systems. DFT revealed that the relative energy barriers of the same electron-transfer (ET) dissociation pathways of [Cu(II)(9-aneN(3))His](*2+) and [Cu(II)(dien)His](*2+) are very similar, with the ET reactions of [Cu(II)(9-aneN(3))His](*2+) leading to the generation of two distinct His(*+) species; in contrast, the proton transfer (PT) dissociation pathways of [Cu(II)(9-aneN(3))His](*2+) and [Cu(II)(dien)His](*2+) differ considerably. The PT reactions of [Cu(II)(9-aneN(3))His](*2+) are associated with substantially higher barriers (>13 kcal/mol) than those of [Cu(II)(dien)His](*2+). Thus, the sterically encumbered auxiliary 9-aneN(3) ligand facilitates ET reactions while moderating PT reactions, allowing the formation of hitherto nonobservable histidine radical cations.

Dissociation of the N-C(alpha) bond and competitive formation of the [z(n) - H](+) and [c(n) + 2H](+) product ions in radical peptide ions containing tyrosine and tryptophan: the influence of proton affinities on product formation.

Dissociations at the N-C(alpha) bond of tryptophan and tyrosine residues are the prevalent pathways in the fragmentations of radical cations of tripeptides that contain such as residues. This process involves a proton transfer from the beta-carbon of the tryptophan or tyrosine residue to the carbonyl oxygen of the amide group, followed by cleavage of the N-C(alpha) bond, generating low-lying proton-bound dimers that dissociate to give each an ionic and a neutral product. Formation of the [z(n) - H](*+) or [c(n) + 2H](+) ion is a competition between the two incipient fragments for the proton in a dissociating proton-bound dimer.

Catalytic oxidation of H2 by N2O in the gas phase: O-atom transport with atomic metal cations.

Twenty-five atomic cations, M (+), that lie within the thermodynamic window for O-atom transport catalysis of the oxidation of hydrogen by nitrous oxide, have been checked for catalytic activity at room temperature with kinetic measurements using an inductively-coupled plasma/selected-ion flow tube (ICP/SIFT) tandem mass spectrometer. Only 4 of these 25 atomic cations were seen to be catalytic: Fe (+), Os (+), Ir (+), and Pt (+). Two of these, Ir (+) and Pt (+), are efficient catalysts, while Fe (+) and Os (+) are not. Eighteen atomic cations (Cr (+), Mn (+), Co (+), Ni (+), Cu (+), Ge (+), Se (+), Mo (+), Ru (+), Rh (+), Sn (+), Te (+), Re (+), Pb (+), Bi (+), Eu (+), Tm (+), and Yb (+)) react too slowly at room temperature either in their oxidation with N 2O to form MO (+) or in the reduction of MO (+) by H 2. Many of these reactions are known to be spin forbidden and a few actually may lie outside the thermodynamic window. Three alkaline-earth metal monoxide cations, CaO (+), SrO (+), and BaO (+), were observed to favor MOH (+) formation in their reactions with H 2. A potential-energy landscape is computed for the oxidation of H 2 with N 2O catalyzed by Fe (+)( (6)D) that vividly illustrates the operation of an ionic catalyst and qualitatively accounts for the relative inefficiency of this catalyst.

Radical-cationic gaseous amino acids: a theoretical study.

Three major forms of gaseous radical-cationic amino acids (RCAAs), keto (COOH), enolic (C(OH)OH), and zwitterionic (COO(-)), as well as their tautomers, are examined for aliphatic Ala(.+), Pro(.+), and Ser(.+), sulfur-containing Cys(.+), aromatic Trp(.+), Tyr(.+), and Phe(.+), and basic His(.+). The hybrid B3LYP exchange-correlation functional with various basis sets along with the highly correlated CCSD(T) method is used. For all RCAAs considered, the main stabilizing factor is spin delocalization; for His(.+), protonation of the basic side chain is equally important. Minor stabilizing factors are hydrogen bonding and 3e-2c interactions. An efficient spin delocalization along the N-C(alpha)-C(O-)O moiety occurs upon H-transfer from C(alpha) to the carboxylic group to yield the captodative enolic form, which is the lowest-energy isomer for Ala(.+), Pro(.+), Ser(.+), Cys(.+), Tyr(.+), and Phe(.+). This H-transfer occurs in a single step as a 1,3-shift through the sigma-system. For His(.+), the lowest-energy isomer is formed upon H-transfer from C(alpha) to the basic side chain, which results in a keto form, with spin delocalized along the N-C(alpha)-C=O fragment. Trp(.+) is the only RCAA that favors spin delocalization over an aromatic system given the low ionization energy of indole. The lowest-energy isomer of Trp(.+) is a keto form, with no H-transfer.

Gas-phase ionic syntheses of amino acids: beta versus alpha.

Both theoretical and experimental studies are reported for the gas-phase reactions of protonated hydroxylamine with acetic and propanoic acids which yield protonated glycine and alanine, GlyH+ and AlaH+, respectively. The key step for these reactions is an insertion of the amino group into a C-H bond. For the formation of AlaH+, the reaction barrier for insertion into a Cbeta-H bond is ca. 5 kcal.mol-1 lower than that for the insertion into a Calpha-H bond; the product beta-AlaH+ is ca. 6 kcal mol-1 lower in energy than alpha-AlaH+. Thus, both kinetics and thermodynamics favor formation of the beta-form. The energetic preference for the beta-form is due to more efficient hydrogen bonding between the amino group and the carbonyl oxygen in the limiting transition structure and in the beta-AlaH+ product. These theoretical results are in excellent accord with selected ion flow tube measurements of the gas-phase synthesis which show striking specificity for the beta-isomer according to multi-collision-induced dissociation of the AlaH+ product ion. The results suggest that Gly and beta-Ala found in carbonaceous chondrite meteorites are products of interstellar chemistry.

Water-catalyzed hydrolysis of the radical cation of ketene in the gas phase: theory and experiment.

Both theoretical and experimental investigations are reported for the gas-phase hydrolysis of the radical cation of ketene, H(2)CCO(*+). Density functional theory (DFT) with the B3LYP/6-311++G(d,p) method indicates that a second water molecule is required as a catalyst for the addition of water across the C=O bond in H(2)CCO(*+) by eliminating the activation barrier for the conversion of [H(2)CCO.H(2)O](*+) to [H(2)CC(OH)(2)](*+). Theory further indicates that [H(2)CC(OH)(2).H(2)O](*+) may recombine with electrons to produce neutral acetic acid. Experimental results of flow-reactor tandem mass spectrometer experiments in which CH(2)CO(*+) ions were produced either directly from ketene by electron transfer or by the chemical reaction of CH(2)(*+) with CO are consistent with formation of an (C(2),H(4),O(2))(*+) ion in a reaction second-order in H(2)O. Furthermore, comparative multi-CID experiments indicate that this ion is likely to be the enolic CH(2)C(OH)(2)(*+) cation. The results suggest a possible mechanism for the formation of acetic acid from ketene and water on icy surfaces in hot cores and interstellar clouds.

Gaseous bradykinin and its singly, doubly, and triply protonated forms: a first-principles study.

The conformers of gaseous bradykinin, BK, (Arg(1)-Pro(2)-Pro(3)-Gly(4)-Phe(5)-Ser(6)-Pro(7)-Phe(8)-Arg(9)) and its protonated forms, [BK + H](+), [BK + 2H](2+), and [BK + 3H](3+), were examined theoretically using a combination of the Merck molecular force field, Hartree-Fock, and density functional theory. Neutral BK, [BK + H](+), and [BK + 2H](2+) exist in zwitterionic forms that are stabilized by internal solvation and have compact structures; [BK + 3H](3+) differs by the absence of a salt bridge and adopts an elongated form. The common structural feature in all four BK species is a beta-turn in the Ser(6)-Pro(7)-Phe(8)-Arg(9) sequence. The gas-phase basicity of [BK + H](+) estimated from the calculated protonation energy is in accord with published experimental basicity; population-weighted collision cross-sections of the three ionic forms are in agreement with experimental cross-sections in the literature.

O-atom transport catalysis by atomic cations in the gas phase: reduction of N2O by CO.

Atomic cations (26), M+, have been shown to lie within a thermodynamic window for O-atom transport catalysis of the reduction of N2O by CO and have been checked for catalytic activity at room temperature with kinetic measurements using an inductively-coupled plasma/selected-ion flow tube (ICP/SIFT) tandem mass spectrometer. Only 10 of these 26 atomic cations were seen to be catalytic: Ca+, Fe+, Ge+, Sr+, Ba+, Os+, Ir+, Pt+, Eu+, and Yb+. The remaining 16 cations that lie in the thermodynamic window (Cr+, Mn+, Co+, Ni+, Cu+, Se+, Mo+, Ru+, Rh+, Sn+, Te+, Re+, Pb+, Bi+, Tm+, and Lu+) react too slowly at room temperature either in the formation of MO+ or in its reduction by CO. Many of these reactions are known to be spin forbidden and a few actually may lie outside the thermodynamic window. A new measure of efficiency is introduced for catalytic cycles that allows the discrimination between catalytic cations on the basis of the efficiencies of the two legs of the catalytic cycle. Also, a potential-energy landscape is computed for the reduction of N2O by CO catalyzed by Fe+(6D) that vividly illustrates the operation of an ionic catalyst.

Existence of doubly charged lead monohydrate: experimental evidence and theoretical examination.

Despite reports to the contrary, doubly charged lead monohydrate is a stable species against both proton and charge transfers. [Pb(H(2)O)](2+) has been observed as a minor product in the ligand-exchange reaction of [Pb(CH(3)CN)](2+) with H(2)O after collisional activation. Density functional theory has been used to examine reaction profiles of [Pb(H(2)O)(n)](2+) where n = 1, 2, and 3.

Theoretical study of the amazing firefly bioluminescence: the formation and structures of the light emitters.

Reaction mechanisms for the formation of the keto-form of oxyluciferin (OxyLH(2)) from the luciferin of fireflies via a dioxetanone intermediate are predicted using the B3LYP/6-31G theoretical method. The ring opening of a model dioxetanone and the decarboxylation proceed in one step via a singlet diradical transition structure with an activation barrier of 18.1 and an exothermicity of 90.8 kcal/mol. The S(0) --> S(1) vertical excitation energies predicted with time dependent density functional theory, TDDFT B3LYP/6-31+G, for the anionic and neutral forms of OxyLH(2) are in the range of 60 to 80 kcal/mol. These energetic results support the generally accepted theory of chemically initiated electron exchange luminescence (CIEEL). The chemical origin of the multicolor bioluminescence from OxyLH(2) is examined theoretically using the TDDFT B3LYP/6-31+G, ZINDO//B3LYP/6-31+G, and CIS/6-31G methods. A change in color of the light emission upon rotation of the two rings in the S(1) excited state of OxyLH(2) is unlikely because both possible emitters, the planar keto- and enol-forms, are minima on the S(1) potential energy surface. The participation of the enol-forms of OxyLH(2) in bioluminescence is plausible but not required to explain the multicolor emission. According to predictions at the TDDFT B3LYP level, the color of the bioluminescence depends on the polarization of the OxyLH(2) in the microenvironment of the enzyme-OxyLH(2) complex.

rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation.

The analysis of gene regulatory networks has become one of the most challenging problems of the postgenomic era. Earlier we developed rSNP_Guide (http://util.bionet.nsc.ru/databases/rsnp.html), a computer system and database devoted to prediction of transcription factor (TF) binding sites (TF sites), which can be responsible for disease phenotypes. The prediction results were confirmed by 70 known relationships between TF sites and diseases, as well as by site-directed mutagenesis data. The rSNP_Guide is being investigated as a tool for TF site annotation. Previously analyzed and characterized cases of altered TF sites were used to annotate potential sites of the same type and at the same location in homologous genes. Based on 20 TF sites with known alterations in TF binding to DNA, we localized 245 potential TF sites in homologous genes. For these potential TF sites, rSNP_Guide estimates TF-DNA interaction according to three categories: 'present', 'weak', and 'absent'. The significance of each assignment is statistically measured.

rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites.

Since the human genome was sequenced in draft, single nucleotide polymorphism (SNP) analysis has become one of the keynote fields of bioinformatics. We have developed an integrated database-tools system, rSNP_Guide (http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/), devoted to prediction of transcription factor (TF) binding sites, alterations of which could be associated with disease phenotype. By inputting data on alterations in DNA sequence and in DNA binding pattern of an unknown TF, rSNP_Guide searches for a known TF with alterations in the recognition score calculated on the basis of TF site's sequence and consistent with the input alterations in DNA binding to the unknown TF. Our system has been tested on many relationships between known TF sites and diseases, as well as on site-directed mutagenesis data. Experimental verification of rSNP_Guide system was made on functionally important SNPs in human TDO2and mouse K-ras genes. Additional examples of analysis are reported involving variants in the human gammaA-globin (HBG1), hsp70(HSPA1A), and Factor IX (F9) gene promoters.

Regioselective silylation of sugars through palladium nanoparticle-catalyzed silane alcoholysis.

Palladium(0)-catalyzed silane alcoholysis was applied to sugars for the first time using tert-butyldimethylsilane (TBDMS-H) and Ph(3)SiH as the silanes. The catalyst is a colloidal solution of Pd(0) generated in situ from PdX(2) (X = Cl(-), OAc(-)) and TBDMS-H in N,N-dimethylacetamide. The colloid has been characterized by dynamic light scattering and transmission electron microscopy and consists of catalytically highly active nanoparticles of approximately 2 nm diameter. The silane alcoholysis reaction is an effective method for the regioselective silylation of methyl and phenyl glycosides and generates hydrogen gas as the only side product. For many of the sugar substrates investigated, the distribution of regioisomers obtained is complementary to that of the traditional R(3)SiCl/base (base = pyridine, imidazole) methodology and gives convenient access to the 3,6- rather than the 2,6-silylated pyranosides, obtained as the main product by the silyl chloride method. The method also allows a selective axial silylation of levoglucosan and 1,3,5-O-methylidene-myo-inositol. In an attempt to rationalize the observed regioselectivities, ab initio predictions (HF/3-21G) have been made on the relative energies of some of the silylated products. They suggest that the observed regioselectivities do not reflect a kinetic vs thermodynamic product distribution but are induced by the silylation agent employed. Models for the possible origin of the observed regioselectivity in both silylation methods (silane- and silyl chloride-based) are discussed.

SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data.

SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. Since in vitro experimental data are evidently system-dependent, the new release of the SELEX_DB has been supplemented by the database SYSTEM storing the experimental design. In addition, the recognition applet package, SELEX_TOOLS, applying in vitro selected data to annotation of the genome DNA, is accompanied by the cross-validation test database CROSS_TEST discriminating the sites (natural or other) related to in vitro selected sites out of random DNA. By cross-validation testing, we have unexpectedly observed that the recognition accuracy increases with the growth of homology between the training and test sets of protein binding sequences. For natural sites, the recognition accuracy was lower than that for the nearest protein homologs and higher than that for distant homologs and non-homologous proteins binding the common site. The current SELEX_DB release is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/.