Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

fac-/mer-[RuCl(3)(NO)(P-N)] (P-N = [o-(N,N-dimethylamino)phenyl]diphenylphosphine): Synthesis, characterization and DFT calculations

Complex fac-[RuCl(3)(NO)(P-N)] (1) was synthesized from the reaction of [RuCl(3)(H(2)O)(2)(NO)] and the P-N ligand, o-[(N,N-dimethylamino)phenyl]diphenylphosphine) in refluxing methanol solution, while complex mer,trans-[RuCl(3)(NO)(P-N)] (2) was obtained by photochemical isomerization of (1) in dichloromethane solution. The third possible isomer mer, cis-[RuCl(3)(NO)(P-N)] (3) was never observed in direct synthesis as well as in photo-or thermal-isomerization reactions. When refluxing a methanol solution of complex (2) a thermally induced isomerization occurs and complex (1) is regenerated. The complexes were characterized by NMR ((31)P{(1)H}, (15)N{1H} and 1H), cyclic voltammetry, FTIR, UV-Vis, elemental analysis and X-ray diffraction structure determination. The (31)P{(1)H} NMR revealed the presence of singlet at 35.6 for (1) and 28.3 ppm for (2). The (1)H NMR spectrum for (1) presented two singlets for the methyl hydrogens at 3.81 and 3.13 ppm, while for (2) was observed only one singlet at 3.29 ppm. FTIR Ru-NO stretching in KBr pellets or CH(2)Cl(2) solution presented 1866 and 1872 cm(-1) for (1) and 1841 and 1860 cm(-1) for (2). Electrochemical analysis revealed a irreversible reduction attributed to Ru(II)-NO(+) -> Ru(II)-NO(0) at -0.81 V and -0.62 V, for (1) and (2), respectively; the process Ru(II) -> Ru(III), as expected, is only observed around 2.0 V, for both complexes. Studies were conducted using (15)NO and both complexes were isolated with (15)N-enriched NO. Upon irradiation, the complex fac-[RuCl(3)(NO)(P-N)] (1) does not exchange (14)NO by (15)NO, while complex mer, trans-[RuCl(3)(NO)(P-N)] (2) does. Complex mer, trans-[RuCl(3)((15)NO)(P-N)] (2`) was obtained by direct reaction of mer, trans-[RuCl(3)(NO)(P-N)] (2) with (15)NO and the complex fac-[RuCl(3)((15)NO)(P-N)] (1`) was obtained by thermal-isomerization of mer, trans-[RuCl(3)((15)NO)(P-N)] (2`). DFT calculation on isomer energies, electronic spectra and electronic configuration were done. For complex (1) the HOMO orbital is essentially Ru (46.6%) and Cl (42.5%), for (2) Ru (57.4%) and Cl (39.0%) while LUMO orbital for (1) is based on NO (52.9%) and is less extent on Ru (38.4%), for (2) NO (58.2%) and Ru (31.5%). (C) 2011 Elsevier B. V. All rights reserved.

The binding of synthetic triiodo L-thyronine analogs to human transthyretin: Molecular basis of cooperative and non-cooperative ligand recognition

Transthyretin (TTR) is a tetrameric beta-sheet-rich transporter protein directly involved in human amyloid diseases. Several classes of small molecules can bind to TTR delaying its amyloid fibril formation, thus being promising drug candidates to treat TTR amyloidoses. In the present study, we characterized the interactions of the synthetic triiodo L-thyronine analogs and thyroid hormone nuclear receptor TR beta-selecfive agonists GC-1 and GC-24 with the wild type and V30M variant of human transthyretin (TTR). To achieve this aim, we conducted in vitro TTR acid-mediated aggregation and isothermal titration calorimetry experiments and determined the TTR:GC-1 and TTR:GC-24 crystal structures. Our data indicate that both GC-1 and GC-24 bind to TTR in a non-cooperative manner and are good inhibitors of TTR aggregation, with dissociation constants for both hormone binding sites (HBS) in the low micromolar range. Analysis of the crystal structures of TTRwt:GC-1(24) complexes and their comparison with the TTRwt X-ray structure bound to its natural ligand thyroxine (T4) suggests, at the molecular level, the basis for the cooperative process displayed by T4 and the non-cooperative process provoked by both GC-1 and GC-24 during binding to TTR. (C) 2010 Elsevier Inc. All rights reserved.

Evaluation of dental pulp repair using low level laser therapy (688 nm and 785 nm) morphologic study in capuchin monkeys

The aim of this study was to evaluate the hypothesis that low-level laser therapy (LLLT) 688 nm and 785 nm accelerate dentin barrier formation and repair process after traumatic pulp exposure. The sample consisted of 45 premolars of capuchin monkeys (Cebus apella) with pulp exposure Class V cavities. All premolars were treated with calcium hydroxide (Ca(OH)(2)), divided in groups of 15 teeth each, and analyzed on 7(th), 25(th), and 60(th) day. Group GI - only Ca(OH)(2), GIF- laser 688 nm, and GIII - laser 785 nm. Laser beam was used in single and punctual dose with the parameters: continuous, 688 nm and 785 nm wavelength, tip`s area of 0.00785 cm(2), power 50 mW, application time 20 s, dose 255 J/cm(2), energy 2 J. Teeth were capped with Ca(OH)(2), Ca(OH)(2) cement and restored with amalgam. All groups presented pulp repair. On 25(th) day the thickness of the formed dentin barrier was different between the groups GI and GII (p < 0.05) and between groups GI and GIII (p < 0.01). On 60(th) day there was difference between GI and GIII (p < 0.01). It may be concluded that, LLLT 688 nm and 785 nm accelerated dentin barrier formation and consequently pulp repair process, with best results using infrared laser 785 nm. (c) 2009 by Astro Ltd. Published exclusively by WLLEY-VCH Verlag GmbH & Co. KGaA

Isolation, chemical composition and anti-inflammatory activity of Copaifera langsdorffii desf. fruit peels essential oil according to successive hydrodistillations

In this study, the isolation and characterization of chemical composition of C. langsdorffii (copaiba) fruit peel volatile oil from Alfenas - MG was carried out according to successive hydrodistillations, likewise the anti-inflammatory activity was evaluated by rat paw edema model. The chemical composition of the oil was determined by GC-MS analysis. The major components were (E)-caryophyllene, germacrene B, 1,5-epoxysalvial-4(14)-ene, caryophyllene oxide and isospathulenol. The inflammatory process was inhibited in 39 +/- 6 % (p<0.05, Tukey-Kramer) by one sample of essential oil. The C. langsdorffii fruit peel is a rich source of essential oil (3.8% w/w), and due to potential industrial interest of its components this ecotype presents feasible crop seeking productivity and it could constitutes in a good alternative to the sustainable use of this specie.

The link between partial melting, granitization and granulite development in central Ribeira Fold Belt, SE Brazil: New evidence from elemental and Sr-Nd isotopic geochemistry

Elemental and Sr-Nd isotopic data on metatexites, diatexites, orthogneisses and charnockites from the central Ribeira Fold Belt indicate that they are LILE-enriched weakly peraluminous granodiorites. Harker and Th-Hf-La correlation trends suggest that these rocks represent a co-genetic sequence, whereas variations on CaO, MnO, Y and HREE for charnockites can be explained by garnet consumption during granulitic metamorphism. Similar REE patterns and isotopic results of epsilon(565)(Nd) = -5.4 to -7.3 and (87)Sr/(86)Sr(565) = 0.706-0.711 for metatexites, diatexites, orthogneisses and charnockites, as well as similar T(DM) ages between 2.0 and 1.5 Ga are consistent with evolution from a relatively homogeneous and enriched common crustal (metasedimentary) protolith. Results suggest a genetic link between metatexites, diatexites, orthogneisses and charnockites and a two-step process for charnockite development: (a) generation of the hydrated igneous protoliths by anatexis of metasedimentary rocks; (b) continuous high-grade metamorphism that transformed the ""S-type granitoids"" (leucosomes and diatexites) into orthogneisses and, as metamorphism and dehydration progressed, into charnockites. (C) 2011 Elsevier Ltd. All rights reserved.