Artur M. S. Silva

PanWeb: A web interface for pan-genomic analysis

With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species. Thus, a new approach to comparative genomics, termed pan-genomics, was developed. In pan-genomics, various organisms of the same species or genus are compared. Currently, there are many tools that can perform pan-genomic analyses, such as PGAP (Pan-Genome Analysis Pipeline), Panseq (Pan-Genome Sequence Analysis Program) and PGAT (Prokaryotic Genome Analysis Tool). Among these software tools, PGAP was developed in the Perl scripting language and its reliance on UNIX platform terminals and its requirement for an extensive parameterized command line can become a problem for users without previous computational knowledge. Thus, the aim of this study was to develop a web application, known as PanWeb, that serves as a graphical interface for PGAP. In addition, using the output files of the PGAP pipeline, the application generates graphics using custom-developed scripts in the R programming language. PanWeb is freely available at http://www.computationalbiology.ufpa.br/panweb.

Characterization of an acetylated heteroxylan from Eucalyptus globulus Labill

A heteroxylan was isolated from Eucalyptus globulus wood by extraction of peracetic acid delignified holocellulose with dimethyl sulfoxide. Besides (1-->4)-linked beta-D-xylopyranosyl units of the backbone and short side chains of terminal (1-->2)-linked 4-O-methyl-alpha-D-glucuronosyl residues (MeGlcA) in a 1:10 molar ratio, this hemicellulose contained galactosyl and glucosyl units attached at O-2 of MeGlcA originating from rhamnoarabinogalactan and glucan backbones, respectively. About 30% of MeGlcA units were branched at O-2. The O-acetyl-(4-O-methylglucurono)xylan showed an acetylation degree of 0.61, as determined by 1H NMR spectroscopy, and a weight-average molecular weight (M(w)) of about 36 kDa (P=1.05) as revealed from size-exclusion chromatography (SEC) analysis. About half of the beta-D-xylopyranosyl units of the backbone were found as acetylated moieties at O-3 (34 mol%), O-2 (15 mol%) or O-2,3 (6 mol%). Practically, all beta-D-xylopyranosyl units linked at O-2 with MeGlcA residues were 3-O-acetylated (10 mol%).

Ion Specific Effects on the Mutual Solubilities of Water and Hydrophobic Ionic Liquids

Ion specific effects on the mutual solubilities between hydrophobic ionic liquids (ILs) and water are complex and not fully understood. The aim of this work is to obtain further evidence about the molecular mechanism behind this phenomenon by evaluating the effect of a large series of inorganic and organic salts on the mutual solubilities of water and the ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C(4)mim][Tf(2)N]. The magnitudes of the salting-in and salting-out effects were assessed by changing either the cation or the anion, in a series of salts, as well as the salt concentration. It was observed that the influence of the ions on the solubility followed the Hofmeister series. Both salting-in and salting-out effects were observed and they showed to be dependent on both the nature of the salt and its concentration, while the pH had only a marginal effect on the studied solubilities. On the basis of the solubility changes of the ionic liquid in water in the presence of salts and on NMR spectroscopic data, it will be shown that salting-out inducing ions (high charge density) and salting-in inducing ions (low charge density) act through different mechanisms. While the former act mainly through an entropic effect resulting from the formation of water-ion hydration complexes which cause the dehydration of the solute and the increase of the surface tension of the cavity, the salting-in results from a direct ion binding of the low charge density ions to the hydrophobic moieties of the solute.

Experimental measurements and theoretical calculations of the chemical shifts and coupling constants of three azines (benzalazine, acetophenoneazine and cinnamaldazine)

Three azines, two of them doubly labeled with 15N, have been studied by multinuclear magnetic resonance in solution and in the solid state. The spectral parameters obtained by iterative analyses have been compared with DFT/B3LYP calculated values (absolute shieldings and coupling constants). The agreement is generally good. Some anomalies have been discussed in relation to the structure of these compounds. Copyright

Chromones and flavanones from artemisia campestris subsp. maritima

Abstract From the acetone extract of Artemisia campestris subsp. maritima six flavanones, two chromones and the coumarin scopoletin were isolated. 5-Hydroxy-7-methoxychromone and 5,7-dimethoxychromone are new compounds, while the flavanone eriodictyol-7,3′-dimethyl ether is reported for the first time in this species. The structures were elucidated by 1D and 2D NMR techniques. The unequivocal assignments of carbon resonances, mainly made by using 1D selective INEPT and 2D HETCOR experiments, allowed us to correct some 1H and 13C resonances of the isolated flavanones and also to differentiate between the flavanone isomers sakuranetin⧹isosakuranetin and eriodictyol-7,3′-dimethyl ether⧹eriodictyol-7,4′-dimethyl ether.

Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains as structural features of coffee arabinogalactans.

The hot water soluble green coffee arabinogalactans, representing nearly 7% of total coffee bean arabinogalactans, were characterized by (1)H and (13)C NMR and, after partial acid hydrolysis, by ESI-MS/MS. Data obtained showed that these are highly branched type II arabinogalactans covalently linked to proteins (AGP), with a protein moiety containing 10% of 4-hydroxyproline residues. They possess a beta-(1-->3)-Galp/beta-(1-->3,6)-Galp ratio of 0.80, with a sugars composition of Rha:Ara:Gal of 0.25:1.0:1.5, and containing 2mol% of glucuronic acid residues. Beyond the occurrence of single alpha-L-Araf residues and [alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] disaccharide residues as side chains, these AGPs contain unusual side chains at O-3 position of the beta-(1-->6)-linked galactopyranosyl residues composed by [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->] and [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] oligosaccharides. Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains are reported for the first time as structural features of plant arabinogalactan-proteins.

Catechols from abietic acid synthesis and evaluation as bioactive compounds.

Catechols from abietic acid were prepared by a short and good yielding chemical process and further evaluated for several biological activities namely, antifungal, antitumoral, antimutagenic, antiviral, antiproliferative and inhibition of nitric oxide. Their properties were compared with those of carnosic acid (6), a naturally occurring catechol with an abietane skeleton and known to possess potent antioxidant activity, as well as anticancer and antiviral properties. From all the synthetic catechols tested compound 2 showed the best activities, stronger than carnosic acid.

Porphyrins in 1,3-dipolar cycloaddition reactions with sugar nitrones. Synthesis of glycoconjugated isoxazolidine-fused chlorins and bacteriochlorins

Glycoconjugated isoxazolidine-fused chlorins and bacteriochlorins were prepared in moderate to good yields by 1,3-dipolar cycloaddition reactions of meso-tetrakis(pentafluorophenyl)porphyrin with glycosyl nitrones.

Structural characterisation of the olive pomace pectic polysaccharide arabinan side chains

An arabinan (97% of Ara and 3% of hexuronic acid) was isolated from the alcohol-insoluble residue (AIR) of olive pomace by treatment with 0.02 M HNO(3), at 80 degrees C, followed by graded precipitation with ethanol. It was separated from acidic pectic polysaccharides by anion-exchange chromatography, and by size-exclusion chromatography its molecular weight was estimated as 8.4 kDa. By methylation analysis, the linkage composition was established as 5:4:3:1 for (1-->5)-Araf, T-Araf, (1-->3,5)-Araf and (1-->3)-Araf, respectively. 13C NMR spectroscopy confirmed this linkage composition, and allowed to assign the alpha anomeric configuration for the arabinofuranosyl residues, except for some terminally linked ones, that were seen to occur as T-beta-Araf. By 2D NMR spectroscopy (1H and 13C), it was possible to conclude that the T-beta-Araf was (1-->5)-linked to a (1-->5)-Araf residue. Also, in the arabinan (1-->5)-Araf backbone, the branched (1-->3,5)-Araf residues were always adjacent to linear (1-->5)-Araf residues. A tentative structure is proposed.

Flavonoids as therapeutic compounds targeting key proteins involved in Alzheimer's disease.

Alzheimers disease is characterized by pathological aggregation of protein tau and amyloid-β peptides, both of which are considered to be toxic to neurons. Naturally occurring dietary flavonoids have received considerable attention as alternative candidates for Alzheimers therapy taking into account their antiamyloidogenic, antioxidative, and anti-inflammatory properties. Experimental evidence supports the hypothesis that certain flavonoids may protect against Alzheimers disease in part by interfering with the generation and assembly of amyloid-β peptides into neurotoxic oligomeric aggregates and also by reducing tau aggregation. Several mechanisms have been proposed for the ability of flavonoids to prevent the onset or to slow the progression of the disease. Some mechanisms include their interaction with important signaling pathways in the brain like the phosphatidylinositol 3-kinase/Akt and mitogen-activated protein kinase pathways that regulate prosurvival transcription factors and gene expression. Other processes include the disruption of amyloid-β aggregation and alterations in amyloid precursor protein processing through the inhibition of β-secretase and/or activation of α-secretase, and inhibiting cyclin-dependent kinase-5 and glycogen synthase kinase-3β activation, preventing abnormal tau phosphorylation. The interaction of flavonoids with different signaling pathways put forward their therapeutic potential to prevent the onset and progression of Alzheimers disease and to promote cognitive performance. Nevertheless, further studies are needed to give additional insight into the specific mechanisms by which flavonoids exert their potential neuroprotective actions in the brain of Alzheimers disease patients.