Phylogenetic analysis of a near-full-length sequence of an erythrovirus genotype 3 strain isolated in Brazil

Human parvovirus B19 is the only member of the genus Erythrovirus that causes human disease. Recent findings of several strains with considerable sequence divergence from B19 have suggested a new classification for parvovirus genotypes as 1 (B19), 2 (A-6 and LaLi) and 3 (V9). In their overall DNA sequence, the three genotypes differ by similar to 10%. Here, we report the isolation of a genotype-3-related strain named BR543 during a prospective study conducted in Sao Paulo, Brazil. Analysis of the nearly full-length genome sequence of BR543 indicates that this B19 variant sequence clusters with Gh2768, a strain from Ghana belonging to subtype 3b, and showed mostly synonymous substitutions.

Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding

Trypanosoma cruzi and Trypanosoma rangeli are human-infective blood parasites, largely restricted to Central and South America. They also infect a wide range of wild and domestic mammals and are transmitted by a numerous species of triatomine bugs. There are significant overlaps in the host and geographical ranges of both species. The two species consist of a number of distinct phylogenetic lineages. A range of PCR-based techniques have been developed to differentiate between these species and to assign their isolates into lineages. However, the existence of at least six and five lineages within T. cruzi and T. rangeli, respectively, makes identification of the full range of isolates difficult and time consuming. Here we have applied fluorescent fragment length barcoding (FFLB) to the problem of identifying and genotyping T. cruzi, T. rangeli and other South American trypanosomes. This technique discriminates species on the basis of length polymorphism of regions of the rDNA locus. FFLB was able to differentiate many trypanosome species known from South American mammals: T. cruzi cruzi. T. cruzi marinkellei, T. dionisii-like, T. evansi, T. lewisi, T. rangeli, T. theileri and T. vivax. Furthermore, all five T. rangeli lineages and many T. cruzi lineages could be identified, except the hybrid lineages TcV and TcVI that could not be distinguished from lineages III and II respectively. This method also allowed identification of mixed infections of T. cruzi and T. rangeli lineages in naturally infected triatomine bugs. The ability of FFLB to genotype multiple lineages of T. cruzi and T. rangeli together with other trypanosome species, using the same primer sets is an advantage over other currently available techniques. Overall, these results demonstrate that FFLB is a useful method for species diagnosis, genotyping and understanding the epidemiology of American trypanosomes. (C) 2010 Elsevier B.V. All rights reserved.

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.

Synthesis of YAP nanopowder by a soft chemistry route

Polycrystalline fine powder of YAlO(3) (YAP) was synthesized by the modified polymeric precursor method. A preliminary gradual pyrolytic decomposition under nitrogen flux was crucial in the removal process of organic residues to avoid the formation of molecular level inhomogeneities. YAP single phase was crystallized at temperatures between 950 degrees C and 1000 degrees C using chemically homogeneous ball-milled amorphous particles and very fast heating rates, corresponding to the lowest synthesis temperature of pure YAP nanopowder by soft chemistry routes. (C) 2009 Elsevier Ltd. All rights reserved.

Synthesis optimization, structural evolution and optical properties of Y(0.9)Er(0.1)Al(3)(BO(3))(4) nanopowders obtained by soft chemistry methods

This paper describes the structural evolution of Y(0.9)Er(0.1)Al(3)(BO(3))(4) nanopowders using two soft chemistry routes, the sol-gel and the polymeric precursor methods. Differential scanning calorimetry, differential thermal analyses, thermogravimetric analyses, X-ray diffraction, Fourier-transform infrared, and Raman spectroscopy techniques have been used to study the chemical reactions between 700 and 1200 degrees C temperature range. From both methods the Y(0.9)Er(0.1)Al(3)(BO(3))(4) (Er:YAB) solid solution was obtained almost pure when the powdered samples were heat treated at 1150 degrees C. Based on the results, a schematic phase formation diagram of Er:YAB crystalline solid solution was proposed for powders from each method. The Er:YAB solid solution could be optimized by adding a small amount of boron oxide in excess to the Er:YAB nominal composition. The nanoparticles are obtained around 210 nm. Photoluminescence emission spectrum of the Er:YAB nanocrystalline powders was measured on the infrared region and the Stark components of the (4)I(13/2) and (4)I(15/2) levels were determined. Finally, for the first time the Raman spectrum of Y(0.9)Er(0.1)Al(3)(BO(3))(4) crystalline phase is also presented. (C) 2008 Elsevier Masson SAS. All rights reserved.

Effects of Crossing Saddle Coil Conductors: Electric Length X Mutual Inductance

In magnetic resonance imaging (MRI), either on human or animal studies, the main requirements for radiofrequency (RF) coils are to produce a homogeneous RF field while used as a transmitter coil and to have the best signal-to-noise ratio (SNR) while used as a receiver. Besides, they need to be easily frequency adjustable and have input impedance matching 50 Omega to several different load conditions. New theoretical and practical concepts are presented here for considerable enhancing of RF coil homogeneity for MRI experiments on small animals. To optimize field homogeneity, we have performed simulations using Blot and Savart law varying the coil`s window angle, achieving the optimum one. However, when the coil`s dimensions are the same order of the wave length and according to transmission line theory, differences in electrical length and effects of mutual inductances between adjacent strip conductors decrease both field homogeneity and SNR. The problematic interactions between strip conductors by means of mutual inductance were eliminated by inserting crossings at half electrical length, avoiding distortion on current density, thus eliminating sources of field inhomogeneity. Experimental results show that measured field maps and simulations are in good agreement. The new coil design, dubbed double-crossed saddle described here have field homogeneity and SNR superior than the linearly driven 8-rung birdcage coil. One of our major findings was that the effects of mutual inductance are more significant than differences in electrical length for this frequency and coil dimensions. In vitro images of a primate Cebus paela brain were acquired, confirming double-crossed saddle superiority. (C) 2010 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 37B: 193-201, 2010

High T/P evolution and metamorphic ages of the migmatitic basement of northern Sierras Pampeanas, Argentina: Characterization of a mid-crustal segment of the Famatinian belt

New petrologic, thermobarometric and U-Pb monazite geochronologic information allowed to resolve the metamorphic evolution of a high temperature mid-crustal segment of an ancient subduction-related orogen. The EI Portezuelo Metamorphic-Igneous Complex, in the northern Sierras Pampeanas, is mainly composed of migmatites that evolved from amphibolite to granulite metamorphic facies, reaching thermal peak conditions of 670-820 degrees C and 4.5-5.3 kbar. The petrographic study combined with conventional and pseudosection thermobarometry led to deducing a short prograde metamorphic evolution within migmatite blocks. The garnet-absent migmatites represent amphibolite-facies rocks, whereas the cordierite-garnet-K-feldspar-sillimanite migmatites represent higher metamorphic grade rocks. U-Pb geochronology on monazite grains within leucosome record the time of migmatization between approximate to 477 and 470 Ma. Thus, the El Portezuelo Metamorphic-Igneous Complex is an example of exhumed Early Ordovician anatectic middle crust of the Famatinian mobile belt. Homogeneous exposure of similar paleo-depths throughout the Famatinian back-arc and isobaric cooling paths suggest slow exhumation and consequent longstanding crustal residence at high temperatures. High thermal gradients uniformly distributed in the Famatinian back-arc can be explained by shallow convection of a low-viscosity asthenosphere promoted by subducting-slab dehydration. (C) 2011 Elsevier Ltd. All rights reserved.

Identification of genes associated with local aggressiveness and metastatic behavior in soft tissue tumors

Soft tissue tumors represent a group of neoplasia with different histologic and biological presentations varying from benign, locally confined to very aggressive and metastatic tumors. The molecular mechanisms responsible for such differences are still unknown. The understanding of these molecular alterations mechanism will be critical to discriminate patients who need systemic treatment from those that can be treated only locally and could also guide the development of new drugs` against this tumors. Using 102 tumor samples representing a large spectrum of these tumors, we performed expression profiling and defined differentially expression genes that are likely to be involved in tumors that are locally aggressive and in tumors with metastatic potential. We described a set of 12 genes (SNRPD3, MEGF9, SPTAN-1, AFAP1L2, ENDOD1, SERPIN5, ZWINTAS, TOP2A, UBE2C, ABCF1, MCM2, and ARL6IP5) showing opposite expression when these two conditions were compared. These genes are mainly related to cell-cell and cell-extracellular matrix interactions and cell proliferation and might represent helpful tools for a more precise classification and diagnosis as well as potential drug targets.

A renewable copper electrode as an amperometric flow detector for nitrate determination in mineral water and soft drink samples

A novel approach was developed for nitrate analysis in a FIA configuration with amperometric detection (E=-0.48 V). Sensitive and reproducible current measurements were achieved by using a copper electrode activated with a controlled potential protocol. The response of the FIA amperometric method was linear over the range from 0.1 to 2.5 mmol L(-1) nitrate with a detection limit of 4.2 mu mol L(-1) (S/N = 3). The repeatability of measurements was determined as 4.7% (n=9) at the best conditions (flow rate: 3.0 mL min(-1), sample volume: 150 mu L and nitrate concentration: 0.5 mmol L(-1)) with a sampling rate of 60 samples h(-1). The method was employed for the determination of nitrate in mineral water and soft drink samples and the results were in agreement with those obtained by using a recommended procedure. Studies towards a selective monitoring of nitrite were also performed in samples containing nitrate by carrying out measurements at a less negative potential (-0.20 V). (C) 2009 Elsevier B.V. All rights reserved.

The soft nucleophilicity of organotellurolates driving the S(N)2-type lactone ring-opening reaction

Lithium and magnesium organotellurolates were reacted with lactones producing the corresponding tellurocarboxylic acids. Treatment of the reaction mixture with lithium aluminum hydride allowed the isolation of the corresponding hydroxytellurides in a one-pot operation. (C) 2009 Published by Elsevier Ltd

Determination of sorbate and benzoate in beverage samples by capillary electrophoresis - Optimization of the method with inspection of ionic mobilities

The aim of this study was to develop a fast capillary electrophoresis method for the determination of benzoate and sorbate ions in commercial beverages. In the method development the pH and constituents of the background electrolyte were selected using the effective mobility versus pH curves. As the high resolution obtained experimentally for sorbate and benzoate in the studies presented in the literature is not in agreement with that expected from the ionic mobility values published, a procedure to determine these values was carried out. The salicylate ion was used as the internal standard. The background electrolyte was composed of 25 mmol L(-1) tris(hydroxymethyl)aminomethane and 12.5 mmol L(-1) 2-hydroxyisobutyric acid, atpH 8.1.Separation was conducted in a fused-silica capillary(32 cm total length and 8.5 cm effective length, 50 mu m I.D.), with short-end injection configuration and direct UV detection at 200 nm for benzoate and salicylate and 254 nm for sorbate ions. The run time was only 28 s. A few figures of merit of the proposed method include: good linearity (R(2) > 0.999), limit of detection of 0.9 and 0.3 mg L(-1) for benzoate and sorbate, respectively, inter-day precision better than 2.7% (n =9) and recovery in the range 97.9-105%. Beverage samples were prepared by simple dilution with deionized water (1:11, v/v). Concentrations in the range of 197-401 mg L(-1) for benzoate and 28-144 mg L(-1) for sorbate were found in soft drinks and tea. (c) 2008 Elsevier B.V. All rights reserved.

Effect of the chain length in the structure of imidazolic ionic liquids and dimethylformamide solutions probed by Raman spectroscopy

The Raman band assigned to the nu(C=O)mode in N,N-dimethylformamide (at ca. 1660 cm(-1)) was used as a probe to study a group of ionic liquids 1-alkyl-3-methylimidazolium bromide ([C(n)Mlm]Br) with different alkyl groups (n = 2, 4, 6, 8 and 10 carbons) in binary equimolar binary mixtures with dimethylformamide. Due to the high electric dipole moment of the group C=O, there is a substantial coupling between adjacent molecules in the solution, and the corresponding Raman band involves both vibrational and reorientational modes. Different chain lengths of the ILs lead to different extents of the uncoupling of adjacent molecules of dimethylformamide, resulting in different shifts for this band in the mixtures. Information about the organization of ionic liquids in solution was obtained and a model of aggregation for these systems is proposed. (C) 2010 Elsevier B.V. All rights reserved.