A Genome-wide Screen for Neurospora crassa Transcription Factors Regulating Glycogen Metabolism

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Composition-resolved size distributions of volcanic aerosols in the Mt. Etna plumes

Particle size distributions for soluble and insoluble species in Mt. Etna's summit plumes were measured across an extended size range (10 nm < d < 100 mu m) using a combination of techniques. Automated scanning electron microscopy (QEMSCAN) was used to chemically analyze many thousands of insoluble particles (collected on pumped filters) allowing the relationships between particle size, shape, and composition to be investigated. The size distribution of fine silicate particles (d < 10 mu m) was found to be lognormal, consistent with formation by bursting of gas bubbles at the surface of the magma. The compositions of fine silicate particles were found to vary between magmatic and nearly pure silica; this is consistent with depletion of metal ions by reactions in the acidic environment of the gas plume and vent. Measurements of the size, shape and composition of fine silicate particles may potentially offer insights into preemission, synemission, and postemission processes. The mass flux of fine silicate particles from Mt. Etna released during noneruptive volcanic degassing in 2004 and 2005 was estimated to be similar to 7000 kg d(-1). Analysis of particles in the range 0.1 < d/mu m < 100 by ion chromatography shows that there are persistent differences in the size distributions of sulfate aerosols between the two main summit plumes. Analysis of particles in the range 0.01 mu m < d < 0.1 mu m by scanning transmission electron microscopy (STEM) shows that there are significant levels of nanoparticles in the Mt. Etna plumes although their compositions remain uncertain.

Anticorpos contra o vírus rábico em seres humanos com atividades no Hospital Veterinário da Universidade Federal de Mato Grosso. Cuiabá, MT, Brasil

Uma caracterização do perfil sorológico de 102 indivíduos com constantes atividades no Hospital Veterinário da Universidade Federal de Mato Grosso foi realizada por meio de fichas epidemiológicas e provas sorológicas para titulação de anticorpos contra o vírus da raiva, no período de novembro de 1999 a novembro de 2000. Dessas pessoas, 27 tinham sido vacinadas em esquema de pré-exposição e 75 não tinham recebido nenhum esquema de vacinação anti-rábica. Os resultados deste estudo puderam classificar os indivíduos em diferentes grupos (G1, G2, G3 e G4). As 19 (18,6%) pessoas do grupo G1, previamente vacinadas contra raiva, apresentaram titulação abaixo de 0,5 UI/mL; no grupo G2, as 8 (7,8%) pessoas, também previamente vacinadas, apresentaram títulos superiores a 0,5UI/mL; no grupo G3, as 67 (65,6%) pessoas, não vacinadas contra o vírus rábico, apresentaram titulação abaixo de 0,5UI/mL; e finalmente no grupo G4, as 8 (7,8%) pessoas, que nunca receberam esquema vacinal, apresentaram títulos acima de 0,5UI/mL. Os resultados obtidos demonstraram que existe necessidade de avaliação epidemiológica e acompanhamento sorológico. de pessoas submetidas a vacinação anti-rábica pré-exposição em hospitais veterinários.

Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa

Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X.fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X.fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X.fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X.fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.

DBMODELING - A database applied to the study of protein targets from genome projects

Genome sequencing efforts are providing us with complete genetic blueprints for hundreds of organisms. We are now faced with assigning, understanding, and modifying the functions of proteins encoded by these genomes. DBMODELING is a relational database of annotated comparative protein structure models and their metabolic pathway characterization, when identified. This procedure was applied to complete genomes such as Mycobacteritum tuberculosis and Xylella fastidiosa. The main interest in the study of metabolic pathways is that some of these pathways are not present in humans, which makes them selective targets for drug design, decreasing the impact of drugs in humans. In the database, there are currently 1116 proteins from two genomes. It can be accessed by any researcher at http://www.biocristalografia.df.ibilce.unesp.br/tools/. This project confirms that homology modeling is a useful tool in structural bioinformatics and that it can be very valuable in annotating genome sequence information, contributing to structural and functional genomics, and analyzing protein-ligand docking.

Equine infectios anemia of traction equids in the Cuiaba Districty, MT, Brazil

The present study it had for objective to search the AIE in equids traction of the city of Cuiaba, of which if it extracted an inquiry epidemiologist and a sampling of blood serum of 113 animals (110 equines and 3 mules) that they transited for the public ways. The sampling of the animals was random how much to the age (of 8 months the 20 years) and sex of the animals where 67 (60.9%) were of females and 46 (41.8%), of males, with a average of 22 working hours per week. The samples of blood had been analyzed by means of the technique of AGID test. The results of the blood tests had indicated that of the 110 examined samples of blood serum of the equines, thirteen (11.8%) were positive, being seven of female (10.4% of the total of females) and 6 males (13.0% of the total of males), all no symptoms animals and the age of the positive animals was concentrated in the band of 6 10 years, representing 84.6% (11 animals). The results of the blood tests had also indicated that of three mules analyzed, 1 (33.3%) was positive.

FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

Background: The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain-specific markers, on which specific primers are designed for pathogen detection purpose.Results: PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for designing common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/similar to primer.Conclusion: PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation showed that this software had a successful prediction rate of 80.4 - 100% for strain specific primer design.

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications.

The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

Os granitóides brasilianos da faixa de dobramentos paraguai, MS e MT

The Brazilian Granitic Province from southeastern Mato Grosso do Sul and Mato Grosso region, central western Brazil, can be divided into two major groups and/or magmatic events related to the evolution of the Paraguay Fold Belt. The southern portion crops out in Mato Grosso do Sul State and is constituted by the Taboco, Rio Negro, Coxim and Sonora massifs forming NE-SW oriented, elongated small intrusions. The north portion crops out in Mato Grosso State and is constituted by the São Vicente, Araguaiana and Lajinha batholiths. Lithogeochemical aspects of the northern granites point to Type-I granites ranging from K calc-alkaline to high-K, peraluminous to metaluminous in composition, generated in an environment of continental collision and/or post- collision decompression. The southern granites are Type-I, from K calc-alkaline to high-K, peraluminous to subordinate metalummous, in a syn-collision continental arc environment with the exception of some pre-collisional facies from the Rio Negro Massif. The southern granites have less SiO 2 and K 2O, and are less differentiated and evolved than granites from the northern region. The four southern granites can be grouped into two subordinate sets with the degree of differentiation increasing from South (Taboco and Rio Negro) to North (Coxim and Sonora). The granitic rocks are characterized by a magmatism generated by melting of material from the lower crust which suggests that in this province the formation from non-cogenetic magmas with diversified compositions and distinct degrees of fractioning reaching more steady consolidated environments at the end of the collisional event in the southeastern Amazonian Craton.

Geologic e geoquímica do batólito Rapakivi Rio Branco, SW do Craton Amazônico - MT

The Rio Branco Rapakivi Batholith belongs to the Cachoeirinha Tectonic Domain, part of the Rio Negro-Juruena Geochronological Province located on the southwestern portion of the Amazonian Craton in Mato Grosso, Central Brasil. A systematic geological mapping on a 1:100.000 scale, coupled with petrographic and geochemical studies allowed to redefine this batholithic unit, to recognize faciological variations and to characterize the geochemical features of this rapakivi magmatism. The batholith is constituted by two major plutonic suites, the first forming a basic suite of fine-grained, equigranular, mesoto melanocratic gray to black lithotypes, with usually discontinuous porphyritic varieties located near the margins of the intrusion. The second one is characterized by acid to intermediate rocks constituted by porphyritic granites, in part granophyric, with rapakivi textures. They have K-feldspar phenocrysts of up to 4cm. Three distinct petrographic facies are recognized in this suite: 1. equigranular to pegmatitic monzogranites; 2. red rapakivi leuco-monzogranites; 3. dark red rapakivi monzogranites to quartz-monzonites. Rocks present SiO2 contents from 67% to 73%, show peraluminous to metaluminous compositions and define a high-K calc-alkaline to shoshonitic magmatism in an I- and A-type, post-orogenic to anorogenic intraplate environment. The magmatic processes are associated with the end of the collisional event that consolidated and stabilized the SW part of the Amazonian Craton.

Mitochondrial genome sequence of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae): Mitochondrial genes utility to investigate the evolutionary history of Coleoptera and its bioluminescence

The Coleoptera order is the richest group among Metazoa, but its phylogenetics remains incompletely understood. Among Coleoptera, bioluminescence is found within the Elateroidea, but the evolution of this character remains a mystery. Mitochondrial DNA has been used extensively to reconstruct phylogenetic relationships, however, the evolution of a single gene does not always correspond to the species evolutionary history and the molecular marker choice is a key step in this type of analysis. To create a solid basis to better understand the evolutionary history of Coleoptera and its bioluminescence, we sequenced and comparatively analyzed the mitochondrial genome of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae). © 2007 Elsevier B.V. All rights reserved.

Contexto tectônico dos granitóides neoproterozóicos da faixa de dobramentos paraguai, MS e MT

The Neoproterozoic Granitic Province from the southeast of Mato Grosso and Mato Grosso do Sul region is constituted by seven distinctive granitic bodies, emplaced in the epimetamorphic rocks of the Cuiabá Group and related to the evolution of Paraguai Folded Belt. The Northern portion crops out in Mato Grosso State and is constituted by São Vicente, Araguaiana and Lajinha batholiths; the Southern portion crops out in the Mato Grosso do Sul State and is represented the Sonora, Coxim Rio Negro and Taboco massifs. The structural evolution is evidenced by the presence of three deformational phases, the first one is characterized by axial planar foliation (S 1), parallel or sub parallel to S 0, with attitude N60E/70NW; the second constitutes the most important phase for the tectonic arrangement and is defined by a slaty and/or crenulation cleavages (S 2), with attitude N10W/30SW and contact metamorphism associated to the emplacement of granitic bodies, the third phase is characterized by a weak retrometamorphic cleavage (S 3) with attitude N10E/ 80NW, that evolves local and gradually to strike-slip shear zones. The geological data suggest that this province was formed syn- to post tectonic to the D2 deformational set associated to the end of the collisional event in the Southeastern of the Amazonian Craton.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.