Optimal clone identifier for genomic shotgun libraries: OC Identifier tool

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray. ©FUNPEC-RP.

Optimal clone identifier based on dynamic rules and process algebra

The rule creation to clone selection in different projects is a hard task to perform by using traditional implementations to control all the processes of the system. The use of an algebraic language is an alternative approach to manage all of system flow in a flexible way. In order to increase the power of versatility and consistency in defining the rules for optimal clone selection, this paper presents the software OCI 2 in which uses process algebra in the flow behavior of the system. OCI 2, controlled by an algebraic approach was applied in the rules elaboration for clone selection containing unique genes in the partial genome of the bacterium Bradyrhizobium elkanii Semia 587 and in the whole genome of the bacterium Xanthomonas axonopodis pv. citri. Copyright© (2009) by the International Society for Research in Science and Technology.

Algebraic approach to optimal clone selection applied in metagenomic projects

Due to the wide diversity of unknown organisms in the environment, 99% of them cannot be grown in traditional culture medium in laboratories. Therefore, metagenomics projects are proposed to study microbial communities present in the environment, from molecular techniques, especially the sequencing. Thereby, for the coming years it is expected an accumulation of sequences produced by these projects. Thus, the sequences produced by genomics and metagenomics projects present several challenges for the treatment, storing and analysis such as: the search for clones containing genes of interest. This work presents the OCI Metagenomics, which allows defines and manages dynamically the rules of clone selection in metagenomic libraries, thought an algebraic approach based on process algebra. Furthermore, a web interface was developed to allow researchers to easily create and execute their own rules to select clones in genomic sequence database. This software has been tested in metagenomic cosmid library and it was able to select clones containing genes of interest. Copyright 2010 ACM.

Presence of a human diarrheagenic escherichia coli clone in captivity kept psittacidaes

Bacterial cultures of cloaca swabs from 86 captivity kept psittacidaes revealed 17 Escherichia coli bearing birds sharing strains which, on the basis of enterobacterial repetitive intergenic consensus (ERIC) PCR analysis, proved to be genetically similar. Further, triplex PCR specific for the genetic markers chuA, yjaA, and TSPE4.C2 was used to assign the strains to the E. coli reference collection (EcoR) B2 group. One strain of each, from the enteropathogenic (EPEC), enteroaggregative (EAEC) and Shiga toxin (STEC) E. coli pathovars were found among these isolates. © Marietto-Gonçalves et al.; Licensee Bentham Open.

Classificação Estrutural e Qualidade da Madeira do Clone GT 1 de Hevea brasiliensis Muell. Arg

Latex is the main product extracted from rubber trees (Hevea brasiliensis). In Brazil, at the end of the production cycle of latex, the wood of rubber tree is traditionally used for energy purposes, but several international studies have reported consolidated practices of adding value to it. The objective of this paper was to evaluate the quality of wood and classify it structurally based on its mechanical properties. Six 20-year-old trees of the clone GT 1 of rubber tree proceeding from Itajobi, State of Sao Paulo, Brazil were sampled. Reduced dimensions specimens in the radial direction of the wood were produced to evaluate the quality by compression parallel to the grain, static bending and Janka hardness tests. Two specimens, one from the lower log (since the ground up to breast height) and one from the higher log (from breast height up to 2.50 m) were produced for structural classification of the wood based on the characteristic strength in compression parallel to the grain (NBR 7190 norm, 1997). The wood was classified as C40 (fc0k ≥ 40 MPa) class. Results revealed that the strength was not statistically different in the radial direction (except for the Janka hardness), though tending to increase from pith to bark.

Interclonal Variations in the Molecular Karyotype of Trypanosoma cruzi: Chromosome Rearrangements in a Single Cell-Derived Clone of the G Strain

Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure. © 2013 Lima et al.

Crescimento inicial de um clone de Eucalyptus grandis em diferentes arranjos de plantio no sistema de curta rotação

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Efeito do espaçamento de plantio na biomassa do fuste de um clone híbrido interespecífico de Eucalyptus grandis e Eucalyptus urophylla

Pós-graduação em Ciência Florestal - FCA

Caracterização fitossanitária e seleção de limeiras ácidas 'Tahiti' clone Quebra-galho candidatas a matrizes

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Adubação nitrogenada, fosfatada e potássica na cultura do eucalipto (clone i144 - E. urograndis)

Pós-graduação em Agronomia - FEIS

Fontes e modos de aplicação de boro na cultura do eucalipto (clone I144)

Pós-graduação em Agronomia - FEIS

Produção de carvão vegetal a partir da madeira de Eucalyptus saligna clone SI70 com tres anos e meio de idade

Charcoal is obtained from carbonization, much used in the steel industry for ore reduction, using as raw material the Eucalyptus. The present study aims to verify whether the main Eucalyptus saligna genetically modified produce quality charcoal with only 3.5 years old. The study was done with material collected from three trees, divided into five discs removed at 0, 25 , 50 , 75 and 100 % of the commercial height of the tree. The procedures adopted were based on standards published by ABNT. The results were satisfactory for the parameters: basic wood density with an average of 0.39 ± 0.0082 g / cm ³; volatile materials from coal with an average of 19.35 ± 3.27 %, fixed carbon content of the coal with an average of 75.62 ± 3.40 % and gross calorific value of coal with an average of 4694.43 cal / g, and unsatisfactory results for ash content averaging 5.03 ± 0.23 when compared to the values found in the literature. It was concluded that the studied wood is able to produce charcoal, but the factors of production should be better observed, such as heating time which exerted direct influence on the determination of ash content

Quality of wood and pulp from a clone of Eucalyptus grandis planted at three locations

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

My life as a clone

Zehar, an extremely popular and dignified man, is a renowned scientist. He has worked extremely hard, and spend two years, on a research to make human cloning.His idea was to produce the creature, simply of its own looking and exactly identical as him. To his satisfaction he had accomplished to make the physical characteristic, simply like his own. Even his experiment on a mentality and emotional aspect of a clone was also a success. But his last and the most vital wish, remained a complete failure. He wanted that the soul of the cloning should also be identical like his own soul, as the physical characteristics. But it was a complete different. The character of the cloning was getting too dangerous and later part he found he has to lose all his sympathy of his own clone, as his clone had became the most dangerous enemy in his life. All his fame and his moral character is being uprooted to the public by his clone. Ultimately he decides to kill it, and clone even takes a motto to kill Zehar, if Zehar decides to kill it, simply because, the clone wants to create his own fame to rule the world. Thus the story, gives an advice, to the world of science, that not to try human clones, in particular.

Prevalence of avian pathogenic Escherichia coli (APEC) clone harboring sfa gene in Brazil

Escherichia coli sfa+ strains isolated from poultry were serotyped and characterized by polymerase chain reaction (PCR) and amplified fragment length polymorphism (AFLP). Isolates collected from 12 Brazilian poultry farms mostly belonged to serogroup O6, followed by serogroups O2, O8, O21, O46, O78, O88, O106, O111, and O143. Virulence genes associated were: iuc 90%, fim 86% neuS 60%, hly 34%, tsh 28%, crl/csg 26%, iss 26%, pap 18%, and 14% cnf. Strains from the same farmpresented more than one genotypic pattern belonging to different profiles in AFLP. AFLP showed a clonal relation between Escherichia coli sfa+ serogroup O6. The virulence genes found in these strains reveal some similarity with extraintestinal E. coli (ExPEC), thus alerting for potential zoonotic risk.