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.

Crescimento inicial do eucalipto em função da aclimatação em viveiro

This study aimed to evaluate the acclimatization effects in the Eucalyptus grandis vs. Eucalyptus urophylla seedlings nursery in their initial growth in two soils types, clay and sandy. The seedlings were planted in Plantmax substrate and in rice hulls plus vermiculite, and managed, after 60 days of the mass propagation (DAE), during the rustication. There were five different frequencies of subsurface drip irrigation, restoring the soil field capacity condition: F1, F2, F3 and F4, which were irrigated once, twice, three and four times a day, respectively, and FD, kept in continue irrigation until planting at 90 DAE. In a randomized block design with four replications, plant height (HPA) were evaluated at 6 and 13 months after planting and the diameter at breast height (DAP) at 13 months after planting. Findings show that water management at hardening phase seedlings had no influence on growth in both soils.

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.

Efeito competicional em testes de progênies de eucalipto

Many studies have recommended the use of small plots for forest experiments, although they do not consider the inter-genotype competition increase. If this competition is not isolated from the mathematics model, it can lead to incorrect selection of genetic materials. The aim of this work was to evaluate the effect of seven competition covariates in two Eucalyptus spp. progeny tests. Data from the two half-sib eucalyptus progenies were analyzed, using the randomized blocks design. The seven analyzed covariates were HegyI's competition index (IC), self-competition (AT), alo competition (AL), self-competition mean (MAT), alo competition mean (MAL), and arithmetic means of four (M4) and eight (M8) nearest neighbors. Individual and combined analyses of covariates were used for the wood volume trait. All the variance components and the changes caused by covariates use were evaluated. The competition affects the results of eucalypt progeny analysis in different ways, according to its type, self or alo competition. Most influential covariates were MAT, MAL and IC. Most promising results of competition effects reduction were observed for the IC/MAT covariates inclusion in eucalypt progeny tests.

Relação do meio físico com o manejo sustentável de plantio de eucalipto em áreas de terrenos acidentados - A Fazenda Santa Edwirges, Vale do Paraíba, Sudeste do Brasil

This study intends to evaluate the effects of landscape physical elements (rocks and relief) associated with silviculture activities. The study was carried out on a small farm (Fazenda Santa Edwirges) covered by Eucalyptus forested situated in the Paraiba do Sul Basin, Southeast Brazil. The methodology consisted of detailed geological and geomorphological studies at 1:10,000 scale, and laboratory analysis of soil physical properties. The results showed three geologic-geomorphologic associations (ridge escarpment with granitic rocks, steep and gentle hills cut by shear zones and gentle hill with alluvial sediments) present high vulnerability for the development of the physical processes such as accelerated erosion landslides and flooding. In contrast, mountains associated with gneissic rocks present smaller vulnerability and high resilience for the development of the physical processes. The results have showed the importance of considering the interactions among landscape physical for the eucalyptus forest management contributing to a better selection area for eucalyptus cultivation and minimize adverse environment impact in road design.

Qualidade de mudas seminais de eucalipto em função dos substratos e fertilização de liberação controlada

For the production of quality seedlings, depending on the physical characteristics of each substrate, more rational nutritional managements, from the of economic-environmental point of view, should be sought. This study aimed to evaluate the development and quality of Eucalyptus grandis × E. urophylla seedlings in terms of substrates and doses of controlledrelease Osmocote® fertilizer. The experiment was conducted with a completely randomized, factorial design, using as substrates: vermiculite+carbonized rice chaff+coconut fiber (1:1:1); vermiculite+coconut fiber (1:1) and vermiculite+coconut fiber (2:1) and doses of 2, 4, 6 and 8kg·m -3 of substrate. The substrates with higher water holding capacity allow seedlings to reach their maximum development in most parameters using lower doses of controlled-release fertilizer. We recommend the application of the controlled-release fertilizer at a dose of 6.0kg·m-3 in vermiculite+carbonized rice chaff+coconut fiber (1:1:1) and vermiculite+coconut fiber (2:1) substrates, and in substrate vermiculite+coconut fiber (1:1) at a dose of 7.0kg·m-3. In each substrate there is a dose range that promotes a greater formation of suitable root systems for planting in the field, which consequently results in seedlings with greater morphological development at nursery.

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.

Resistência de genótipos de eucalipto a ceratocystis spp

Eucalyptus is the most important plantation forest species in Brazil. Wilt and canker caused by Ceratocystis fimbriata on eucalyptus were first reported in 1998 in plantations of an E. grandis × E. urophylla hybrid in southern Bahia, Brazil. This work aimed at studying the reaction of different eucalyptus genotypes after inoculation with C. fimbriata isolates, in order to find a possible source of resistance. The study included four isolates of Ceratocystis collected from eucalyptus in different regions. One disc of fungal mycelium with 1-cm-diameter (from colonies growing for 10 days on malt extract agar medium-MEA) was inoculated on the stem of thus injured eucalyptus plants (six months old). A cotton wool moistened with sterile distilled water was wrapped with plastic film. Control plants were inoculated with discs of MEA without fungal colonies. The inoculated plants were kept in a greenhouse. Wilt symptoms were observed 90 days after inoculation. The seedlings were cut in the longitudinal direction of the stem in order to observe the colonization of fungus in the plant xylem. We tested twenty eucalyptus genotypes, but only five showed resistance to all isolates of Ceratocystis, belonging to different species of Eucalyptus: E. urophylla (C2 and C9), E. grandis (C3), E. saligna (C6 and C13) Most E. gramdis genotypes were more susceptible to all four fungal isolates. These results support future studies related to eucalyptus resistance to Ceratocystis.

Uma abordagem probabilística do número de reprodução básica em modelos epidemiológicos com aplicação na ferrugem do eucalipto

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Potencial do eucalipto na fitorremediação de um solo contaminado por chumbo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Caracterização física e química do solo e avaliação do desenvolvimento de plantas de eucalipto em função do espaçamento e da adubação, visando a colheita precoce para utilização em bioenergia

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Relação entre estresse de radiação ultravioleta-b e óxido nítrico em plantas de eucalipto

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Controle químico de doenças de Eucalyptus spp. em viveiros e seus efeitos morfo-fisiológicos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise de extração de madeira de eucalipto com forwarder em floresta de primeira e segunda rotação

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