Transcriptional Profile of Bradyrhizobium elkanii Semia 587 in Symbiosis with Soybean (Glycine max L. Merrill) Analyzed by DNA Microarray

Marcondes, Jackson; Cantão, Maurício Egídio; Alves, L. M. C.; Lemos, Eliana Gertrudes Macedo

doi:10.1007/978-1-4020-8252-8_116

Cited by 2 publications

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“…The amplicons were labeled using the Post CyScribe cDNA Labeling kit (Amersham Biosciences) with the following fluorophores: Cy3 as reference for samples S1, S2, and S3; Cy5 as test for samples S1_T, S2_1N and S3_8N. The hybridization and washing steps were performed in the GeneTac hybridization station (TM Genomic Solutions, Ann Arbor, Michigan, USA) according to Marcondes et al (2008). Images were acquired by scanning.…”

Section: Microarray Screeningmentioning

confidence: 99%

Impact of sewage sludge on the soil bacterial communities by DNA microarray analysis

Val-Moraes

Marcondes

Alves

et al. 2011

World J Microbiol Biotechnol

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Sewage sludge has been used as organic manure to replace chemical fertilizer. The aim of this study was to evaluate the effect of doses of sewage sludge on the soil bacterial community by DNA microarray analysis. A microarray phylochip containing 1,560 partial sequences of 16S rRNA from the most common strains of bacteria was developed for bioprospection. Soil plots from an experimental field in Brazil were assessed with or without sludge treatment containing different doses of nitrogen based on that recommended for maize cultivation. The microarray technique was useful for quickly assessing changes in the bacterial communities and a high variation was observed, mainly in soil treated with high doses of sludge. While sludge containing 25 kg N/ha favored an in crease in the number of members in various phyla, on the other hand sludge with the higher dose regarding to 200 kg N/ha caused a reduction in the number of members in almost all phyla. Proteobacteria often dominant in soils was specifically affected. This study highlights the spread of bacteria to new environments and provides direct information about bacterial composition at specific habitats. Our results have shown that bacterial community structure was greatly affected by sludge application.

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Section: Microarray Screeningmentioning

confidence: 99%

Impact of sewage sludge on the soil bacterial communities by DNA microarray analysis

Val-Moraes

Marcondes

Alves

et al. 2011

World J Microbiol Biotechnol

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Abordagem algébrica para seleção de clones ótimos em projetos genomas e metagenomas

Cantão¹

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Agradeço também ao pessoal do Laboratório de Banco de Dados do IME-USP, em especial ao Luciano Araújo, que considero uma pessoa extraordinária como pessoa, profissional e amigo.Aos companheiros de república Maurílio Garcia, André Pádua Durante, Eric Motoiama, pela amizade e convivência.Enfim, a todos aqueles que de forma direta ou indireta colaboraram para a realização deste trabalho. Muito obrigado! iv ResumoDevido à grande diversidade de microrganismos desconhecidos no meio ambiente, 99% deles não podem ser cultivados nos meios de cultura tradicionais dos laboratórios. Para isso, projetos metagenômicos são propostos para estudar comunidades microbianas presentes no meio ambiente, a partir de técnicas moleculares, em especial o seqüenciamento. Dessa forma, para os próximos anos é esperado um acúmulo de seqüências produzidas por esses projetos.As seqüências produzidas pelos projetos genomas e metagenomas apresentam vários desafios para o tratamento, armazenamento e análise, como exemplo: a busca de clones contendo genes de interesse.Este trabalho apresenta uma abordagem algébrica que define e gerencia de forma dinâmica as regras para a seleção de clones em bibliotecas genômicas e metagenômicas, que se baseiam em álgebra de processos. Além disso, uma interface web foi desenvolvida para permitir que os pesquisadores criem e executem facilmente suas próprias regras de seleção de clones em bancos de dados de seqüências genômicas e metagenômicas. Este software foi testado em bibliotecas genômicas e metagenômicas e foi capaz de selecionar clones contendo genes de interesse.v AbstractDue 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 an algebraic approach that defines it dynamically and manages the rules of the selection of clones in genomic and metagenomic libraries, which are 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 and metagenomic sequence database. This software was tested in genomics and metagenomics libraries and it was able to select clones containing genes of interest. Figura 9 -Representa um fragmento de um genoma com duas ORFs, uma seqüência de "rRNA 5S" e 8 clones identificados pelas letras "A" a "H". O clone "B" encontra-se interno à "ORF 4", enquanto que o clone "F" está localizado externamente à "ORF 5". O clone "E" representa a "ORF 5" e contém 7 bases da seqüência do "rRNA 5S" na seqüência no sentido forward ........ 54Figura 10 ...

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Transcriptional Profile of Bradyrhizobium elkanii Semia 587 in Symbiosis with Soybean (Glycine max L. Merrill) Analyzed by DNA Microarray

Cited by 2 publications

References 0 publications

Impact of sewage sludge on the soil bacterial communities by DNA microarray analysis

Impact of sewage sludge on the soil bacterial communities by DNA microarray analysis

Abordagem algébrica para seleção de clones ótimos em projetos genomas e metagenomas

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