Genotipagem por sequenciamento para identificação de SNPs e associação com características agronômicas em Coffea canephora

A genotipagem por sequenciamento (GBS) é capaz de identificar e genotipar milhares de polimorfismos do tipo SNPs de forma simultânea. Objetiva-se contribuir para o melhoramento genético do cafeeiro Conilon através da caracterização da ocorrência de SNPs no genoma de Coffea canephora e de associações destes com características de interesse agronômico. Os145 indivíduos de duas famílias de irmãos completos (clones 109x120/120x109 e 76x48) do programa de melhoramento do Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural (Incaper)foram fenotipados e os DNAs foram multiplexados em sequenciador Ilumina na Universidade de Cornell. Detectaram-se 91.105 SNPs antes de aplicar os parâmetros de filtragem, sendo que após os filtros houve redução de 64%. Ampla distribuição dos SNPs foi encontrada, sendo que foram detectados em média 1330 SNPs gênicos e 2955 intergênicos, por pseudocromossomo. Verificou-se que o padrão de distribuição dos SNPs nas regiões do genoma difere. A menor ocorrência de SNPs detectada em regiões gênicas é esperada como consequência da pressão de seleção, que limita as alterações de aminoácidos nas sequências proteicas. Os estudos de associação permitiram encontrar 18 SNPs associados a características fenotípicas de Coffea canephora (S2_9329731, S2_4579518, S2_41329025, S2_17821870, S2_20934616, S3_23227842, S4_22978689, S5_10964474, S6_9949547, S7_13991105, S7_13991086, S7_13991077, S9_4618814, S9_18527411, S10_24840747, S11_30063996, S11_23828233). Localizam-se em regiões intergênicas 33% dos SNPs, sendo que os demais se distribuem em região de íntrons, éxons e 3UTR. Os SNPs em região codificadora são responsáveis por alterações não sinônimas em 82% das ocorrências. Os resultados encontrados são importantes para a cafeicultura e podem contribuir para a seleção assistida por marcadores. Palavras-chave: cafeeiro, sequenciamento, SNP, genotipagem, estudos de associação

Efeito de leguminosas herbáceas perenes consorciadas com a bananeira, sobre a ocorrência de plantas espontâneas em agroecossistema sob manejo ecológico.

bitstream/item/69048/1/052-padovan-efeito.pdfPublicado também no Cadernos de Agroecologia, v. 7, n.2, 2012

Acúmulo de massa e nutrientes em leguminosas herbáceas perenes consorciadas com bananeira em agroecossistema sob manejo ecológico em Mato Grosso do Sul.

Publicado também na: Revista Brasileira de Agroecologia, v. 6. n. 2, dez. 2011

Quantitative magneto-optical investigation of superconductor/ferromagnet hybrid structures

We present a detailed quantitative magneto-optical imaging study of several superconductor/ferromagnet hybrid structures, including Nb deposited on top of thermomagnetically patterned NdFeB, and permalloy/niobium with erasable and tailored magnetic landscapes imprinted in the permalloy layer. The magneto-optical imaging data is complemented with and compared to scanning Hall probe microscopy measurements. Comprehensive protocols have been developed for calibrating, testing, and converting Faraday rotation data to magnetic field maps. Applied to the acquired data, they reveal the comparatively weaker magnetic response of the superconductor from the background of larger fields and field gradients generated by the magnetic layer.Comment: 21 pages, including 2 pages of supplementary materia

Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise?

<p>Abstract</p> <p>Background</p> <p>A major effort of the scientific community has been to obtain complete pictures of the genomes of many organisms. This has been accomplished mainly by annotation of structural and functional elements in the genome sequence, a process that has been centred in the gene concept and, as a consequence, biased toward protein coding sequences. Recently, the explosion of transcriptome data generated and the discovery of many functional non-protein coding RNAs have painted a more detailed and complex scenario for the genome. Here we analyzed the mouse carboxypeptidase M <it>locus </it>in this broader perspective in order to define the mouse CPM gene structure and evaluate the existence of other transcripts from the same genomic region.</p> <p>Results</p> <p>Bioinformatic analysis of nucleotide sequences that map to the mouse CPM <it>locus </it>suggests that, in addition to the mouse CPM mRNA, it expresses at least 33 different transcripts, many of which seem to be non-coding RNAs. We randomly chose to evaluate experimentally four of these extra transcripts. They are expressed in a tissue specific manner, indicating that they are not artefacts or transcriptional noise. Furthermore, one of these four extra transcripts shows expression patterns that differed considerably from the other ones and from the mouse CPM gene, suggesting that there may be more than one transcriptional unit in this <it>locus</it>. In addition, we have confirmed the mouse CPM gene RefSeq sequence by rapid amplification of cDNA ends (RACE) and directional cloning.</p> <p>Conclusion</p> <p>This study supports the recent view that the majority of the genome is transcribed and that many of the resulting transcripts seem to be non-coding RNAs from introns of genes or from independent transcriptional units. Although some of the information on the transcriptome of many organisms may actually be artefacts or transcriptional noise, we argue that it can be experimentally evaluated and used to find and define biological functional elements on the genome. Furthermore, the transcription of other functional RNAs besides the protein coding RNA from a specific genomic <it>locus </it>imposes extra care when designing and interpreting experiments involving genetic manipulations or expression detection and quantification.</p

Performance do feijoeiro cultivado em sucessão a adubos verdes num agroecossistema sob manejo ecológico em Dourados, Mato Grosso do Sul.

bitstream/item/68484/1/077-Performance-do-feijoeiro-cultivado-em-sucessao-a-adubos-verdes.pdfPublicado também no Cadernos de Agroecologia, v. 7, n. 2, 2012

Unified treatment of the total angular momentum of single photons via generalized quantum observables

In this paper, we provide a consistent framework to address the notorious difficult decomposition of the single-photon total angular momentum (TAM) into a spin (SAM) and an orbital (OAM) component. We discuss the canonical decomposition into SAM and OAM components, which are the generators of internal and spatial rotations in the space of physical states. We find that those operators are mutually compatible but unsharp quantum observables, therefore Positive Operator-Valued Measures describe their joint measurements. We present another decomposition of the TAM, which we denote as a non-canonical one. The operators resulting from this decomposition are mutually incompatible but sharp quantum observables, thus Projector-Valued Measurements. This fact reflects their consistency with the transversality condition of single-photon wavefunctions, thus explains the underlying physics from a quantum information theoretic view. Furthermore, we discuss the implementations on joint measurements for both decompositions and provide an explicit calculation of all these quantities for circularly polarized Gaussian single-photon states. The difference between the canonical and non-canonical momenta leads to observable differences in higher-order statistical moments

Desempenho de variedades de cana-de-açúcar consorciadas com Crotalaria juncea sob manejo ecológico em solo de Cerrado, em Dourados, Mato Grosso do Sul.

Publicado também na: Revista Brasileira de Agroecologia, v. 6. n. 2, dez. 2011