921 resultados para ChIP-Seq


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El artículo forma parte de una sección de la revista dedicada a innovación educativa

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This paper analyzes the convergence behavior of the least mean square (LMS) filter when used in an adaptive code division multiple access (CDMA) detector consisting of a tapped delay line with adjustable tap weights. The sampling rate may be equal to or higher than the chip rate, and these correspond to chip-spaced (CS) and fractionally spaced (FS) detection, respectively. It is shown that CS and FS detectors with the same time-span exhibit identical convergence behavior if the baseband received signal is strictly bandlimited to half the chip rate. Even in the practical case when this condition is not met, deviations from this observation are imperceptible unless the initial tap-weight vector gives an extremely large mean squared error (MSE). This phenomenon is carefully explained with reference to the eigenvalues of the correlation matrix when the input signal is not perfectly bandlimited. The inadequacy of the eigenvalue spread of the tap-input correlation matrix as an indicator of the transient behavior and the influence of the initial tap weight vector on convergence speed are highlighted. Specifically, a initialization within the signal subspace or to the origin leads to very much faster convergence compared with initialization in the a noise subspace.

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Gene Chips are finding extensive use in animal and plant science. Generally microarrays are of two kind, cDNA or oligonucleotide. cDNA microarrays were developed at Stanford University, whereas oligonucleotide were developed by Affymetrix. The construction of cDNA or oligonucleotide on a glass slide helps to compare the gene expression level of treated and control samples by labeling mRNA with green (Cy3) and red (Cy5) dyes. The hybridized gene chip emit fluorescence whose intensity and colour can be measured. RNA labeling can be done directly or indirectly. Indirect method involves amino allyle modified dUTP instead of pre-labelled nucleotide. Hybridization of gene chip generally occurs in a minimum volume possible and to ensure the hetroduplex formation, a ten fold more DNA is spotted on slide than in the solutions. A confocal or semi confocal laser technologies coupled with CCD camera are used for image acquisition. For standardization, house keeping genes are used or cDNA are spotted in gene chip that are not present in treated or control samples. Moreover, statistical analysis (image analysis) and cluster analysis softwares have been developed by Stanford University. The gene-chip technology has many applications like expression analysis, gene expression signatures (molecular phenotypes) and promoter regulatory element co-expression.

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The transcriptome of the developing starchy endosperm of hexaploid wheat (Triticum aestivum) was determined using RNA-Seq isolated at five stages during grain fill. This resource represents an excellent way to identify candidate genes responsible for the starchy endosperm cell wall, which is dominated by arabinoxylan (AX), accounting for 70% of the cell wall polysaccharides, with 20% (1,3; 1,4)-beta-D-glucan, 7% glucomannan, and 4% cellulose. A complete inventory of transcripts of 124 glycosyltransferase (GT) and 72 glycosylhydrolase (GH) genes associated with cell walls is presented. The most highly expressed GT transcript (excluding those known to be involved in starch synthesis) was a GT47 family transcript similar to Arabidopsis (Arabidopsis thaliana) IRX10 involved in xylan extension, and the second most abundant was a GT61. Profiles for GT43 IRX9 and IRX14 putative orthologs were consistent with roles in AX synthesis. Low abundances were found for transcripts from genes in the acyl-coA transferase BAHD family, for which a role in AX feruloylation has been postulated. The relative expression of these was much greater in whole grain compared with starchy endosperm, correlating with the levels of bound ferulate. Transcripts associated with callose (GSL), cellulose (CESA), pectin (GAUT), and glucomannan (CSLA) synthesis were also abundant in starchy endosperm, while the corresponding cell wall polysaccharides were confirmed as low abundance (glucomannan and callose) or undetectable (pectin) in these samples. Abundant transcripts from GH families associated with the hydrolysis of these polysaccharides were also present, suggesting that they may be rapidly turned over. Abundant transcripts in the GT31 family may be responsible for the addition of Gal residues to arabinogalactan peptide.

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Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes.

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Com o advento dos processos submicrônicos, a capacidade de integração de transistores tem atingido níveis que possibilitam a construção de um sistema completo em uma única pastilha de silício. Esses sistemas, denominados sistemas integrados, baseiam-se no reuso de blocos previamente projetados e verificados, os quais são chamados de núcleos ou blocos de propriedade intelectual. Os sistemas integrados atuais incluem algumas poucas dezenas de núcleos, os quais são interconectados por meio de arquiteturas de comunicação baseadas em estruturas dedicadas de canais ponto-a-ponto ou em estruturas reutilizáveis constituídas por canais multiponto, denominadas barramentos. Os futuros sistemas integrados irão incluir de dezenas a centenas de núcleos em um mesmo chip com até alguns bilhões de transistores, sendo que, para atender às pressões do mercado e amortizar os custos de projeto entre vários sistemas, é importante que todos os seus componentes sejam reutilizáveis, incluindo a arquitetura de comunicação. Das arquiteturas utilizadas atualmente, o barramento é a única que oferece reusabilidade. Porém, o seu desempenho em comunicação e o seu consumo de energia degradam com o crescimento do sistema. Para atender aos requisitos dos futuros sistemas integrados, uma nova alternativa de arquitetura de comunicação tem sido proposta na comunidade acadêmica. Essa arquitetura, denominada rede-em-chip, baseia-se nos conceitos utilizados nas redes de interconexão para computadores paralelos. Esta tese se situa nesse contexto e apresenta uma arquitetura de rede-em-chip e um conjunto de modelos para a avaliação de área e desempenho de arquiteturas de comunicação para sistemas integrados. A arquitetura apresentada é denominada SoCIN (System-on-Chip Interconnection Network) e apresenta como diferencial o fato de poder ser dimensionada de modo a atender a requisitos de custo e desempenho da aplicação alvo. Os modelos desenvolvidos permitem a estimativa em alto nível da área em silício e do desempenho de arquiteturas de comunicação do tipo barramento e rede-em-chip. São apresentados resultados que demonstram a efetividade das redes-em-chip e indicam as condições que definem a aplicabilidade das mesmas.