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1.
Springerplus ; 3: 439, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25184108

RESUMO

The goal of metabolomics data pre-processing is to eliminate systematic variation, such that biologically-related metabolite signatures are detected by statistical pattern recognition. Although several methods have been developed to tackle the issue of batch-to-batch variation, each method has its advantages and disadvantages. In this study, we used a reference sample as a normalization standard for test samples within the same batch, and each metabolite value is expressed as a ratio relative to its counterpart in the reference sample. We then applied this approach to a large multi-batch data set to facilitate intra- and inter-batch data integration. Our results demonstrate that normalization to a single reference standard has the potential to minimize batch-to-batch data variation across a large, multi-batch data set.

2.
J Agric Food Chem ; 62(13): 2997-3009, 2014 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-24564827

RESUMO

Profiling techniques such as microarrays, proteomics, and metabolomics are used widely to assess the overall effects of genetic background, environmental stimuli, growth stage, or transgene expression in plants. To assess the potential regulatory use of these techniques in agricultural biotechnology, we carried out microarray and metabolomic studies of 3 different tissues from 11 conventional maize varieties. We measured technical variations for both microarrays and metabolomics, compared results from individual plants and corresponding pooled samples, and documented variations detected among different varieties with individual plants or pooled samples. Both microarray and metabolomic technologies are reproducible and can be used to detect plant-to-plant and variety-to-variety differences. A pooling strategy lowered sample variations for both microarray and metabolomics while capturing variety-to-variety variation. However, unknown genomic sequences differing between maize varieties might hinder the application of microarrays. High-throughput metabolomics could be useful as a tool for the characterization of transgenic crops. However, researchers will have to take into consideration the impact on the detection and quantitation of a wide range of metabolites on experimental design as well as validation and interpretation of results.


Assuntos
Perfilação da Expressão Gênica/métodos , Metabolômica/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Plantas Geneticamente Modificadas/genética , Zea mays/genética , Inocuidade dos Alimentos , Alimentos Geneticamente Modificados/classificação , Plantas Geneticamente Modificadas/classificação , Plantas Geneticamente Modificadas/metabolismo , Zea mays/classificação , Zea mays/metabolismo
3.
Genetics ; 163(3): 1221-5, 2003 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-12663558

RESUMO

The centromeres of Arabidopsis thaliana chromosomes contain megabases of complex DNA consisting of numerous types of repetitive DNA elements. We developed a chromatin immunoprecipitation (ChIP) technique using an antibody against the centromeric H3 histone, HTR12, in Arabidopsis. ChIP assays showed that the 180-bp centromeric satellite repeat was precipitated with the antibody, suggesting that this repeat is the key component of the centromere/kinetochore complex in Arabidopsis.


Assuntos
Arabidopsis/genética , Centrômero/genética , Cromatina/isolamento & purificação , Repetições de Microssatélites/genética , Proteínas de Arabidopsis/genética , Clonagem Molecular , DNA de Plantas/genética
4.
Plant Cell ; 14(11): 2825-36, 2002 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-12417704

RESUMO

Maize centromeres are composed of CentC tandem repeat arrays, centromeric retrotransposons (CRs), and a variety of other repeats. One particularly well-conserved CR element, CRM, occurs primarily as complete and uninterrupted elements and is interspersed thoroughly with CentC at the light microscopic level. To determine if these major centromeric DNAs are part of the functional centromere/kinetochore complex, we generated antiserum to maize centromeric histone H3 (CENH3). CENH3, a highly conserved protein that replaces histone H3 in centromeres, is thought to recruit many of the proteins required for chromosome movement. CENH3 is present throughout the cell cycle and colocalizes with the kinetochore protein CENPC in meiotic cells. Chromatin immunoprecipitation demonstrates that CentC and CRM interact specifically with CENH3, whereas knob repeats and Tekay retroelements do not. Approximately 38 and 33% of CentC and CRM are precipitated in the chromatin immunoprecipitation assay, consistent with data showing that much, but not all, of CENH3 colocalizes with CentC.


Assuntos
Centrômero/genética , DNA Satélite/genética , Histonas/genética , Cinetocoros/metabolismo , Retroelementos/genética , Zea mays/genética , Sequência de Aminoácidos , Ciclo Celular/genética , Ciclo Celular/fisiologia , Sequência Conservada/genética , Histonas/metabolismo , Sequências Repetitivas Dispersas/genética , Dados de Sequência Molecular , Sequências de Repetição em Tandem/genética
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