植物生理

Highly variable intergenic spacer and intron regions from nuclear and cytoplasmic DNA have been used for species identification. Noncoding internal transcribed spacers (ITSs) located in 18S-5.8S-26S, and 5S ribosomal RNA genes (rDNAs) represent suitable region for medicinal pl ...

Among the PCR-based markers that are most widely used in molecular genetic studies, SCARs (sequence characterized amplified regions) have the advantage of being less sensitive to the conditions of a standard PCR due to its primer size when compared to RAPD (random amplified polymorphic DNA) ...

Annotation of plant genomic sequences can be separated into structural and functional annotation. Structural annotation is the foundation of all genomics as without accurate gene models understanding gene function or evolution of genes across taxa can be impeded. Structural anno ...

The progress made in DNA marker technology has been remarkable and exciting in recent years. DNA markers have proved valuable tools in various analyses in plant breeding, for example, early generation selection, enrichment of complex F1s, choice of donor parent in backcrossing, recovery of ...

By mid-2007, the three-dimensional (3D) structures of some 45,000 proteins have been solved, over a period where the linear structures of millions of genes have been defined. Technical challenges associated with X-ray crystallography are being overcome and high-throughput methods b ...

In recognition of the fact that a relatively small percentage of ‘named’ genes in databases have any experimental proof for their annotation, attention is shifting towards the more accurate assignment of functions to individual genes in a genome. The central objective will be to reduce our re ...

In the post-genomic era, it is necessary to adapt methods for gene expression and functional analyses to more high-throughput levels of processing. mRNA in situ hybridization (ISH) remains a powerful tool for obtaining information regarding a gene’s temporal and spatial expression pat ...

Databases have become an integral part of all aspects of biological research, including basic and applied plant biology. The importance of databases continues to increase as the volume of data from direct and indirect genomics approaches expands. What is not always obvious to users of datab ...

Although new technologies in genomics are powerful tools for discovering genes and gaining insight into their function, discovery of a gene itself does not ensure its practical application. Commercialization of transgenic crop plants has now taken place for more than a decade. Plant bio ...

In the following chapter we describe methods and protocols to analyze the interaction of proteins with DNA using footprinting and related techniques based on the modification of DNA with either hydroxyl radicals or methylating agents. Footprinting, based on the protection from chemi ...

Chromatin immunoprecipitation (ChIP) is a valuable tool to detect the interaction in vivo between a DNA-associated protein and DNA fragments. Combined with approaches to assess gene expression in response to accumulation of a transcription factor, it is possible to identify direct re ...

DNA-binding proteins, including transcription factors, play essential roles in many biological processes. The identification of the DNA sequences to which these proteins bind is a first, yet still challenging, step for determining their functions. SELEX provides an excellent tool ...

Transcription factors are modular in nature in all organisms. In general, they have a DNA binding domain, one or more transcription activation and/or repressor domain, and often a dimerization domain. In many cases, transcription factors also have other protein–protein interaction do ...

Most transcription factors fulfill their role in protein complexes. As a consequence, information about their interaction capacity sheds light on a protein’s function and the molecular mechanism underlying this activity. The yeast two-hybrid GAL4 (Y2H) assay is a powerful method to un ...

Non-cell-autonomous (NCA) control of plant development is an emerging field. Transcription factors (TFs) are the most important plant proteins involved in development and cell fate determination. In plants specialized intercellular symplastic channels, called plasmodes ...

Similar to the activities of transcription factors (TFs) in other eukaryotes, activities of many plant TFs are determined via regulated proteolysis by the ubiquitin/26S proteasome system. Thus, to fully understand the function of a TF, it is important to determine the fate of the active TF prot ...

Defining protein complexes is critical to virtually all aspects of cell biology because most cellular processes are regulated by stable or more dynamic protein interactions. Elucidation of the protein–protein interaction network around transcription factors is essential to f ...

Protein–protein interactions are an important aspect of the gene regulation process. The expression of a gene in response to certain stimuli, within a specific cell type or at a particular developmental stage, involves a complex network of interactions between different regulatory pr ...

Microarray analysis is widely used to identify transcriptional changes associated with genetic perturbation or signaling events. Here we describe its application in the identification of plant transcription factor target genes with emphasis on the design of suitable DNA const ...

Regulation of gene expression by transcription factors is a fundamental mechanism in essentially all aspects of cellular processes. Transient expression assay of a reporter plasmid containing a reporter gene driven by a promoter of interest and an effector plasmid expressing a tran ...