植物生理

The extent to which physical properties and intranuclear locations of chromatin can influence transcription output remains unclear and poorly quantified. Because the scale and resolution at which structural parameters can be queried are usually so different from the scale that tr ...

Barbara McClintock first showed that transposable elements in maize can induce major chromosomal rearrangements, including duplications, deletions, inversions, and translocations. More recently, researchers have made significant progress in elucidating the mechan ...

Plant genetic engineering has become one of the most important molecular tools in the modern molecular breeding of crops. Over the last decade, significant progress has been made in the development of new and efficient transformation methods in plants. Despite a variety of available DNA del ...

The plastids of higher plants have their own ∼120–160-kb genome that is present in 1,000–10,000 copies per cell. Engineering of the plastid genome (ptDNA) is based on homologous recombination between the plastid genome and cloned ptDNA sequences in the vector. A uniform population of enginee ...

Homologous recombination (HR) is a central cellular process involved in many aspects of genome maintenance such as DNA repair, replication, telomere maintenance, and meiotic chromosomal segregation. HR is highly conserved among eukaryotes, contributing to genome stability as w ...

Fluorescence in situ hybridization (FISH) is an invaluable tool for chromosome analysis and engineering. The ability to visually localize endogenous genes, transposable elements, transgenes, naturally occurring organellar DNA insertions – essentially any unique sequen ...

In plant cells, DICER-LIKE4 processes perfectly double-stranded RNA (dsRNA) into short interfering (si) RNAs, and DICER-LIKE1 generates micro (mi) RNAs from primary miRNA transcripts (pri-miRNA) that form fold-back structures of imperfectly dsRNA. Both si and miRNAs direct the endo ...

The goal of this chapter is to describe in simple terms how the use of ordinary differential equation (ODE) modeling, in conjunction with experimentation, can be utilized to improve our understanding of the dynamics of gene silencing and virus resistance in plants.

In plants, several classes of non-coding small RNA (sRNA) have been shown to be important regulators of gene expression in a wide variety of biological processes. The two main classes of sRNA, the small-interfering RNA (siRNA) and microRNA (miRNA) classes, are well documented and several exper ...

In this chapter, we detail some of the methods available to the researcher for isolating and analyzing virus-derived small RNAs (vsRNAs). These methods have been successfully used for four plant viruses: Cucumber mosaic virus (CMV), including the CMV Y-Satellite, Turnip mosaic virus (TuMV ...

Genetically engineered resistance to protect plants against virus infections can be based on protein- and RNA-mediated defense mechanisms. RNA silencing that leads to high-level virus resistance is triggered by virus-specific double-stranded (ds)RNA. The most efficient means ...

RNA silencing is a natural plant defense system against foreign genetic elements including viruses. This natural antiviral mechanism has been adopted to develop virus-resistant plants by the expression of long stretches of viral sequences in perfectly paired double-stranded or s ...

Small RNAs, defined as noncoding 20–30-nt-long RNAs, are instrumental regulators of cellular processes in most eukaryotes. In this chapter we describe three methods for extracting small RNA from cells: a general method, one plant specific and a third particular to conifers. Further, proto ...

When Diener discovered Potato spindle tuber viroid in 1971 (Diener, Virology 45:411–428, 1971), only a limited number of techniques were available for plant virus detection and purification. Biological assays using indicator hosts showing characteristic symptoms of infection a ...

RNA-dependent RNA polymerases (RDRPs) are encoded by RNA viruses as well as eukaryotic organisms such as plants. The function of these cellular RDRPs has been associated with the synthesis of short interfering RNAs (siRNAs), which are essential regulators of genomic integrity and plant v ...

Understanding the biology of a system requires the association of gene functions to phenotypes and vice versa. Although a large number of resources and genomic tools are available for studies in the crop plant soybean, investigations related to gene function have been lacking. This is large ...

Viroids and satellite RNAs, which are the smallest infectious agents in plants, have noncoding RNA genomes and characteristic secondary structures. Some satellite RNAs (satRNAs) cause disease symptoms that are different from those induced by their helper virus. This phenomenon has ...

RNA interference, or RNAi, is arguably one of the most significant discoveries in biology in the last several decades. First recognized in plants (where it was called post-transcriptional gene silencing, PTGS) RNAi is a gene down-regulation mechanism since demonstrated to exist in all euk ...

Gene silencing has been used widely in gene function studies and crop plant modification. Long hairpin RNA (lhRNA) results in high efficiency of gene silencing; however, constructing multiple lhRNA vectors using traditional approaches is both time consuming and costly. Also, most of the e ...

Dark green islands (DGIs) form in some plant virus infections as areas that are resistant to infection. This resistance has been demonstrated to act through a sequence-specific, RNA degradation mechanism termed RNAi. In addition to the virus that induces the initial DGI, a second, infectious ...