Springer protocols feed by Plant Sciences 
This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.
This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Plastid Gene Transcription: Promoters and RNA Polymerases
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) ...
Source: Springer protocols feed by Plant Sciences - March 6, 2014 Category: Biology Source Type: news
Next-Generation Technologies to Determine Plastid Genome Sequences
Sequencing of chloroplast genomes is a key tool for analysis of chloroplasts and the impact of manipulation of chloroplast genomes by biotechnology. Advances in genome sequencing allow the complete sequencing of the chloroplast genome and assessment of variation in the chloroplast genome sequences within a plant. Isolation of chloroplast DNA has been a traditional starting point in these analyses, but the capacity of current sequencing technologies allows effective analysis of the chloroplast genome sequence by shotgun sequencing of a preparation of total DNA from the plant. Chloroplast insertions in the nuclear genome can...
Source: Springer protocols feed by Plant Sciences - March 6, 2014 Category: Biology Source Type: news
The Plastid Genomes of Flowering Plants
The plastid genome (plastome) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations are allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter we present an overview of some of the seminal and cont...
Source: Springer protocols feed by Plant Sciences - March 6, 2014 Category: Biology Source Type: news
Detection of mRNA Expression Patterns by Nonradioactive In Situ Hybridization on Histological Sections of Floral Tissue
We describe how the samples are fixed, embedded, and sectioned in preparation for in situ hybridization, how RNA probes are prepared, and how hybridization and detection is carried out. While the described protocol is optimized for inflorescence meristems, it can possibly be used for other tissues as well. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
The GUS Reporter System in Flower Development Studies
The β-glucuronidase (GUS) reporter gene system is an important technique with versatile uses in the study of flower development. Transcriptional and translational GUS fusions are used to characterize gene and protein expression patterns, respectively, during reproductive development. Additionally, GUS reporters can be used to map cis-regulatory elements within promoter sequences and to investigate whether genes are regulated posttranscriptionally. Gene trap/enhancer trap GUS constructs can be used to identify novel genes involved in flower development and marker lines useful in mutant characterization. Flower developm...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
A Floral Induction System for the Study of Early Arabidopsis Flower Development
Assessing the molecular changes that occur over the course of flower development is hampered by difficulties in isolating sufficient amounts of floral tissue at specific developmental stages. This is especially problematic when investigating molecular events at very early stages of Arabidopsis flower development, as the floral buds are minute and are initiated sequentially such that a single flower on an inflorescence is at a given developmental stage. Moreover, young floral buds are hidden by older buds, which present an additional challenge for dissection. To circumvent these issues, a floral induction system that allows...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Fluorescence Activated Cell Sorting of Shoot Apical Meristem Cell Types
Growing tips of plants harbor a set of stem cells in structures called shoot apical meristems (SAMs) which provide cells for development of aboveground biomass. Despite a periodic differentiation of stem cell progenitors into leaves, the stem cell pool remains constant over time. Genetic analysis has revealed molecular pathways involved in stem-cell specification, cell division patterns, and organ differentiation. Stem cells within SAMs are few in number, which imposes a limitation to the experimental approaches that can be used for deciphering the gene regulatory networks that underlie cell fate transitions. Here, I provi...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Identification of Arabidopsis Knockout Lines for Genes of Interest
Determining gene function through reverse genetics has been an important experimental approach in the field of flower development. The method largely relies on the availability of knockout lines for the gene of interest. Insertional mutagenesis can be performed using either T-DNA or transposable elements, but the former has been more frequently employed in Arabidopsis. A primary concern for working with insertional mutant lines is whether the respective insertion results in a complete or rather a partial loss of gene function. The effect of the insertion largely depends on its position with respect to the structure of the ...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Gene Expression Analysis by Quantitative Real-time PCR for Floral Tissues
Real-time, or quantitative, reverse transcription polymerase chain reaction (qRT-PCR), is a powerful method for rapid and reliable quantification of mRNA abundance. Although it has not featured prominently in flower development research in the past, the availability of novel techniques for the synchronized induction of flower development, or for the isolation of cell-specific mRNA populations, suggests that detailed quantitative analyses of gene expression over time and in specific tissues and cell types by qRT-PCR will become more widely used. In this chapter, we discuss specific considerations for studying gene expressio...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Misexpression Approaches for the Manipulation of Flower Development
The generation of dominant gain-of-function mutants through activation tagging is a forward genetic approach that complements the screening of loss-of-function mutants and that has been successfully applied to studying the mechanisms of flower development. In addition, the functions of genes of interest can be further analyzed through reverse genetics. A commonly used method is gene overexpression, where strong, often ectopic expression can result in an opposite phenotype to that caused by a loss-of-function mutation. When overexpression is detrimental, the misexpression of a gene using tissue-specific promoters can be use...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Next-Generation Sequencing Applied to Flower Development: RNA-Seq
Genome-wide study of gene expression, or transcriptome profiling, is critical for our understanding of biological functions, including developmental processes. Recent breakthroughs in high-throughput sequencing technologies have revolutionized gene expression profiling to study the transcriptome at the nucleotide level, which is known as RNA-seq. RNA-seq, also called “whole transcriptome shotgun sequencing,” uses next-generation sequencing technologies to sequence cDNA in order to infer a sample’s RNA content. Here we describe a detailed bench-ready protocol to generate RNA-seq libraries for high-throughp...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Next-Generation Sequencing Applied to Flower Development: ChIP-Seq
Over the past 20 years, classic genetic approaches have shown that the developmental program underlying flower formation involves a large number of transcriptional regulators. However, the target genes of these transcription factors, as well as the gene regulatory networks they control, remain largely unknown. Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-Seq), which allows the identification of transcription factor binding sites on a genome-wide scale, has been successfully applied to a number of transcription factors in Arabidopsis. The ChIP-Seq procedure involves chemical cross-linking of pro...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Live-Imaging of the Arabidopsis Inflorescence Meristem
The aboveground tissues of higher plants are derived from a small population of stem cells located at the shoot apex within a structure called the shoot apical meristem (SAM). The SAM not only includes the stem cells but also incorporates a region from which lateral organs arise. The SAM is therefore of prime interest for understanding plant growth and development. In this chapter we outline methods for using confocal microscopy to image the Arabidopsis inflorescence SAM. This method enables detailed examination of cell division and growth patterns (Reddy et al., Development 131:4225–4237, 2004) as well as gene expre...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Gene Regulatory Network Models for Floral Organ Determination
Understanding how genotypes map unto phenotypes implies an integrative understanding of the processes regulating cell differentiation and morphogenesis, which comprise development. Such a task requires the use of theoretical and computational approaches to integrate and follow the concerted action of multiple genetic and nongenetic components that hold highly nonlinear interactions. Gene regulatory network (GRN) models have been proposed to approach such task. GRN models have become very useful to understand how such types of interactions restrict the multi-gene expression patterns that characterize different cell-fates. M...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
Genetic and Phenotypic Analyses of Carpel Development in Arabidopsis
Carpels are the female reproductive organs of the flower, organized in a gynoecium, which is arguably the most complex organ of a plant. The gynoecium provides protection for the ovules, helps to discriminate between male gametophytes, and facilitates successful pollination. After fertilization, it develops into a fruit, a specialized organ for seed protection and dispersal. To carry out all these functions, coordinated patterning and tissue specification within the developing gynoecium have to be achieved. In this chapter, we describe different methods to characterize defects in carpel patterning and morphogenesis associa...
Source: Springer protocols feed by Plant Sciences - January 11, 2014 Category: Biology Source Type: news
