Abstract：
BACKGROUND:Kinome profiling aims at the parallel analysis of kinase activities in a cell. Novel developed arrays containing consensus substrates for kinases are used to assess those kinase activities. The arrays described in this paper were already used to determine kinase activities in mammalian systems, but since substrates from many organisms are present we decided to test these arrays for the determination of kinase activities in the model plant species Arabidopsis thaliana. RESULTS:Kinome profiling using Arabidopsis cell extracts resulted in the labelling of many consensus peptides by kinases from the plant, indicating the usefulness of this kinome profiling tool for plants. Method development showed that fresh and frozen plant material could be used to make cell lysates containing active kinases. Dilution of the plant extract increased the signal to noise ratio and non-radioactive ATP enhances full development of spot intensities. Upon infection of Arabidopsis with an avirulent strain of the bacterial pathogen Pseudomonas syringae pv. tomato, we could detect differential kinase activities by measuring phosphorylation of consensus peptides. CONCLUSION:We show that kinome profiling on arrays with consensus substrates can be used to monitor kinase activities in plants. In a case study we show that upon infection with avirulent P. syringae differential kinase activities can be found. The PepChip can for example be used to purify (unknown) kinases that play a role in P. syringae infection. This paper shows that kinome profiling using arrays of consensus peptides is a valuable new tool to study signal-transduction in plants. It complements the available methods for genomics and proteomics research.
journal_name
Plant Methodsjournal_title
Plant methodsauthors
Ritsema T,Joore J,van Workum W,Pieterse CMdoi
10.1186/1746-4811-3-3subject
Has Abstractpub_date
2007-02-12 00:00:00pages
3issn
1746-4811pii
1746-4811-3-3journal_volume
3pub_type
杂志文章相关文献
Plant Methods文献大全abstract：BACKGROUND:When conducting plant research, the measurement of photosynthetic pigments can provide basic information on the physiological status of a plant. High-pressure liquid chromatography (HPLC) is becoming widely used for this purpose because it provides an accurate determination of a variety of photosynthetic pig...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-9-19
更新日期：2013-06-19 00:00:00
abstract：BACKGROUND:Mitochondria play critical roles in plant growth, development and stress tolerance. Numerous researchers have carried out studies on the plant mitochondrial genome structure, mitochondrial metabolism and nuclear-cytoplasmic interactions. However, classical plant mitochondria extraction methods are time-consu...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00690-6
更新日期：2020-11-04 00:00:00
abstract：BACKGROUND:Starch is the most important source of calories for human nutrition and the majority of it is produced by cereal farming. Starch is also used as a renewable raw material in a range of industrial sectors. It can be chemically modified to introduce new physicochemical properties. In this way starch is adapted ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-36
更新日期：2012-09-07 00:00:00
abstract：Background:To investigate potential effects of herbicide phytotoxic on crops, a major challenge is a lack of non-destructive and rapid methods to detect plant growth that could allow characterization of herbicide-resistant plants. In such a case, hyperspectral imaging can quickly obtain the spectrum for each pixel in t...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00576-7
更新日期：2020-03-05 00:00:00
abstract：Background:Many agronomic traits have been bred into modern wheat varieties, but wheat (Triticum aestivum L.) continues to be vulnerable to heat stress, with high night-time temperature (HNT) stress shown to have large negative impact on yield and quality. Global mean temperature during the day is consistently warming ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0424-x
更新日期：2019-04-24 00:00:00
abstract：BACKGROUND:The elucidation of complex biological systems requires integration of multiple molecular parameters. Accordingly, high throughput methods like transcriptomics, proteomics, metabolomics and lipidomics have emerged to provide the tools for successful system-wide investigations. Unfortunately, optimized analysi...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0146-2
更新日期：2016-11-10 00:00:00
abstract：Background:In-field measurement of yield and growth rate in pasture species is imprecise and costly, limiting scientific and commercial application. Our study proposed a LiDAR-based mobile platform for non-invasive vegetative biomass and growth rate estimation in perennial ryegrass (Lolium perenne L.). This included de...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0456-2
更新日期：2019-07-10 00:00:00
abstract：BACKGROUND:Protein phosphorylation is accepted as a major regulatory pathway in plants. More than 1000 protein kinases are predicted in the Arabidopsis proteome, however, only a few studies look systematically for in vivo protein phosphorylation sites. Owing to the low stoichiometry and low abundance of phosphorylated ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-1-9
更新日期：2005-11-01 00:00:00
abstract：: Generating and identifying transformants is essential for many studies of gene function. In Arabidopsis thaliana, a revolutionary protocol termed floral dip is now the most widely used transformation method. Although robust, it involves a number of relatively time-consuming and laborious steps, including manipulating...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-5-3
更新日期：2009-02-27 00:00:00
abstract：BACKGROUND:It is well known that preparation of biological (plant and animal) tissues for Scanning Electron Microscopy (SEM) by chemical fixation and critical point drying results in shrinkage of tissues, often by up to 20-30%, depending on the tissue type and fixation protocol used. We sought to identify a protocol th...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-9-36
更新日期：2013-10-02 00:00:00
abstract：BACKGROUND:Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene express...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0123-9
更新日期：2016-04-26 00:00:00
abstract：Background:Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0362-z
更新日期：2018-10-24 00:00:00
abstract：BACKGROUND:Transient gene expression systems are indispensable tools in molecular biology. Yet, their routine application is limited to few plant species often requiring substantial equipment and facilities. High chloroplast and chlorophyll content may further impede downstream applications of transformed cells from gr...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-14
更新日期：2012-05-04 00:00:00
abstract：Background:Monitoring the timing of seedling emergence and early development via high-throughput phenotyping with computer vision is a challenging topic of high interest in plant science. While most studies focus on the measurements of leaf area index or detection of specific events such as emergence, little attention ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00647-9
更新日期：2020-07-30 00:00:00
abstract：Background:Plant parasitic weeds belonging to the genus Striga are a major threat for food production in Sub-Saharan Africa and Southeast Asia. The parasite's life cycle starts with the induction of seed germination by host plant-derived signals, followed by parasite attachment, infection, outgrowth, flowering, reprodu...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00602-8
更新日期：2020-05-01 00:00:00
abstract：: Large-scale genetic screens in Arabidopsis are a powerful approach for molecular dissection of complex signaling networks. However, map-based cloning can be time-consuming or even hampered due to low chromosomal recombination. Current strategies using next generation sequencing for molecular identification of mutatio...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-12
更新日期：2012-03-30 00:00:00
abstract：BACKGROUND:The main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter wa...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-017-0191-5
更新日期：2017-05-22 00:00:00
abstract：Background:Wheat is one of the most widely grown crop in temperate climates for food and animal feed. In order to meet the demands of the predicted population increase in an ever-changing climate, wheat production needs to dramatically increase. Spike and grain traits are critical determinants of final yield and grain ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-017-0229-8
更新日期：2017-11-01 00:00:00
abstract：Background:Image processing techniques have been widely used in the analysis of leaf characteristics. Earlier techniques for processing digital RGB color images of plant leaves had several drawbacks, such as inadequate de-noising, and adopting normal-probability statistical estimation models which have few parameters a...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-0561-2
更新日期：2020-02-26 00:00:00
abstract：BACKGROUND:Protoplasts isolated from leaves are useful materials in plant research. One application, the transient expression of recombinant genes using Arabidopsis mesophyll protoplasts (TEAMP), is currently commonly used for studies of subcellular protein localization, promoter activity, and in vivo protein-protein i...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-5-16
更新日期：2009-11-24 00:00:00
abstract：BACKGROUND:The cultivar Micro-Tom (MT) is regarded as a model system for tomato genetics due to its short life cycle and miniature size. However, efforts to improve tomato genetic transformation have led to protocols dependent on the costly hormone zeatin, combined with an excessive number of steps. RESULTS:Here we re...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-6-23
更新日期：2010-10-07 00:00:00
abstract：BACKGROUND:Establishment and maintenance of mutualistic plant-microbial interactions in the rhizosphere and within plant roots involve several root cell types. The processes of host-microbe recognition and infection require complex signal exchange and activation of downstream responses. These molecular events coordinat...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0105-y
更新日期：2016-01-22 00:00:00
abstract：:Intact protein complexes can be separated by apparent molecular mass using a standard polyacrylamide gel electrophoresis system combining mild detergents and the dye Coomassie Blue. Referring to the blue coloured gel and the gentle method of solubilization yielding native and enzymatically active protein complexes, th...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-1-11
更新日期：2005-11-16 00:00:00
abstract：: Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA la...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-18
更新日期：2012-06-13 00:00:00
abstract：BACKGROUND:In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published r...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-7-8
更新日期：2011-03-29 00:00:00
abstract：Motivation:In 2005, researchers from the French National Research Institute for Agriculture, Food and Environment (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, INRAE) started a collaboration with the French farmers' seed network Réseau Semences Paysannes (RSP) on bread wheat par...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00640-2
更新日期：2020-07-23 00:00:00
abstract：BACKGROUND:Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulat...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-015-0087-1
更新日期：2015-09-04 00:00:00
abstract：BACKGROUND:In eukaryotic cells, the proteasome maintains homeostasis by selectively degrading regulatory and misfolded proteins, and in doing so contributes to the amino acid pool. Inhibition of the proteasome in yeast and human cells decreases de novo protein synthesis. However, it is not know if proteasome inhibition...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0120-z
更新日期：2016-03-16 00:00:00
abstract：: We report on a detailed chromatin immunoprecipitation (ChIP) protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide s...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-7-35
更新日期：2011-11-03 00:00:00
abstract：Background:Most bacteria are not culturable, but can be identified through molecular methods such as metagenomics studies. Due to specific metabolic requirements and symbiotic relationships, these bacteria cannot survive on typical laboratory media. Many economically and medically important bacteria are unculturable; i...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0465-1
更新日期：2019-07-31 00:00:00
