Abstract:
:One should perhaps start off by asking the question, 'But what wood is it we want to see?' There are so many trees that make up the wood; within a post-genomics context, genes, transcripts, proteins, and metabolites are the more tangible ones. Rather than studying these components in isolation, a more holistic approach is to unravel the interactions between the myriad of subcellular components and this is vital to systems biology. Moreover, this will help define the phenotype of the organism under investigation. Metabolomics is complementary to transcriptomics and proteomics, and despite the immense metabolite diversity observed in plants, metabolomics has been embraced by the plant community and in particular for studying metabolic networks. Whilst post-genomic science is producing vast data torrents, it is well known that data do not equal knowledge and so the extraction of the most meaningful parts of these data is key to the generation of useful new knowledge. A metabolomics experiment is guaranteed to generate thousands of data points (e.g. samples multiplied by the levels of particular metabolites) of which only a handful might be needed to describe the problem adequately. Evolutionary computational-based methods such as genetic algorithms and genetic programming are ideal strategies for mining such high-dimensional data to generate useful relationships, rules, and predictions. This article describes these techniques and highlights their usefulness within metabolomics.
journal_name
J Exp Botjournal_title
Journal of experimental botanyauthors
Goodacre Rdoi
10.1093/jxb/eri043keywords:
subject
Has Abstractpub_date
2005-01-01 00:00:00pages
245-54issue
410eissn
0022-0957issn
1460-2431pii
eri043journal_volume
56pub_type
杂志文章,评审abstract::Six MaMADS-box genes have been cloned from the banana fruit cultivar Grand Nain. The similarity of these genes to tomato LeRIN is low and neither MaMADS2 nor MaMADS1 complement the tomato rin mutation. Nevertheless, the expression patterns, specifically in fruit and the induction during ripening and in response to eth...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erq017
更新日期:2010-03-01 00:00:00
abstract::It is generally believed that an osmotically generated pressure gradient drives the phloem mass flow. So far, this widely accepted Münch theory has required remarkably few adaptations, but the debate on alternative and additional hypotheses is still ongoing. Recently, a possible shortcoming of the Münch theory has bee...
journal_title:Journal of experimental botany
pub_type: 杂志文章,评审
doi:10.1093/jxb/ert302
更新日期:2013-11-01 00:00:00
abstract::As a PLC activity was implicated in the light transduction pathway that controls C(4) photosynthesis in Digitaria sanguinalis, a full length PLC cDNA (DsPLC2) was cloned. The proteins encoded by the two possible open reading frames were produced in Escherichia coli; they both harbour a PLC activity but with different ...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:
更新日期:2002-06-01 00:00:00
abstract::Here, a comprehensive proteomic analysis of the chromoplasts purified from sweet orange using Nycodenz density gradient centrifugation is reported. A GeLC-MS/MS shotgun approach was used to identify the proteins of pooled chromoplast samples. A total of 493 proteins were identified from purified chromoplasts, of which...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/err140
更新日期:2011-11-01 00:00:00
abstract::At present and more so in the future, irrigated agriculture will take place under water scarcity. Insufficient water supply for irrigation will be the norm rather than the exception, and irrigation management will shift from emphasizing production per unit area towards maximizing the production per unit of water consu...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erl165
更新日期:2007-01-01 00:00:00
abstract::The activity of the protein kinase STN7, involved in phosphorylation of the light-harvesting complex II (LHCII) proteins, has been reported as being co-operatively regulated by the redox state of the plastoquinone pool and the ferredoxin-thioredoxin (Trx) system. The present study aims to investigate the role of plast...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/ery415
更新日期:2019-02-05 00:00:00
abstract::Leaf senescence is a very important trait that limits yield and biomass accumulation of agronomic crops and reduces post-harvest performance and the nutritional value of horticultural crops. Significant advance in physiological and molecular understanding of leaf senescence has made it possible to devise ways of manip...
journal_title:Journal of experimental botany
pub_type: 杂志文章,评审
doi:10.1093/jxb/eru248
更新日期:2014-07-01 00:00:00
abstract::Improving photosynthesis is considered a promising way to increase crop yield to feed a growing population. Realizing this goal requires non-destructive techniques to quantify photosynthetic variation among crop cultivars. Despite existing remote sensing-based approaches, it remains a question whether solar-induced fl...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/eraa537
更新日期:2020-12-19 00:00:00
abstract::Seed size is a key determinant of evolutionary fitness, and is also one of the most important components of seed yield. In angiosperms, seed development begins with double fertilization, which leads to the formation of a diploid embryo and a triploid endosperm. The outermost layer of the seed is the seed coat, which d...
journal_title:Journal of experimental botany
pub_type: 杂志文章,评审
doi:10.1093/jxb/eru549
更新日期:2015-02-01 00:00:00
abstract::The state of etiolation is generally defined by the presence of non-green plastids (etioplasts) in plant tissues that would normally contain chloroplasts. In the commonly used dark-grown seedling system, etiolation is coupled with a type of growth called skotomorphogenesis. Upon illumination, de-etiolation occurs, mar...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erz496
更新日期:2020-02-19 00:00:00
abstract::Jasmonates are signaling compounds that regulate plant responses to stress. Jasmonic acid (JA) is the direct precursor of the bioactive plant hormone JA-isoleucine (JA-Ile), the ligand of the CORONATINE INSENSITIVE 1-jasmonate ZIM-domain (COI1-JAZ) co-receptor complex. JA, its methyl ester, and three furanonyl esters ...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/ery114
更新日期:2018-05-25 00:00:00
abstract::The endosperm is an essential part of the seed which sustains embryo development and contains storage reserves. Endosperm development involves a series of nuclear divisions in the absence of cytokinesis. In this study, it is shown that a mutant Arabidopsis plant carrying the disrupted At4g24900 gene exhibits severe de...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/ers243
更新日期:2012-10-01 00:00:00
abstract::Magnesium-chelatase H subunit [CHLH/putative abscisic acid (ABA) receptor ABAR] positively regulates guard cell signalling in response to ABA, but the molecular mechanism remains largely unknown. A member of the sucrose nonfermenting 1 (SNF1)-related protein kinase 2 family, SnRK2.6/open stomata 1 (OST1)/SRK2E, which ...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erv341
更新日期:2015-10-01 00:00:00
abstract::The high efficiency of C4 photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C4 tissues along a developing leaf gradient. This method treat...
journal_title:Journal of experimental botany
pub_type: 杂志文章,meta分析
doi:10.1093/jxb/erw463
更新日期:2017-01-01 00:00:00
abstract::Although the mechanisms of nodule N(2) fixation in legumes are now well documented, some uncertainty remains on the metabolic consequences of water deficit. In most cases, little consideration is given to other organs and, therefore, the coordinated changes in metabolism in leaves, roots, and nodules are not well know...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/ers367
更新日期:2013-02-01 00:00:00
abstract::This paper gives a summary of a project to characterize a tobacco aquaporin. The cDNA and gene, including the 5' upstream region, for the tobacco aquaporin NtAQP1 has been isolated and the encoded protein characterized. The significance of promoter regions for an abscisic acid- and gibberellic acid-induced gene expres...
journal_title:Journal of experimental botany
pub_type: 杂志文章,评审
doi:10.1093/jexbot/52.363.1953
更新日期:2001-10-01 00:00:00
abstract::One of the earliest symptoms of boron (B) deficiency is the inhibition of root elongation which can reasonably be attributed to the damaging effects of B deprivation on cell wall integrity. It is shown here that exposure of wild-type Arabidopsis thaliana seedlings to B deficiency for 4h led to a drastic inhibition of ...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erv186
更新日期:2015-07-01 00:00:00
abstract::Oilseed rape is one of the most important dicotyledonous field crops in the world, where it plays a key role in productive cereal crop rotations. However, its production requires high nitrogen fertilization and its nitrogen footprint exceeds that of most other globally important crops. Hence, increased nitrogen use ef...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erz044
更新日期:2019-03-27 00:00:00
abstract::In Crocus vernus, a spring bulbous species, prolonged growth at low temperatures results in the development of larger perennial organs and delayed foliar senescence. Because corm growth is known to stop before the first visual sign of leaf senescence, it is clear that factors other than leaf duration alone determine f...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erp103
更新日期:2009-01-01 00:00:00
abstract::Soil salinity and drought compromise water uptake and lead to osmotic adjustment in xero-halophyte plant species. These important environmental constraints may also have specific effects on plant physiology. Stress-induced accumulation of osmocompatible solutes was analysed in two Tunisian populations of the Mediteran...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/ern040
更新日期:2008-01-01 00:00:00
abstract::The measurement of the response of net photosynthesis to leaf internal CO2 (i.e. A-Ci curves) is widely used for ecophysiological studies. Most studies did not consider CO2 exchange between the chamber and the surrounding air, especially at the two extremes of A-Ci curves, where large CO2 gradients are created, leadin...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erm027
更新日期:2007-01-01 00:00:00
abstract::Dry matter partitioning is the end result of the flow of assimilates from source organs via a transport path to the sink organs. The dry matter partitioning among the sinks of a plant is primarily regulated by the sinks themselves. The effect of source strength on dry matter partitioning is often not a direct one, but...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/47.Special_Issue.1281
更新日期:1996-08-01 00:00:00
abstract::The phloem is a well-known target of sucking and piercing insects that utilize the transported fluid as their major nutrient source. In addition to small molecules like sugars and amino acids, phloem sap of higher land plants contains proteins that can accumulate up to high concentrations. Although the knowledge about...
journal_title:Journal of experimental botany
pub_type: 杂志文章,评审
doi:10.1093/jxb/erj087
更新日期:2006-01-01 00:00:00
abstract::PaHB1 (for Picea abies Homeobox1), an evolutionarily conserved HD-GL2 homeobox gene, specifically expressed in the protoderm during somatic embryogenesis in the gymnosperm Norway spruce has been reported previously. An additional HD-GL2 gene designated PaHB2 is reported here. During somatic embryogenesis, the PaHB2 ge...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erg145
更新日期:2003-05-01 00:00:00
abstract::The hypersensitive response (HR) is one mechanism of the resistance of plants to pathogen infection. It involves the generation of reactive oxygen species (ROS) which have crucial roles in signal transduction or as toxic agents leading to cell death. Often, ROS generation is accompanied by an ultraweak photon emission...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erl215
更新日期:2007-01-01 00:00:00
abstract::Fructans are water-soluble fructose oligomers and polymers that are based on sucrose, and have been implicated in protecting plants against water stress. Rice (Oryza sativa L.) is highly sensitive to chilling temperatures, and is not able to synthesize fructans. Two wheat fructan-synthesizing enzymes, sucrose:sucrose ...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erm367
更新日期:2008-01-01 00:00:00
abstract::An increased concentration of cytosolic Ca2+ is an early response of plant cells to heat shock. Arabidopsis cyclic nucleotide-gated ion channel 6 (CNGC6) mediates heat-induced Ca2+ influx and is activated by cAMP. However, it remains unclear how the Ca2+ conductivity of CNGC6 is negatively regulated under the elevated...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erz445
更新日期:2020-01-01 00:00:00
abstract::Anthocyanin production is a characteristic response of flowering plants to unfavourable environmental conditions. The potential roles of flavonoids and anthocyanins in plant growth were investigated by growing Arabidopsis thaliana anthocyanin production mutants (transparent testa) under limiting nitrogen and high ligh...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/ers328
更新日期:2013-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are important transcriptional and post-transcriptional modulators of gene expression that play crucial roles in the responses to diverse stresses. To explore jasmonic acid (JA)-dependent miRNA-mediated regulatory networks that are responsive to root-knot nematode (RKN), two small RNA libraries were ...
journal_title:Journal of experimental botany
pub_type: 杂志文章
doi:10.1093/jxb/erv238
更新日期:2015-08-01 00:00:00
abstract::Successful sexual reproduction often relies on the ability of plants to recognize self- or genetically-related pollen and prevent pollen tube growth soon after germination in order to avoid self-fertilization. Angiosperms have developed different reproductive barriers, one of the most extended being self-incompatibili...
journal_title:Journal of experimental botany
pub_type: 杂志文章,评审
doi:10.1093/jxb/erv083
更新日期:2015-05-01 00:00:00