Toward supportive data collection tools for plant metabolomics.

Abstract:

:Over recent years, a number of initiatives have proposed standard reporting guidelines for functional genomics experiments. Associated with these are data models that may be used as the basis of the design of software tools that store and transmit experiment data in standard formats. Central to the success of such data handling tools is their usability. Successful data handling tools are expected to yield benefits in time saving and in quality assurance. Here, we describe the collection of datasets that conform to the recently proposed data model for plant metabolomics known as ArMet (architecture for metabolomics) and illustrate a number of approaches to robust data collection that have been developed in collaboration between software engineers and biologists. These examples also serve to validate ArMet from the data collection perspective by demonstrating that a range of software tools, supporting data recording and data upload to central databases, can be built using the data model as the basis of their design.

journal_name

Plant Physiol

journal_title

Plant physiology

authors

Jenkins H,Johnson H,Kular B,Wang T,Hardy N

doi

10.1104/pp.104.058875

subject

Has Abstract

pub_date

2005-05-01 00:00:00

pages

67-77

issue

1

eissn

0032-0889

issn

1532-2548

pii

138/1/67

journal_volume

138

pub_type

杂志文章
  • Sulfur economy and cell wall biosynthesis during sulfur limitation of Chlamydomonas reinhardtii.

    abstract::We have identified two novel periplasmic/cell wall polypeptides that specifically accumulate during sulfur limitation of Chlamydomonas reinhardtii. These polypeptides, present at high levels in the extracellular polypeptide fraction from a sulfur-deprived, cell wall-minus C. reinhardtii strain, have apparent molecular...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:

    authors: Takahashi H,Braby CE,Grossman AR

    更新日期:2001-10-01 00:00:00

  • Arabidopsis putative selenium-binding protein1 expression is tightly linked to cellular sulfur demand and can reduce sensitivity to stresses requiring glutathione for tolerance.

    abstract::Selenium-Binding Protein1 (SBP1) gene expression was studied in Arabidopsis (Arabidopsis thaliana) seedlings challenged with several stresses, including cadmium (Cd), selenium {selenate [Se(VI)] and selenite [Se(IV)]}, copper (Cu), zinc (Zn), and hydrogen peroxide (H(2)O(2)) using transgenic lines expressing the lucif...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.109.144808

    authors: Hugouvieux V,Dutilleul C,Jourdain A,Reynaud F,Lopez V,Bourguignon J

    更新日期:2009-10-01 00:00:00

  • Expression of tobacco carbonic anhydrase in the C4 dicot flaveria bidentis leads to increased leakiness of the bundle sheath and a defective CO2-concentrating mechanism

    abstract::Flaveria bidentis (L.) Kuntze, a C4 dicot, was genetically transformed with a construct encoding the mature form of tobacco (Nicotiana tabacum L.) carbonic anhydrase (CA) under the control of a strong constitutive promoter. Expression of the tobacco CA was detected in transformant whole-leaf and bundle-sheath cell (bs...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.117.3.1071

    authors: Ludwig M,von Caemmerer S,Dean Price G,Badger MR,Furbank RT

    更新日期:1998-07-01 00:00:00

  • Differential Effects of a Substituted Pyridazinone, BASF 13-338, on Pathways of Monogalactosyldiacylglycerol Synthesis in Arabidopsis.

    abstract::We have examined the effects of the substituted pyridazinone herbicide, 4-chloro-5-(dimethylamino)-2-phenyl-3(2H)pyridazinone (BASF 13-338, Sandoz 9785), on the desaturation of linoleic acid (18:2) on different molecular species of monogalactosyldiacylglycerol (MGDG) and phosphatidylcholine (PC) in leaf tissue of Arab...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.85.3.684

    authors: Norman HA,John JB

    更新日期:1987-11-01 00:00:00

  • Inhibition by fusicoccin of germination of pea seeds.

    abstract::Fusicoccin inhibits the germination of pea (Pisum sativum L. cv Progress 9) seeds by decreasing the growth of the embryonal axis and by stimulating the fresh weight increase of the cotyledons. The growth of isolated embryonal axes in the presence of sucrose and KCl is stimulated by fusicoccin. The effect of fusicoccin...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.76.3.819

    authors: Lioi L,Petruzzelli L,Morgutti S,Cocucci SM

    更新日期:1984-11-01 00:00:00

  • Targeting tryptophan decarboxylase to selected subcellular compartments of tobacco plants affects enzyme stability and in vivo function and leads to a lesion-mimic phenotype.

    abstract::Tryptophan decarboxylase (TDC) is a cytosolic enzyme that catalyzes an early step of the terpenoid indole alkaloid biosynthetic pathway by decarboxylation of L-tryptophan to produce the protoalkaloid tryptamine. In the present study, recombinant TDC was targeted to the chloroplast, cytosol, and endoplasmic reticulum (...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.010889

    authors: Di Fiore S,Li Q,Leech MJ,Schuster F,Emans N,Fischer R,Schillberg S

    更新日期:2002-07-01 00:00:00

  • Knockout of a bacterial-type ATP-binding cassette transporter gene, AtSTAR1, results in increased aluminum sensitivity in Arabidopsis.

    abstract::ATP-binding cassette (ABC) transporters represent a large family in plants, but the functions of most of these transporters are unknown. Here we report a gene, AtSTAR1, only encoding an ATP-binding domain of a bacterial-type ABC transporter in Arabidopsis (Arabidopsis thaliana). AtSTAR1 is an ortholog of rice (Oryza s...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.110.155028

    authors: Huang CF,Yamaji N,Ma JF

    更新日期:2010-08-01 00:00:00

  • Development of the Potential for Cyanogenesis in Maturing Black Cherry (Prunus serotina Ehrh.) Fruits.

    abstract::Biochemical changes related to cyanogenesis (hydrogen cyanide production) were monitored during maturation of black cherry (Prunus serotina Ehrh.) fruits. At weekly intervals from flowering until maturity, fruits (or selected parts thereof) were analyzed for (a) fresh and dry weights, (b) prunasin and amygdalin levels...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.98.4.1423

    authors: Swain E,Li CP,Poulton JE

    更新日期:1992-04-01 00:00:00

  • Mitochondrial and nuclear localization of a novel pea thioredoxin: identification of its mitochondrial target proteins.

    abstract::Plants contain several genes encoding thioredoxins (Trxs), small proteins involved in the regulation of the activity of many enzymes through dithiol-disulfide exchange. In addition to chloroplastic and cytoplasmic Trx systems, plant mitochondria contain a reduced nicotinamide adenine dinucleotide phosphate-dependent T...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.109.138073

    authors: Martí MC,Olmos E,Calvete JJ,Díaz I,Barranco-Medina S,Whelan J,Lázaro JJ,Sevilla F,Jiménez A

    更新日期:2009-06-01 00:00:00

  • Soft X-Ray Imaging of Cellular Carbon and Nitrogen Distributions in Heterocystous Cyanobacteria.

    abstract::Soft x-ray microscopy (SXM) is a minimally invasive technique for single-cell high-resolution imaging as well as the visualization of intracellular distributions of light elements such as carbon, nitrogen, and oxygen. We used SXM to observe photosynthesis and nitrogen fixation in the filamentous cyanobacterium Anabaen...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.17.01767

    authors: Teramoto T,Azai C,Terauchi K,Yoshimura M,Ohta T

    更新日期:2018-05-01 00:00:00

  • Phosphorylation of wheat germ initiation factors and ribosomal proteins.

    abstract::The ability of the wheat germ initiation factors and ribosomes to serve as substrates for a wheat germ protein kinase (Yan and Tao 1982 J Biol Chem 257: 7037-7043) has been investigated. The wheat germ kinase catalyzes the phosphorylation of the 42,000 dalton subunit of eukaryotic initiation factor (eIF)-2 and the 107...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.77.2.370

    authors: Browning KS,Yan TF,Lauer SJ,Aquino LA,Tao M,Ravel JM

    更新日期:1985-02-01 00:00:00

  • Characterization of nucleoside triphosphatase activity in isolated pea nuclei and its photoreversible regulation by light.

    abstract::A nucleoside triphosphatase (NTPase) present in highly purified preparations of pea nuclei was partially characterized. The activity of this enzyme was stimulated by divalent cations (Mg2+ = Mn2+ > Ca2+), but was not affected by the monovalent cations, Na+ and K+. The Mg(2+)-dependent activity was further stimulated...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.81.2.609

    authors: Chen YR,Roux SJ

    更新日期:1986-01-01 00:00:00

  • Localization, solubilization and characterization of plant membrane-associated calcium-dependent protein kinases.

    abstract::Membrane fractions from mature silver beet (Beta vulgaris) deveined leaf and leaf stem homogenates have associated Ca(2+) -dependent protein kinase. The Ca(2+) -dependent protein kinase activity is associated with plasma membranes (density 1.14-1.18 grams per cubic centimeter) as determined from copurification on isop...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.88.1.164

    authors: Klucis E,Polya GM

    更新日期:1988-09-01 00:00:00

  • Replication of cauliflower mosaic virus DNA in leaves and suspension culture protoplasts of cotton.

    abstract::Cauliflower mosaic virus (CaMV) replicated in protoplasts and in inoculated leaves of the non-host, cotton (Gossypium hirsutum, L.). Protoplasts prepared from suspension-cultured cotton cells were infected by incubation with liposome-encapsulated CaMV virions. During a 1-week culture period the amount of CaMV nucleic ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.83.3.633

    authors: Hussain MM,Melcher U,Whittle T,Williams A,Brannan CM,Mitchell ED

    更新日期:1987-03-01 00:00:00

  • A transglutaminase immunologically related to tissue transglutaminase catalyzes cross-linking of cell wall proteins in Chlamydomonas reinhardtii.

    abstract::The addition of primary amines to the growth medium of the unicellular green alga Chlamydomonas reinhardtii disrupts cell wall assembly in both vegetative and zygotic cells. Primary amines are competitive inhibitors of the protein-cross-linking activity of transglutaminases. Two independent assays for transglutaminase...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.121.3.1003

    authors: Waffenschmidt S,Kusch T,Woessner JP

    更新日期:1999-11-01 00:00:00

  • Carotenogenesis Is Regulated by 5'UTR-Mediated Translation of Phytoene Synthase Splice Variants.

    abstract::Phytoene synthase (PSY) catalyzes the highly regulated, frequently rate-limiting synthesis of the first biosynthetically formed carotene. While PSY constitutes a small gene family in most plant taxa, the Brassicaceae, including Arabidopsis (Arabidopsis thaliana), predominantly possess a single PSY gene. This monogenic...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.16.01262

    authors: Álvarez D,Voß B,Maass D,Wüst F,Schaub P,Beyer P,Welsch R

    更新日期:2016-12-01 00:00:00

  • The cytokinin type-B response regulator PtRR13 is a negative regulator of adventitious root development in Populus.

    abstract::Adventitious root formation at the base of plant cuttings is an innate de novo organogenesis process that allows massive vegetative propagation of many economically and ecologically important species. The early molecular events following shoot excision are not well understood. Using whole-genome microarrays, we detect...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.109.137505

    authors: Ramírez-Carvajal GA,Morse AM,Dervinis C,Davis JM

    更新日期:2009-06-01 00:00:00

  • Photosynthetic Decline from High Temperature Stress during Maturation of Wheat : II. Interaction with Source and Sink Processes.

    abstract::High temperature stress reduces grain growth in wheat (Triticum aestivum L.) by altering source activity and sink capacity. The impact of stress on source and sink interactions in two wheat cultivars of differing source thermotolerance was monitored by analysis of chlorophyll fluorescence transients, Fv (variable fluo...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.92.3.654

    authors: Harding SA,Guikema JA,Paulsen GM

    更新日期:1990-03-01 00:00:00

  • Temperature Dependence of Photosynthesis in Agropyron smithii Rydb. : I. FACTORS AFFECTING NET CO(2) UPTAKE IN INTACT LEAVES AND CONTRIBUTION FROM RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE MEASURED IN VIVO AND IN VITRO.

    abstract::As part of an extensive analysis of the factors regulating photosynthesis in Agropyron smithii Rydb., a C(3) grass, we have examined the response of leaf gas exchange and ribulose-1,5-bisphosphate (RuBP) carboxylase activity to temperature. Emphasis was placed on elucidating the specific processes which regulate the t...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.69.4.921

    authors: Monson RK,Stidham MA,Williams GJ,Edwards GE,Uribe EG

    更新日期:1982-04-01 00:00:00

  • The histidine kinase Hik34 is involved in thermotolerance by regulating the expression of heat shock genes in synechocystis.

    abstract::Histidine kinases (Hiks) in Synechocystis sp. PCC 6803 are involved in the transduction of signals associated with various kinds of environmental stress. To examine the potential role in thermotolerance of Hiks, we used genome microarray analysis to screen a Hik knockout library for mutations that affected the express...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.104.059097

    authors: Suzuki I,Kanesaki Y,Hayashi H,Hall JJ,Simon WJ,Slabas AR,Murata N

    更新日期:2005-07-01 00:00:00

  • Comparison of the Ability of Salicylic Acid and Ferricyanide to Induce Flowering in the Long-day Plant, Lemna Gibba G3.

    abstract::Both salicylic acid and ferricyanide induce flowering in the long-day plant Lemna gibba L., strain G3 under 8- and 9-hour short days. In both cases the effect is daylength-dependent. Salicylic acid is ineffective on daylengths less than 8 hours and ferricyanide is ineffective on daylengths less than 5 hours. When both...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.65.6.1058

    authors: Tanaka O,Cleland CF

    更新日期:1980-06-01 00:00:00

  • Stomatal Responses to Light and Drought Stress in Variegated Leaves of Hedera helix.

    abstract::Direct and indirect mechanisms underlying the light response of stomata were studied in variegated leaves of the juvenile phase of Hedera helix L. Dose response curves of leaf conductance were measured with blue and red light in leaves kept in normal or in an inverted position. In the green portions of the leaves, the...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.81.3.768

    authors: Aphalo PJ,Sánchez RA

    更新日期:1986-07-01 00:00:00

  • Extracellular Matrix Assembly in Diatoms (Bacillariophyceae) (I. A Model of Adhesives Based on Chemical Characterization and Localization of Polysaccharides from the Marine Diatom Achnanthes longipes and Other Diatoms).

    abstract::Extracellular adhesives from the diatoms Achnanthes longipes, Amphora coffeaeformis, Cymbella cistula, and Cymbella mexicana were characterized by monosaccharide and methylation analysis, lectin-fluorescein isothiocyanate localization, and cytochemical staining. Polysaccharide was the major component of adhesives form...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.113.4.1059

    authors: Wustman BA,Gretz MR,Hoagland KD

    更新日期:1997-04-01 00:00:00

  • Predicting Stomatal Closure and Turgor Loss in Woody Plants Using Predawn and Midday Water Potential.

    abstract::Knowledge about physiological stress thresholds provides crucial information about plant performance and survival under drought. In this study, we report on the triphasic nature of the relationship between plant water potential (Ψ) at predawn and midday and describe a method that predicts Ψ at stomatal closure and tur...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.20.00500

    authors: Knipfer T,Bambach N,Hernandez MI,Bartlett MK,Sinclair G,Duong F,Kluepfel DA,McElrone AJ

    更新日期:2020-10-01 00:00:00

  • Transient accumulation of asparagine in sycamore cells after a long period of sucrose starvation.

    abstract::The mobilization of stored carbohydrates (sucrose and starch) and proteins during sucrose starvation was studied with sycamore (Acer pseudoplatanus L.) cells. When almost all the intracellular carbohydrate pools had disappeared, the cell protein content declined progressively whereas asparagine determined by either (1...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.94.2.717

    authors: Genix P,Bligny R,Martin JB,Douce R

    更新日期:1990-10-01 00:00:00

  • Integrated Analysis of Engineered Carbon Limitation in a Quadruple CO2/HCO3- Uptake Mutant of Synechocystis sp. PCC 6803.

    abstract::Cyanobacteria have efficient carbon concentration mechanisms and suppress photorespiration in response to inorganic carbon (Ci) limitation. We studied intracellular Ci limitation in the slow-growing CO2/HCO3 (-)-uptake mutant ΔndhD3 (for NADH dehydrogenase subunit D3)/ndhD4 (for NADH dehydrogenase subunit D4)/cmpA (fo...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.15.01289

    authors: Orf I,Klähn S,Schwarz D,Frank M,Hess WR,Hagemann M,Kopka J

    更新日期:2015-11-01 00:00:00

  • Stimulation of delta-Aminolevulinic Acid Formation in Algal Extracts by Heterologous RNA.

    abstract::Formation of the chlorophyll and heme precursor delta-aminolevulinic acid (ALA) from glutamate in soluble extracts of Chlorella vulgaris, Euglena gracilis, and Cyanidium caldarium was stimulated by addition of low molecular weight RNA derived from greening algae or plant tissue. Enzyme extracts were prepared for the A...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.82.4.1096

    authors: Weinstein JD,Mayer SM,Beale SI

    更新日期:1986-12-01 00:00:00

  • State transitions in Chlamydomonas reinhardtii. The role of the Mehler reaction in state 2-to-state 1 transition.

    abstract::The light intensity-dependent transition to state 1 of dark-adapted anaerobic state 2 Chlamydomonas reinhardtii cells is stimulated by oxygen and by other electron acceptors for photosystem I, such as oxaloacetate and methylviologen. This suggests that the transition to state 1 requires the oxidation of the intersyste...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.104.048256

    authors: Forti G,Caldiroli G

    更新日期:2005-02-01 00:00:00

  • Identification of hydroxypyruvate and glyoxylate reductases in maize leaves.

    abstract::At least two hydroxypyruvate reductases (HPRs), differing in specificity for NAD(P)H and (presumably) utilizing glyoxylate as a secondary substrate, were identified by fractionation of crude maize leaf extracts with ammonium sulfate. The NADH-preferring enzyme, which most probably represented peroxisomal HPR, was prec...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.91.1.278

    authors: Kleczkowski LA,Edwards GE

    更新日期:1989-09-01 00:00:00

  • Effects of Air Pollutants on the Composition of Stable Carbon Isotopes, deltaC, of Leaves and Wood, and on Leaf Injury.

    abstract::Air pollutants are known to cause visible leaf injury as well as impairment of photosynthetic CO(2) fixation. Here we evaluate whether the effects on photosynthesis are large enough to cause changes in the relative composition of stable carbon isotopes, delta(13)C, of plant tissue samples, and, if so, how the changes ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.88.1.218

    authors: Martin B,Bytnerowicz A,Thorstenson YR

    更新日期:1988-09-01 00:00:00