bluuebunny/crossref_metadata_2025_split huggingface dataset:
GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox
Authors: Zimmermann Philip , Hirsch-Hoffmann Matthias , Hennig Lars , Gruissem Wilhelm 
Published: September 2004

Abstract
High-throughput gene expression analysis has become a frequent and powerful research tool in biology. At present, however, few software applications have been developed for biologists to query large microarray gene expression databases using a Web-browser interface. We present GENEVESTIGATOR, a database and Web-browser data mining interface for Affymetrix GeneChip data. Users can query the database to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs. Reversely, mining tools allow users to identify genes specifically expressed during selected stresses, growth stages, or in particular organs. Using GENEVESTIGATOR, the gene expression profiles of more than 22,000 Arabidopsis genes can be obtained, including those of 10,600 currently uncharacterized genes. The objective of this software application is to direct gene functional discovery and design of new experiments by providing plant biologists with contextual information on the expression of genes. The database and analysis toolbox is available as a community resource at https://www.genevestigator.ethz.ch.
TheElm1(ZmHy2) Gene of Maize Encodes a Phytochromobilin Synthase
Authors: Sawers Ruairidh J.H. , Linley Philip J. , Gutierrez-Marcos Jose F. , Delli-Bovi Teegan , Farmer Phyllis R. , Kohchi Takayuki , Terry Matthew J. , Brutnell Thomas P. 
Published: September 2004

AbstractThe light insensitive maize (Zea mays) mutant elongated mesocotyl1 (elm1) has previously been shown to be deficient in the synthesis of the phytochrome chromophore 3E-phytochromobilin (PΦB). To identify the Elm1 gene, a maize homolog of the Arabidopsis PΦB synthase gene AtHY2 was isolated and designated ZmHy2. ZmHy2 encodes a 297-amino acid protein of 34 kD that is 50% identical to AtHY2. ZmHY2 was predicted to be plastid localized and was targeted to chloroplasts following transient expression in tobacco (Nicotiana plumbaginifolia) leaves. Molecular mapping indicated that ZmHy2 is a single copy gene in maize that is genetically linked to the Elm1 locus. Sequence analysis revealed that the ZmHy2 gene of elm1 mutants contains a single G to A transition at the 3′ splice junction of intron III resulting in missplicing and premature translational termination. However, flexibility in the splicing machinery allowed a small pool of in-frame ZmHy2 transcripts to accumulate in elm1 plants. In addition, multiple ZmHy2 transcript forms accumulated in both wild-type and elm1 mutant plants. ZmHy2 splice variants were expressed in Escherichia coli and products examined for activity using a coupled apophytochrome assembly assay. Only full-length ZmHY2 (as defined by homology to AtHY2) was found to exhibit PΦB synthase activity. Thus, the elm1 mutant of maize is deficient in phytochrome response due to a lesion in a gene encoding phytochromobilin synthase that severely compromises the PΦB pool.
Light Regulation of the Arabidopsis Respiratory Chain. Multiple Discrete Photoreceptor Responses Contribute to Induction of Type II NAD(P)H Dehydrogenase Genes
Authors: Escobar Matthew A. , Franklin Keara A. , Svensson Å. Staffan , Salter Michael G. , Whitelam Garry C. , Rasmusson Allan G. 
Published: September 2004

AbstractControlled oxidation reactions catalyzed by the large, proton-pumping complexes of the respiratory chain generate an electrochemical gradient across the mitochondrial inner membrane that is harnessed for ATP production. However, several alternative respiratory pathways in plants allow the maintenance of substrate oxidation while minimizing the production of ATP. We have investigated the role of light in the regulation of these energy-dissipating pathways by transcriptional profiling of the alternative oxidase, uncoupling protein, and type II NAD(P)H dehydrogenase gene families in etiolated Arabidopsis seedlings. Expression of the nda1 and ndc1 NAD(P)H dehydrogenase genes was rapidly up-regulated by a broad range of light intensities and qualities. For both genes, light induction appears to be a direct transcriptional effect that is independent of carbon status. Mutant analyses demonstrated the involvement of two separate photoreceptor families in nda1 and ndc1 light regulation: the phytochromes (phyA and phyB) and an undetermined blue light photoreceptor. In the case of the nda1 gene, the different photoreceptor systems generate distinct kinetic induction profiles that are integrated in white light response. Primary transcriptional control of light response was localized to a 99-bp region of the nda1 promoter, which contains an I-box flanked by two GT-1 elements, an arrangement prevalent in the promoters of photosynthesis-associated genes. Light induction was specific to nda1 and ndc1. The only other substantial light effect observed was a decrease in aox2 expression. Overall, these results suggest that light directly influences the respiratory electron transport chain via photoreceptor-mediated transcriptional control, likely for supporting photosynthetic metabolism.
Seed-Specific Heterologous Expression of a Nasturtium FAE Gene in Arabidopsis Results in a Dramatic Increase in the Proportion of Erucic Acid
Authors: Mietkiewska Elzbieta , Giblin E. Michael , Wang Song , Barton Dennis L. , Dirpaul Joan , Brost Jennifer M. , Katavic Vesna , Taylor David C. 
Published: September 2004

Abstract
The fatty acid elongase [often designated FAE or β-(or 3-) ketoacyl-CoA synthase] is a condensing enzyme and is the first component of the elongation complex involved in synthesis of erucic acid (22:1) in seeds of garden nasturtium (Tropaeolum majus). Using a degenerate primers approach, a cDNA of a putative embryo FAE was obtained showing high homology to known plant elongases. This cDNA contains a 1,512-bp open reading frame that encodes a protein of 504 amino acids. A genomic clone of the nasturtium FAE was isolated and sequence analyses indicated the absence of introns. Northern hybridization showed the expression of this nasturtium FAE gene to be restricted to the embryo. Southern hybridization revealed the nasturtium β-ketoacyl-CoA synthase to be encoded by a small multigene family. To establish the function of the elongase homolog, the cDNA was introduced into two different heterologous chromosomal backgrounds (Arabidopsis and tobacco [Nicotiana tabacum]) under the control of a seed-specific (napin) promoter and the tandem 35S promoter, respectively. Seed-specific expression resulted in up to an 8-fold increase in erucic acid proportions in Arabidopsis seed oil, while constitutive expression in transgenic tobacco tissue resulted in increased proportions of very long chain saturated fatty acids. These results indicate that the nasturtium FAE gene encodes a condensing enzyme involved in the biosynthesis of very long chain fatty acids, utilizing monounsaturated and saturated acyl substrates. Given its strong and unique preference for elongating 20:1-CoA, the utility of the FAE gene product for directing or engineering increased synthesis of erucic acid is discussed.
Embryo-Specific Reduction of ADP-Glc Pyrophosphorylase Leads to an Inhibition of Starch Synthesis and a Delay in Oil Accumulation in Developing Seeds of Oilseed Rape
Authors: Vigeolas Helene , Möhlmann Torsten , Martini Norbert , Neuhaus H. Ekkehard , Geigenberger Peter 
Published: September 2004

Abstract
In oil-storing Brassica napus (rape) seeds, starch deposition occurs only transiently in the early stages of development, and starch is absent from mature seeds. This work investigates the influence of a reduction of ADP-Glc pyrophosphorylase (AGPase) on storage metabolism in these seeds. To manipulate the activity of AGPase in a seed-specific manner, a cDNA encoding the small subunit of AGPase was expressed in the sense or antisense orientation under the control of an embryo-specific thioesterase promoter. Lines were selected showing an embryo-specific decrease in AGPase due to antisense and cosuppression at different stages of development. At early developmental stages (25 days after flowering), a 50% decrease in AGPase activity was accompanied by similar decreases in starch content and the rate of starch synthesis measured by injecting 14C-Suc into seeds in planta. In parallel to inhibition of starch synthesis, the level of ADP-Glc decreased, whereas Glc 1-phosphate levels increased, providing biochemical evidence that inhibition of starch synthesis was due to repression of AGPase. At 25 days after flowering, repression of starch synthesis also led to a decrease in the rate of 14C-Suc degradation and its further metabolism via other metabolic pathways. This was not accompanied by an increase in the levels of soluble sugars, indicating that Suc import was inhibited in parallel. Flux through glycolysis, the activities of hexokinase, and inorganic pyrophosphate-dependent phosphofructokinase, and the adenylate energy state (ATP to ADP ratio) of the transgenic seeds decreased, indicating inhibition of glycolysis and respiration compared to wild type. This was accompanied by a marked decrease in the rate of storage lipid (triacylglycerol) synthesis and in the fatty acid content of seeds. In mature seeds, glycolytic enzyme activities, metabolite levels, and ATP levels remained unchanged, and the fatty acid content was only marginally lower compared to wild type, indicating that the influence of AGPase on carbon metabolism and oil accumulation was largely compensated for in the later stages of seed development. Results indicate that AGPase exerts high control over starch synthesis at early stages of seed development where it is involved in establishing the sink activity of the embryo and the onset of oil accumulation.
Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen
Authors: Scheible Wolf-Rüdiger , Morcuende Rosa , Czechowski Tomasz , Fritz Christina , Osuna Daniel , Palacios-Rojas Natalia , Schindelasch Dana , Thimm Oliver , Udvardi Michael K. , Stitt Mark 
Published: September 2004

Abstract
Transcriptome analysis, using Affymetrix ATH1 arrays and a real-time reverse transcription-PCR platform for &gt;1,400 transcription factors, was performed to identify processes affected by long-term nitrogen-deprivation or short-term nitrate nutrition in Arabidopsis. Two days of nitrogen deprivation led to coordinate repression of the majority of the genes assigned to photosynthesis, chlorophyll synthesis, plastid protein synthesis, induction of many genes for secondary metabolism, and reprogramming of mitochondrial electron transport. Nitrate readdition led to rapid, widespread, and coordinated changes. Multiple genes for the uptake and reduction of nitrate, the generation of reducing equivalents, and organic acid skeletons were induced within 30 min, before primary metabolites changed significantly. By 3 h, most genes assigned to amino acid and nucleotide biosynthesis and scavenging were induced, while most genes assigned to amino acid and nucleotide breakdown were repressed. There was coordinate induction of many genes assigned to RNA synthesis and processing and most of the genes assigned to amino acid activation and protein synthesis. Although amino acids involved in central metabolism increased, minor amino acids decreased, providing independent evidence for the activation of protein synthesis. Specific genes encoding expansin and tonoplast intrinsic proteins were induced, indicating activation of cell expansion and growth in response to nitrate nutrition. There were rapid responses in the expression of many genes potentially involved in regulation, including genes for trehalose metabolism and hormone metabolism, protein kinases and phosphatases, receptor kinases, and transcription factors.
The Capacity of Green Oilseeds to Utilize Photosynthesis to Drive Biosynthetic Processes
Authors: Ruuska Sari A. , Schwender Jörg , Ohlrogge John B. 
Published: September 2004

Abstract
Seeds of many plant species are green during embryogenesis. To directly assess the influence of light on the physiological status of green oilseeds in planta, Brassica napus and soybean (Glycine max) seeds were rapidly dissected from plants growing in the light or dark. The activation state of malate dehydrogenase, which reflects reduced thioredoxin and NADP/NADPH ratios, was found to be as high in seeds exposed to light as in leaves and to decrease in the dark. Rubisco was highly activated (carbamylated) in both light and dark, most likely reflecting high seed CO2 concentrations. Activities of Rubisco and phosphoribulokinase were sufficient to account for significant refixation of CO2 produced during B. napus oil biosynthesis. To determine the influence of light on oil synthesis in planta, siliques on intact plants in full sunlight or detached siliques fed 3H2O were partly covered with aluminum foil. Seeds from light and dark sections were analyzed, and fatty acid accumulation was found to be higher in seeds exposed to light than seeds from dark sections. The spectrum of light filtering through silique walls and the pigment composition of developing B. napus embryos were determined. In addition to a low chlorophyll a/b ratio, the carotenoid pigments of seeds can provide additional capture of the green light that filters through siliques. Together, these results demonstrate that even the low level of light reaching seeds plays a substantial role in activating light-regulated enzymes, increasing fatty acid synthesis, and potentially powering refixation of CO2.
Protection of Plasma Membrane K+ Transport by the Salt Overly Sensitive1 Na+-H+ Antiporter during Salinity Stress
Authors: Qi Zhi , Spalding Edgar P. 
Published: September 2004

Abstract
Physicochemical similarities between K+ and Na+ result in interactions between their homeostatic mechanisms. The physiological interactions between these two ions was investigated by examining aspects of K+ nutrition in the Arabidopsis salt overly sensitive (sos) mutants, and salt sensitivity in the K+ transport mutants akt1 (Arabidopsis K+ transporter) and skor (shaker-like K+ outward-rectifying channel). The K+-uptake ability (membrane permeability) of the sos mutant root cells measured electrophysiologically was normal in control conditions. Also, growth rates of these mutants in Na+-free media displayed wild-type K+ dependence. However, mild salt stress (50 mm NaCl) strongly inhibited root-cell K+ permeability and growth rate in K+-limiting conditions of sos1 but not wild-type plants. Increasing K+ availability partially rescued the sos1 growth phenotype. Therefore, it appears that in the presence of Na+, the SOS1 Na+-H+ antiporter is necessary for protecting the K+ permeability on which growth depends. The hypothesis that the elevated cytoplasmic Na+ levels predicted to result from loss of SOS1 function impaired the K+ permeability was tested by introducing 10 mm NaCl into the cytoplasm of a patch-clamped wild-type root cell. Complete loss of AKT1 K+ channel activity ensued. AKT1 is apparently a target of salt stress in sos1 plants, resulting in poor growth due to impaired K+ uptake. Complementary studies showed that akt1 seedlings were salt sensitive during early seedling development, but skor seedlings were normal. Thus, the effect of Na+ on K+ transport is probably more important at the uptake stage than at the xylem loading stage.
Age‐related decline in forest production: modelling the effects of growth limitation, neighbourhood competition and self‐thinning
Authors: BERGER UTA , HILDENBRANDT HANNO , GRIMM VOLKER 
Published: September 2004

SummaryIn growing forest stands, above‐ground net primary production peaks early in stand development and then declines. The causes for this decline are not yet well understood, but hypotheses include physiological and ecophysiological effects, as well as changes in stand structure due to local competition among neighbouring trees.The majority of existing studies address mono‐causal explanations of this decline. Here we study the combined effects of intrinsic growth limitation of individual trees, growth limitation due to neighbourhood competition, and self‐thinning.We use an individual‐based model to analyse forest wood production of a mangrove species described by a sigmoidal growth function, and two hypothetical species with exponential or linear growth. The model reproduces a decline for all species investigated, even when individual growth rates did not become limited.We conclude that individual, sigmoidal growth curves are sufficient but not necessary to explain the production decline in natural forests where neighbourhood competition is appreciably active.We show that the causes for production decline change during forest development. Whereas growth reduction through neighbourhood competition is the main process at the beginning, imbalanced wood loss dominates the later stage of the decline.
Occurrence of non‐mycorrhizal plant species in south Swedish rocky habitats is related to exchangeable soil phosphate
Authors: OLSSON PÅL AXEL , TYLER GERMUND 
Published: September 2004

Summary

Plant species that do not typically form mycorrhiza are most likely to be successful under conditions where mycorrhizal fungi are not important for plant coexistence or where the costs of symbiosis outweigh the benefits. The relative occurrence of non‐mycorrhizal species was investigated in relationship to exchangeable soil P in herbaceous vegetation, where arbuscular mycorrhizal (AM) associations are generally common. We investigated a total of 439 sites in rocky habitats with sparse vegetation and 110 meadows with dense vegetation.
In both rocky habitats and meadows, soil pH was inversely related to exchangeable P. In rocky habitats plant species richness increased greatly between pH 3 and 5 and was also inversely related to P.
Plant communities in rocky habitats contained a relatively larger proportion of non‐mycorrhizal species than those in meadows. More non‐mycorrhizal species occurred at high soil P in the rocky habitats, but no such relation was found in meadows.
Non‐mycorrhizal species in rocky habitats were most common at low soil pH (high P availability). Plant species that thrived at extreme soil pH were often non‐mycorrhizal.
The occurrence of fewer non‐mycorrhizal plants in meadows than in rocky habitats supports the hypothesis that AM associations are more important in ecosystems with intense competition among plants. In rocky habitats, where abiotic stress may restrict photosynthesis more than nutrient limitation does, it is adaptive for plant species to utilize strategies other than mycorrhiza, particularly at low pH sites where P availability is likely to be adequate.
Height growth response of tree line black spruce to recent climate warming across the forest‐tundra of eastern Canada
Authors: GAMACHE ISABELLE , PAYETTE SERGE 
Published: September 2004

Summary

The northward expansion of the boreal forest vegetation zone is generally predicted under a warmer doubled CO2, but the delay associated with vegetation development processes often has been overlooked. In the subarctic forest‐tundra of northern Québec, reforestation of tundra uplands appears currently limited by the poor reproductive capacity of shrubby black spruce (Picea mariana), and the development of erect stems through accelerated height growth should be the first registered response to 20th century climate warming. The subarctic forest‐tundra is characterized by small‐ and large‐scale heterogeneity in topography, vegetation structure and climate. This spatial heterogeneity, added to the complexity of tree growth–climate relationships, can cause various growth responses of subarctic tree line black spruce to 20th century climate change.
Twenty spruce populations at subarctic tree lines and seven isolated clones at the species limit were sampled along a > 300‐km latitudinal transect from the southern forest‐tundra to the shrub tundra. Height growth patterns of black spruce at tree line and above tree line were examined (i) over their life span, using dendrochronological dating of stem cross‐sections, and (ii) for the recent decades, using leader shoot elongation measurements. Indexed elongation chronologies were compared with regional climate data.
Height growth of tree line trees generally decreased with increasing latitude. However, tree line trees in the northern forest‐tundra have experienced an acceleration of height growth since the 1970s, with their growth comparable to that of trees in the southern forest‐tundra. Height growth response of spruce trees appeared increasingly delayed from the northern forest‐tundra to the species limit. Above the subarctic tree line, wind‐exposed conditions obscured the decrease in height growth with latitude observed for tree line trees.
Leader shoot elongation of spruce trees established on tundra hilltops appeared more controlled by summer heat sums than those at tree line all over the forest‐tundra, except at the arctic tree line. Winter precipitation also was linked to leader shoot elongation in some forest‐tundra sites. The increasing snow cover associated with recent warming appeared to have reduced the shoot elongation of spruce at forest margins showing the steepest slopes, hence subjected to snow overloading.
In the northern forest‐tundra sites, the recent increase in height growth and positive trend in leader shoot elongation, consistent with a 1990s’ increase in heat sums, point to the development of spruce krummholz into erect growth forms. In the southern forest‐tundra, reforestation of tundra hilltops and northward expansion of the boreal forest predicted under doubled CO2 conditions could be delayed, as suggested by suppressed height growth of spruce above tree line.