bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding Unexpected Patterns in Microarray Data
Authors: Perelman Susana , Mazzella María Agustina , Muschietti Jorge , Zhu Tong , Casal Jorge J. 
Published: December 2003

Abstract
We describe the performance of a protocol based on the sequential application of unsupervised and supervised methods to analyze microarray samples defined by a combination of factors. Correspondence analysis is used to visualize the emerging patterns of three set of novel or previously published data: photoreceptor mutants of Arabidopsis grown under different light/dark conditions, Arabidopsis exposed to different types of biotic and abiotic stress, and human acute leukemia. We find, for instance, that light has a dramatic effect on plants despite the absence of the four major photoreceptors, that bacterial-, fungal-, and viral-induced responses converge at later stages of attack, and that sample preparation procedures used in different hospitals have large effects on transcriptome patterns. We use canonical discriminant analysis to identify the genes associated with these patters and hierarchical clustering to find groups of coregulated genes that are easily visualized in a second round of correspondence analysis and ordered tables. The unconventional combination of standard descriptive multivariate methods offers a previously unrecognized tool to uncover unexpected information.
Phytochrome Modulation of Blue Light-Induced Chloroplast Movements in Arabidopsis
Authors: DeBlasio Stacy L. , Mullen Jack L. , Luesse Darron R. , Hangarter Roger P. 
Published: December 2003

AbstractPhotometric analysis of chloroplast movements in various phytochrome (phy) mutants of Arabidopsis showed that phyA, B, and D are not required for chloroplast movements because blue light (BL)-dependent chloroplast migration still occurs in these mutants. However, mutants lacking phyA or phyB showed an enhanced response at fluence rates of BL above 10 μmol m-2 s-1. Overexpression of phyA or phyB resulted in an enhancement of the low-light response. Analysis of chloroplast movements within the range of BL intensities in which the transition between the low- and high-light responses occur (1.5-15 μmol m-2 s-1) revealed a transient increase in light transmittance through leaves, indicative of the high-light response, followed by a decrease in transmittance to a value below that measured before the BL treatment, indicative of the low-light response. A biphasic response was not observed for phyABD leaves exposed to the same fluence rate of BL, suggesting that phys play a role in modulating the transition between the low- and high-light chloroplast movement responses of Arabidopsis.
Effect of Manganese Toxicity on the Proteome of the Leaf Apoplast in Cowpea
Authors: Fecht-Christoffers Marion M. , Braun Hans-Peter , Lemaitre-Guillier Christelle , VanDorsselaer Alain , Horst Walter J. 
Published: December 2003

AbstractExcess manganese (Mn) supply causes formation of visible brown depositions in the cell walls of leaves of cowpea (Vigna unguiculata), which consist of oxidized Mn and oxidized phenols. Because oxidation of Mn and phenolic compounds in the leaf apoplast was proposed to be catalyzed by apoplastic peroxidases (PODs), induction of these enzymes by Mn excess was investigated. POD activity increased upon prolonged Mn treatment in the leaf tissue. Simultaneously, a significant increase in the concentration of soluble apoplastic proteins in “apoplastic washing fluid” was observed. The identity of the released proteins was systematically characterized by analysis of the apoplast proteome using two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry. Some of the identified proteins exhibit sequence identity to acidic PODs from other plants. Several other proteins show homologies to pathogenesis-related proteins, e.g. glucanase, chitinase, and thaumatin-like proteins. Because pathogenesis-related-like proteins are known to be induced by various other abiotic and biotic stresses, a specific physiological role of these proteins in response to excess Mn supply remains to be established. The specific role of apoplastic PODs in the response of plants to Mn stress is discussed.
How Do Plants Achieve Tolerance to Phosphorus Deficiency? Small Causes with Big Effects
Authors: Wissuwa Matthias 
Published: December 2003

Abstract
Genotypic differences in phosphorus (P) uptake from P-deficient soils may be due to higher root growth or higher external root efficiency (micrograms of P taken up per square centimeter of root surface area). Both factors are highly interrelated because any additional P provided by externally efficient roots will also stimulate root growth. It will be necessary to separate both factors to identify a primary mechanism to formulate hypotheses on pathways and genes causing genotypic differences in P uptake. For this purpose, a plant growth model was developed for rice (Oryza sativa) grown under highly P-deficient conditions. Model simulations showed that small changes in root growth-related parameters had big effects on P uptake. Increasing root fineness or the internal efficiency for root dry matter production (dry matter accumulated per unit P distributed to roots) by 22% was sufficient to increase P uptake by a factor of three. That same effect could be achieved by a 33% increase in external root efficiency. However, the direct effect of increasing external root efficiency accounted for little over 10% of the 3-fold increase in P uptake. The remaining 90% was due to enhanced root growth as a result of higher P uptake per unit root size. These results demonstrate that large genotypic differences in P uptake from a P-deficient soil can be caused by rather small changes in tolerance mechanisms. Such changes will be particularly difficult to detect for external efficiency because they are likely overshadowed by secondary root growth effects.
Identification of AtNDI1, an Internal Non-Phosphorylating NAD(P)H Dehydrogenase in Arabidopsis Mitochondria
Authors: Moore Catherine S. , Cook-Johnson Rebecca J. , Rudhe Charlotta , Whelan James , Day David A. , Wiskich Joseph T. , Soole Kathleen L. 
Published: December 2003

Abstract
Plant mitochondria contain non-phosphorylating NAD(P)H dehydrogenases (DHs) that are not found in animal mitochondria. The physiological function, substrate specificity, and location of enzymes within this family have yet to be conclusively determined. We have linked genome sequence information to protein and biochemical data to identify that At1g07180 (SwissProt Q8GWA1) from the Arabidopsis Genome Initiative database encodes AtNDI1, an internal NAD(P)H DH in Arabidopsis mitochondria. Three lines of evidence are presented: (a) The predicted protein sequence of AtNDI1 has high homology with other designated NAD(P)H DHs from microorganisms, (b) the capacity for matrix NAD(P)H oxidation via the rotenone-insensitive pathway is significantly reduced in the Atndi1 mutant plant line, and (c) the in vitro translation product of AtNDI1 is imported into isolated mitochondria and located on the inside of the inner membrane.
A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during Seedling Development
Authors: Jiao Yuling , Yang Hongjuan , Ma Ligeng , Sun Ning , Yu Haiyuan , Liu Tie , Gao Ying , Gu Hongya , Chen Zhangliang , Wada Masamitsu , Gerstein Mark , Zhao Hongyu , Qu Li-Jia , Deng Xing Wang 
Published: December 2003

AbstractA microarray based on PCR amplicons of 1,864 confirmed and predicted Arabidopsis transcription factor genes was produced and used to profile the global expression pattern in seedlings, specifically their light regulation. We detected expression of 1,371 and 1,241 genes in white-light- and dark-grown 6-d-old seedlings, respectively. Together they account for 84% of the transcription factor genes examined. This array was further used to study the kinetics of transcription factor gene expression change of dark-grown seedlings in response to blue light and the role of specific photoreceptors in this blue-light regulation. The expression of about 20% of those transcription factor genes are responsive to blue-light exposure, with 249 and 115 genes up or down-regulated, respectively. A large portion of blue-light-responsive transcription factor genes exhibited very rapid expression changes in response to blue light, earlier than the bulk of blue-light-regulated genes. This result suggests the involvement of transcription cascades in blue-light control of genome expression. Comparative analysis of the expression profiles of wild type and various photoreceptor mutants demonstrated that during early seedling development cryptochromes are the major photoreceptors for blue-light control of transcription factor gene expression, whereas phytochrome A and phototropins play rather limited roles.
Distinct Ultraviolet-Signaling Pathways in Bean Leaves. DNA Damage Is Associated with β-1,3-Glucanase Gene Induction, But Not with Flavonoid Formation
Authors: Kucera Birgit , Leubner-Metzger Gerhard , Wellmann Eckard 
Published: December 2003

AbstractThe enzyme β-1,3-glucanase (βGlu) was found to be strongly induced by ultraviolet (UV-B; 280-320 nm) radiation in primary leaves of French bean (Phaseolus vulgaris). This was demonstrated on the level of gene transcription, protein synthesis, and enzyme activity and was due to the expression of bean class I βGlu (βGlu I). In contrast to other proteins of the family of pathogenesis-related proteins, the induction of βGlu I by UV correlated with the formation of photoreversible DNA damage, i.e. pyrimidine dimer formation. In conditions that allowed photorepair of this damage, βGlu I induction was blocked. Therefore, UV-induced DNA damage seems to constitute a primary signal in the pathway leading to the induction of the βGlu I gene(s). The induction was a local response because in partly irradiated leaves βGlu I was selectively found in leaf parts exposed to UV. Although short wavelength UV (λ &lt; 295 nm) was most efficient in βGlu I induction, longer wavelength UV (λ &gt; 295 nm) as present in natural radiation was still effective. In contrast to UV induction of βGlu I, the induction of flavonoids in bean leaves was optimally triggered by much more moderate fluences from the UV wavelength range no longer effective in βGlu I induction. UV induction of the flavonoid pathway shows no correlation with DNA damage and thus should be mediated via a different signal transduction pathway.
The Cape Verde Islands Allele of Cryptochrome 2 Enhances Cotyledon Unfolding in the Absence of Blue Light in Arabidopsis
Authors: Botto Javier F. , Alonso-Blanco Carlos , Garzarón Ignacio , Sánchez Rodolfo A. , Casal Jorge J. 
Published: December 2003

AbstractWe analyzed the natural genetic variation between Landsburg erecta (Ler) and Cape Verde Islands (Cvi) accessions by studying 105 recombinant inbred lines to search for players in the regulation of sensitivity to light signals perceived by phytochromes in etiolated seedlings of Arabidopsis. In seedlings grown under hourly pulses of far-red (FR) light, we identified three quantitative trait loci (QTLs; VLF3, VLF4, and VLF5) for hypocotyl growth inhibition and three different QTLs (VLF6, VLF7, and VLF1) for cotyledon unfolding. This indicates that different physiological outputs have selective regulation of sensitivity during de-etiolation. Ler alleles, compared with Cvi alleles, of VLF3, VLF4, VLF5, VLF7, and VLF1 enhanced, whereas the Ler allele of VLF6 reduced, the response to pulses of FR. We confirmed and narrowed down the position of some QTLs by using near-isogenic lines. VLF6 mapped close to the CRY2 (cryptochrome 2) gene. Transgenic Ler seedlings expressing the Cvi allele of CRY2 showed enhanced cotyledon unfolding under hourly pulses of FR compared with the wild type or transgenics expressing the CRY2-Ler allele. This response required phytochrome A. The cry1 cry2 double mutant lacking both cryptochromes showed reduced cotyledon unfolding under FR pulses. Because the CRY2-Cvi is a gain-of-function allele compared with CRY2-Ler, cryptochrome activity correlates positively with cotyledon unfolding under FR pulses. We conclude that the blue light photoreceptor cryptochrome 2 can modulate seedling photomorphogenesis in the absence of blue light. In addition to the nuclear loci, we identified cytoplasmic effects on seedling de-etiolation.
Increased Phytochrome B Alleviates Density Effects on Tuber Yield of Field Potato Crops
Authors: Boccalandro Hernán E. , Ploschuk Edmundo L. , Yanovsky Marcelo J. , Sánchez Rodolfo A. , Gatz Christiane , Casal Jorge J. 
Published: December 2003

AbstractThe possibility that reduced photomorphogenic responses could increase field crop yield has been suggested often, but experimental support is still lacking. Here, we report that ectopic expression of the Arabidopsis PHYB (phytochrome B) gene, a photoreceptor involved in detecting red to far-red light ratio associated with plant density, can increase tuber yield in field-grown transgenic potato (Solanum tuberosum) crops. Surprisingly, this effect was larger at very high densities, despite the intense reduction in the red to far-red light ratios and the concomitant narrowed differences in active phytochrome B levels between wild type and transgenics at these densities. Increased PHYB expression not only altered the ability of plants to respond to light signals, but they also modified the light environment itself. This combination resulted in larger effects of enhanced PHYB expression on tuber number and crop photosynthesis at high planting densities. The PHYB transgenics showed higher maximum photosynthesis in leaves of all strata of the canopy, and this effect was largely due to increased leaf stomatal conductance. We propose that enhanced PHYB expression could be used in breeding programs to shift optimum planting densities to higher levels.
Blue Light and Phytochrome-Mediated Stomatal Opening in the npq1 and phot1 phot2 Mutants of Arabidopsis
Authors: Talbott Lawrence D. , Shmayevich Irene J. , Chung Yooshun , Hammad Jamila W. , Zeiger Eduardo 
Published: December 2003

Abstract
Recent studies have shown that blue light-specific stomatal opening is reversed by green light and that far-red light can be used to probe phytochrome-dependent stomatal movements. Here, blue-green reversibility and far-red light were used to probe the stomatal responses of the npq1 mutant and the phot1 phot2 double mutant of Arabidopsis. In plants grown at 50 μmol m-2 s-1, red light (photosynthetic)-mediated opening in isolated stomata from wild type (WT) and both mutants saturated at 100 μmol m-2 s-1. Higher fluence rates caused stomatal closing, most likely due to photo-inhibition. Blue light-specific opening, probed by adding blue light (10 μmol m-2 s-1) to a 100 μmol m-2 s-1 red background, was found in WT, but not in npq1 or phot1 phot2 double mutant stomata. Under 50 μmol m-2 s-1 red light, 10 μmol m-2 s-1 blue light opened stomata in both WT and npq1 mutant stomata but not in the phot1 phot2 double mutant. In npq1, blue light-stimulated opening was reversed by far-red but not green light, indicating that npq1 has a phytochrome-mediated response and lacks a blue light-specific response. Stomata of the phot1 phot2 double mutant opened in response to 20 to 50 μmol m-2 s-1 blue light. This opening was green light reversible and far-red light insensitive, indicating that stomata of the phot1 phot2 double mutant have a detectable blue light-specific response.
Blue-Light- and Phosphorylation-Dependent Binding of a 14-3-3 Protein to Phototropins in Stomatal Guard Cells of Broad Bean
Authors: Kinoshita Toshinori , Emi Takashi , Tominaga Misumi , Sakamoto Koji , Shigenaga Ayako , Doi Michio , Shimazaki Ken-ichiro 
Published: December 2003

Abstract
Phototropins are blue-light (BL) receptor serine (Ser)/threonine kinases, and contain two light, oxygen, and voltage (LOV) domains, and are members of the PAS domain superfamily. They mediate phototropism, chloroplast movement, leaf expansion, and stomatal opening of higher plants in response to BL. In stomatal guard cells, genetic analysis has revealed that phototropins mediate activation of the plasma membrane H+-ATPase by phosphorylation and drive stomatal opening. However, biochemical evidence for the involvement of phototropins in the BL response of stomata is lacking. Using guard cell protoplasts, we showed that broad bean (Vicia faba) phototropins (Vfphots) were phosphorylated by BL, and that this phosphorylation of Vfphots reached to the maximum level earlier than that of the H+-ATPase. Phosphorylation of both Vfphots and H+-ATPase showed similar sensitivity to BL and were similarly suppressed by protein kinase and flavoprotein inhibitors. We found that a 14-3-3 protein was bound to Vfphots upon phosphorylation, and this binding occurred earlier than the H+-ATPase phosphorylation. Vfphots (Vfphot1a and Vfphot1b) were expressed in Escherichia coli, and phosphorylation sites were determined to be Ser-358 for Vfphot1a and Ser-344 for Vfphot1b, which are localized between LOV1 and LOV2. We conclude that Vfphots act as BL receptors in guard cells and that phosphorylation of a Ser residue between LOV1 and LOV2 and subsequent 14-3-3 protein binding are likely to be key steps of BL response in stomata. The binding of a 14-3-3 protein to Vfphot was found in etiolated seedlings and leaves in response to BL, suggesting that this event was common to phototropin-mediated responses.
Light Control of Nuclear Gene mRNA Abundance and Translation in Tobacco
Authors: Tang Li , Bhat Sumana , Petracek Marie E. 
Published: December 2003

Abstract
Photosynthetic signals modulate expression of nuclear genes at the levels of mRNA transcription, mRNA stability, and translation. In transgenic tobacco (Nicotiana tabacum), the pea (Pisum sativum) Ferredoxin 1 (Fed-1) mRNA dissociates from polyribosomes and becomes destabilized when photosynthesis is inhibited by photosynthetic electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea. We used polymerase chain reaction suppressive-subtractive hybridization to identify similarly regulated endogenous tobacco genes. This screen identified 14 nuclear-encoded tobacco mRNAs whose light-induced increase in abundance is suppressed in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Sequence analysis of the cognate cDNAs revealed that nine of the mRNAs encode putative chloroplast-targeted proteins. We asked whether the abundance of these mRNAs was regulated transcriptionally or posttranscriptionally. Of the five mRNAs with sufficient abundance to detect using nuclear run-on assays, we observed transcriptional regulation of α-tubulin, thiazole biosynthetic enzyme, and pSKA10 (an unknown gene). Photosystem A subunit L and, to a lesser extent, α-tubulin and pSKA10 mRNAs, may also be stabilized in the light. In contrast, Rubisco small subunit mRNA abundance appears to be transcriptionally up-regulated but posttranscriptionally down-regulated in the light. To determine whether, like Fed-1 mRNA, the mRNAs identified in this screen were translationally responsive to light, we characterized the polyribosome association of these mRNAs in the light and after a 15-min dark treatment. A subset of the mRNAs showed dramatic dark-induced polyribosome dissociation, similar to Fed-1 mRNA, and all of the mRNAs showed at least slight polyribosome dissociation. Thus, both posttranscriptional and translational regulation appear to be important mechanisms regulating the expression of many nuclear-encoded mRNAs encoding proteins involved in photosynthesis.
Photomorphogenic Responses in Maize Seedling Development
Authors: Markelz Nicole H. , Costich Denise E. , Brutnell Thomas P. 
Published: December 2003

AbstractAs an emerging maize (Zea mays) seedling senses light, there is a decrease in the rate of mesocotyl elongation, an induction of root growth, and an expansion of leaves. In leaf tissues, mesophyll and bundle sheath cell fate is determined, and the proplastids of each differentiate into the dimorphic chloroplasts typical of each cell type. Although it has been inferred from recent studies in several model plant species that multiple photoreceptor systems mediate this process, surprisingly little is known of light signal transduction in maize. Here, we examine two photomorphogenic responses in maize: inhibition of mesocotyl elongation and C4 photosynthetic differentiation. Through an extensive survey of white, red, far-red, and blue light responses among a diverse collection of germplasm, including a phytochrome-deficient mutant elm1, we show that light response is a highly variable trait in maize. Although all inbreds examined appear to have a functional phytochrome signal transduction pathway, several lines showed reduced sensitivity to blue light. A significant correlation was observed between light response and subpopulation, suggesting that light responsiveness may be a target of artificial selection. An examination of C4 gene expression patterns under various light regimes in the standard W22 inbred and elm1 indicate that cell-specific patterns of C4 gene expression are maintained in fully differentiated tissues independent of light quality. To our knowledge, these findings represent the first comprehensive survey of light response in maize and are discussed in relation to maize breeding strategies.
Inorganic Carbon Limitation Induces Transcripts Encoding Components of the CO2-Concentrating Mechanism in Synechococcus sp. PCC7942 through a Redox-Independent Pathway
Authors: Woodger Fiona J. , Badger Murray R. , Price G. Dean 
Published: December 2003

Abstract
The cyanobacterial CO2-concentrating mechanism (CCM) allows photosynthesis to proceed in CO2-limited aquatic environments, and its activity is modulated in response to inorganic carbon (Ci) availability. Real-time reverse transcriptase-PCR analysis was used to examine the transcriptional regulation of more than 30 CCM-related genes in Synechococcus sp. strain PCC7942 with an emphasis on genes encoding high-affinity Ci transporters and carboxysome-associated proteins. This approach was also used to test hypotheses about sensing of Ci limitation in cyanobacteria. The transcriptional response of Synechococcus sp. to severe Ci limitation occurs rapidly, being maximal within 30 to 60 min, and three distinct temporal responses were detected: (a) a rapid, transient induction for genes encoding carboxysome-associated proteins (ccmKLMNO, rbcLS, and icfA) and the transcriptional regulator, cmpR; (b) a slow sustained induction of psbAII; and (c) a rapid sustained induction of genes encoding the inducible Ci transporters cmpABCD, sbtA, and ndhF3-D3-chpY. The Ci-responsive transcripts investigated had half-lives of 15 min or less and were equally stable at high and low Ci. Through the use of a range of physiological conditions (light and Ci levels) and inhibitors such as 3-(3,4-dichlorophenyl)-1,1dimethylurea, glycolaldehyde, dithiothreitol, and ethoxyzolamide, we found that no strict correlation exists between expression of genes known to be induced under redox stress, such as psbAII, and the expression of the Ci-responsive CCM genes. We argue that redox stress, such as that which occurs under high-light stress, is unlikely to be a primary signal for sensing of Ci limitation in cyanobacteria. We discuss the data in relation to current theories of CO2 sensing in cyanobacteria.