| evolutionary divergence of monocot and dicot methyl-cpg-binding domain proteins. | the covalent modification of eukaryotic dna by methylation of the 5' carbon of cytosine residues is frequently associated with transcriptional silencing. in mammals, a potential mechanism for transducing dna methylation patterns into altered transcription levels occurs via binding of methyl-cpg-binding domain (mbd) proteins. mammalian mbd-containing proteins bind specifically to methylated dna and recruit chromatin-modifying complexes containing histone deacetylase activities. sequence similarit ... | 2005 | 15888682 |
| genome cluster database. a sequence family analysis platform for arabidopsis and rice. | the genome-wide protein sequences from arabidopsis (arabidopsis thaliana) and rice (oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. the two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. functional names for the identified families were assigned with an efficient computational approach that uses the description of the most co ... | 2005 | 15888677 |
| the institute for genomic research osa1 rice genome annotation database. | we have developed a rice (oryza sativa) genome annotation database (osa1) that provides structural and functional annotation for this emerging model species. using the sequence of o. sativa subsp. japonica cv nipponbare from the international rice genome sequencing project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. genes were iden ... | 2005 | 15888674 |
| comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. | a detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species oryza sativa, zea mays, triticum aestivum and arabidopsis thaliana. the average gc content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. the results of nc-plots and neutrality plots suggested that nuc ... | 2005 | 15876584 |
| cloning and characterization of micrornas from rice. | micrornas (mirnas) are a growing family of small noncoding rnas that downregulate gene expression in a sequence-specific manner. the identification of the entire set of mirnas from a model organism is a critical step toward understanding mirna-guided gene regulation. rice (oryza sativa) and arabidopsis thaliana, two plant model species with fully sequenced genomes, are representatives of monocotyledonous and dicotyledonous flowering plants, respectively. thus far, experimental identification of ... | 2005 | 15805478 |
| conservation of arabidopsis flowering genes in model legumes. | the model plants arabidopsis (arabidopsis thaliana) and rice (oryza sativa) have provided a wealth of information about genes and genetic pathways controlling the flowering process, but little is known about the corresponding pathways in legumes. the garden pea (pisum sativum) has been used for several decades as a model system for physiological genetics of flowering, but the lack of molecular information about pea flowering genes has prevented direct comparison with other systems. to address th ... | 2005 | 15778459 |
| circadian-associated rice pseudo response regulators (osprrs): insight into the control of flowering time. | a small family of plant proteins, designated pseudo response regulators (prrs), is crucial for a better understanding of the molecular link between circadian rhythm and photoperiodic control of flowering time in the dicotyledonous model plant arabidopsis thaliana. recently, we showed that the monocotyledonous model plant oryza sativa also has homologous members of the osprr family (oryza sativa prr). in the previous experiments with rice, we mainly characterized a japonica variety (nipponbare). ... | 2005 | 15725670 |
| computational identification of novel family members of microrna genes in arabidopsis thaliana and oryza sativa. | micrornas (mirnas) are a class of endogenous small rnas that play important regulatory roles in both animals and plants. mirna genes have been intensively studied in animals, but not in plants. in this study, we adopted a homology search approach to identify homologs of previously validated plant mirnas in arabidopsis thaliana and oryza sativa. we identified 20 potential mirna genes in arabidopsis and 40 in o. sativa, providing a relatively complete enumeration of family members for these mirnas ... | 2005 | 15685364 |
| exploring the plant transcriptome through phylogenetic profiling. | publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. by contrast, an enormous amount of expressed sequence tags (ests) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. integrating protein and est sequences in comparative and evolutionary analyses is not straightforward because of the heteroge ... | 2005 | 15644465 |
| [molecular cloning and sequence analyzing of cytoplasmic ribosomal protein gene osrps7 from rice (oryza sativa)]. | using the cdna of rye cytoplasmic ribosomal protein scrps7 as a query probe, a highly homologous rice genomic contig was obtained from huada rice genome database. the full-length cdna sequence of rice cytoplasmic ribosomal protein s7 was assembled by informatics based on the contig. furthermore, with the two primers designed according to this assembled cdna, the full-length cdna of rice ribosomal protein was cloned by rt-pcr and named as osrps7. the cdna was 919bp in length and contained a compl ... | 2004 | 15639984 |
| molecular analysis of the crinkly4 gene family in arabidopsis thaliana. | the maize (zea mays l.) crinkly4 (cr4) gene encodes a serine/threonine receptor-like kinase that controls an array of developmental processes in the plant and endosperm. the arabidopsis thaliana (l.) heynh. genome encodes an ortholog of cr4, acr4, and four crinkly4-related (crr) proteins: atcrr1, atcrr2, atcrr3 and atcrk1. the available genome sequence of rice (oryza sativa l.) encodes a cr4 ortholog, oscr4, and four crr proteins: oscrr1, oscrr2, oscrr3 and oscrr4, not necessarily orthologous to ... | 2005 | 15549374 |
| genomic basis for cell-wall diversity in plants. a comparative approach to gene families in rice and arabidopsis. | monocotyledons and dicotyledons are distinct, not only in their body plans and developmental patterns, but also in the structural features of their cell walls. the recent completion of the rice (oryza sativa) genomic sequence and publication of the sequence data, together with the completed database of the arabidopsis thaliana genome, provide the first opportunity to compare the full complement of cell-wall-related genes from the two distinct classes of flowering plants. we made this comparison ... | 2004 | 15509833 |
| the gene floral organ number1 regulates floral meristem size in rice and encodes a leucine-rich repeat receptor kinase orthologous to arabidopsis clavata1. | the regulation of floral organ number is closely associated with floral meristem size. mutations in the gene floral organ number1 (fon1) cause enlargement of the floral meristem in oryza sativa (rice), resulting in an increase in the number of all floral organs. ectopic floral organs develop in the whorl of each organ and/or in the additional whorls that form. inner floral organs are more severely affected than outer floral organs. many carpel primordia develop indeterminately, and undifferentia ... | 2004 | 15509765 |
| photoperiod-regulated expression of the ppcol1 gene encoding a homolog of co/col proteins in the moss physcomitrella patens. | the constans (co) protein is a critical regulator of the photoperiodic control of flowering in arabidopsis thaliana and oryza sativa. we isolated a cdna ppcol1 encoding a homolog of the co/co-like (col) family proteins from a cryptogam physcomitrella patens. the predicted ppcol1 protein has n-terminal zinc finger and c-terminal cct domains, which are conserved in the angiosperm co/col proteins. structurally, ppcol1 is the most closely related to the group ia or ic proteins, which include atco an ... | 2004 | 15504355 |
| calculation of binding length of base-specific dna dyes by comparison of sequence and flow cytometric data. application to oryza sativa and arabidopsis thaliana. | from biochemical experiments it has been found that at- and gc-specific dyes need a certain number of consecutive bases of the same type for binding one dye molecule. from known base sequences the amount of bases included in dye binding can be calculated and compared with experimental data from flow cytometry. oryza sativa and arabidopsis thaliana are the first higher plants which are nearly completely (>90%) sequenced. from the published sequences the theoretical fluorescence intensity of base- ... | 2005 | 15498596 |
| inventory and comparative analysis of rice and arabidopsis atp-binding cassette (abc) systems. | atp-binding cassette (abc) proteins constitute a large superfamily found in all kingdoms of living organisms. the recent completion of two draft sequences of the rice (oryza sativa) genome allowed us to analyze and classify its abc proteins and to compare to those in arabidopsis thaliana. we identified a similar number of abc proteins in rice and arabidopsis (121 versus 120), despite the rice genome being more than three times the size of arabidopsis. both arabidopsis and rice have representativ ... | 2004 | 15381434 |
| simple statistical models predict c-to-u edited sites in plant mitochondrial rna. | rna editing is the process whereby an rna sequence is modified from the sequence of the corresponding dna template. in the mitochondria of land plants, some cytidines are converted to uridines before translation. despite substantial study, the molecular biological mechanism by which c-to-u rna editing proceeds remains relatively obscure, although several experimental studies have implicated a role for cis-recognition. a highly non-random distribution of nucleotides is observed in the immediate v ... | 2004 | 15373947 |
| prediction and identification of arabidopsis thaliana micrornas and their mrna targets. | a class of eukaryotic non-coding rnas termed micrornas (mirnas) interact with target mrnas by sequence complementarity to regulate their expression. the low abundance of some mirnas and their time- and tissue-specific expression patterns make experimental mirna identification difficult. we present here a computational method for genome-wide prediction of arabidopsis thaliana micrornas and their target mrnas. this method uses characteristic features of known plant mirnas as criteria to search for ... | 2004 | 15345049 |
| pectin methylesterases: sequence-structural features and phylogenetic relationships. | pectin methylesterases (pmes) are enzymes produced by bacteria, fungi and higher plants. they belong to the carbohydrate esterase family ce-8. this study deals with comparison of 127 amino acid sequences of this family containing the five characteristic sequence segments: 44_gxyxe, 113_qaval, 135_qdtl, 157_dfifg, 223_lgrpw (daucus carota numbering). six strictly conserved residues (gly44, gly154, asp157, gly161, arg225 and trp227) and six conservative ones (ile39, ser86, ser137, ile152, ile159 a ... | 2004 | 15337457 |
| detection of 91 potential conserved plant micrornas in arabidopsis thaliana and oryza sativa identifies important target genes. | micrornas (mirnas) are an extensive class of tiny rna molecules that regulate the expression of target genes by means of complementary base pair interactions. although the first mirnas were discovered in caenorhabditis elegans, >300 mirnas were recently documented in animals and plants, both by cloning methods and computational predictions. we present a genome-wide computational approach to detect mirna genes in the arabidopsis thaliana genome. our method is based on the conservation of short se ... | 2004 | 15272084 |
| enhancer detection and gene trapping as tools for functional genomics in plants. | although more than 25,000 genes of arabidopsis thaliana have been sequenced and mapped, adequate expression or functional information is available for less than 15% of them. in the case of oryza sativa (rice), about half of more than 55,000 predicted genes have been assigned to a vague functional category on the basis of their sequence, but fewer than 100 have been ascribed a precise, verified function after the identification of a mutant phenotype caused by the molecular disruption of the corre ... | 2004 | 15269439 |
| plant two-component systems: principles, functions, complexity and cross talk. | two-component systems have emerged as important sensing/response mechanisms in higher plants. they are composed of hybrid histidine kinases, histidine-containing phosphotransfer domain proteins and response regulators that are biochemically linked by his-to-asp phosphorelay. in plants two-component systems play a major role in cytokinin perception and signalling and contribute to ethylene signal transduction and osmosensing. furthermore, developmental processes like megagametogenesis in arabidop ... | 2004 | 15232695 |
| computational identification of plant micrornas and their targets, including a stress-induced mirna. | micrornas (mirnas) are approximately 21-nucleotide rnas, some of which have been shown to play important gene-regulatory roles during plant development. we developed comparative genomic approaches to systematically identify both mirnas and their targets that are conserved in arabidopsis thaliana and rice (oryza sativa). twenty-three mirna candidates, representing seven newly identified gene families, were experimentally validated in arabidopsis, bringing the total number of reported mirna genes ... | 2004 | 15200956 |
| cloning and sequence analysis of a low temperature-induced gene from trifoliate orange with unusual pre-mrna processing. | exposure of cold-hardy rubidoux trifoliate orange [poncirus trifoliata (l) raf.] plants to temperatures from 28 degrees c to -5 degrees c enabled us to isolate and characterize a novel citrus low-temperature gene (clt) with two transcripts, called clta and cltb, from leaves and stems. clta was produced when plants were subjected to low temperatures (starting at 10 degrees c), while cltb was constitutively expressed. both clta and cltb have the same open reading frame (orf) of 165 nucleotides and ... | 2004 | 15138696 |
| comparative analysis of the receptor-like kinase family in arabidopsis and rice. | receptor-like kinases (rlks) belong to the large rlk/pelle gene family, and it is known that the arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. surprisingly, we found that rice (oryza sativa) has nearly twice as many rlk/pelle members as arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. from the inferred phylogeny of all arabidopsis and rice rlk/pelle members, we ... | 2004 | 15105442 |
| cloning of a putative monogalactosyldiacylglycerol synthase gene from rice (oryza sativa l.) plants and its expression in response to submergence and other stresses. | suppression subtractive hybridization was used to construct a subtractive cdna library from plants of non-submerged and 7-day-submerged rice (oryza sativa l., fr13a, a submergence-tolerant cultivar). one clone of the subtractive cdna library, s23, was expressed abundantly during submergence. the full length of s23 was amplified using 5'- and 3'-rapid amplification of cdna ends, and found to consist of 1,671 bp with an open reading frame of 1,077 bp (181-1257) encoding 358 amino acids. its deduce ... | 2004 | 15088147 |
| comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity. | the importance of angiosperms to sustaining humanity by providing a wide range of 'ecosystem services' warrants increased exploration of their genomic diversity. the nearly completed sequences for two species representing the major angiosperm subclasses, specifically the dicot arabidopsis thaliana and the monocot oryza sativa, provide a foundation for comparative analysis across the angiosperms. the angiosperms also exemplify some challenges to be faced as genomics makes new inroads into describ ... | 2004 | 15081049 |
| ehd1, a b-type response regulator in rice, confers short-day promotion of flowering and controls ft-like gene expression independently of hd1. | two evolutionarily distant plant species, rice (oryza sativa l.), a short-day (sd) plant, and arabidopsis thaliana, a long-day plant, share a conserved genetic network controlling photoperiodic flowering. the orthologous floral regulators-rice heading date 1 (hd1) and arabidopsis constans (co)-integrate circadian clock and external light signals into mrna expression of the flowering locus t (ft) group floral inducer. here, we report that the rice early heading date 1 (ehd1) gene, which confers s ... | 2004 | 15078816 |
| comprehensive analysis of nac family genes in oryza sativa and arabidopsis thaliana. | the nac domain was originally characterized from consensus sequences from petunia nam and from arabidopsis ataf1, ataf2, and cuc2. genes containing the nac domain (nac family genes) are plant-specific transcriptional regulators and are expressed in various developmental stages and tissues. we performed a comprehensive analysis of nac family genes in oryza sativa (a monocot) and arabidopsis thaliana (a dicot). we found 75 predicted nac proteins in full-length cdna data sets of o. sativa (28,469 c ... | 2003 | 15029955 |
| cloning of a cdna encoding an etr2-like protein (os-erl1) from deep water rice (oryza sativa l.) and increase in its mrna level by submergence, ethylene, and gibberellin treatments. | a cdna from deep water rice treated with ethylene, encoding an ethylene receptor homologous to arabidopsis thaliana etr2 and ein4, was isolated using differential display and race techniques. the cdna (2880 bp), corresponding to the os-erl1 gene (oryza sativa ethylene response 2 like 1; genbank accession number ab107219), contained an open reading frame of 2289 bp coding for 763 amino acids. the protein os-erl1 has 50% and 52% similarity to arabidopsis etr2 and ein4, respectively. the os-erl1 ge ... | 2004 | 15020633 |
| a surprising diversity and abundance of xyloglucan endotransglucosylase/hydrolases in rice. classification and expression analysis. | a search of the recently completed genomic database of rice (oryza sativa) identified a 29-member xyloglucan endotransglucosylase/hydrolase (osxth) gene family. this first report of a complete xth family from a monocotyledonous species reveals that the osxth family is comparable in size with that of the dicotyledon arabidopsis thaliana, which consists of 33 atxth genes. this is surprising because xyloglucan, the specific substrate of xths, is considerably less abundant in cell walls of monocotyl ... | 2004 | 14988479 |
| transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and arabidopsis. | we collected and completely sequenced 32,127 full-length complementary dna clones from oryza sativa l. ssp. japonica cv. "nipponbare." mapping of these clones to genomic dna revealed approximately 20,500 transcriptional units (tus) in the rice genome. for each tu, we selected 60-mers using an algorithm that took into account some dna conditions such as base composition and sequence complexity. using in situ synthesis technology, we constructed oligonucleotide arrays with these tus on glass slide ... | 2004 | 14982972 |
| overexpression of the rice osmyb4 gene increases chilling and freezing tolerance of arabidopsis thaliana plants. | the expression of the gene osmyb4, detected at low level in rice (oryza sativa) coleoptiles grown for 3 days at 29 degrees c, is strongly induced by treatments at 4 degrees c. at sublethal temperatures of 10 and 15 degrees c, its expression in rice seedlings is already evident, but this effect cannot be vicariated by other stresses or aba treatment. we demonstrate by transient expression that myb4 transactivates the pal2, scd9 sad and cor15a cold-inducible promoters. the osmyb4 function in vivo ... | 2004 | 14675437 |
| the evolutionarily conserved osprr quintet: rice pseudo-response regulators implicated in circadian rhythm. | in arabidopsis thaliana, a number of circadian-associated factors have been identified, including toc1 (timing of cab expression 1) that is believed to be a component of the central oscillator. toc1 is a member of a small family of proteins, designated as arabidopsis pseudo-response regulators (aprr1/toc1, aprr3, aprr5, aprr7, and aprr9). as demonstrated previously, these aprr1/toc1 quintet members are crucial for a better understanding of the molecular links between circadian rhythms, control o ... | 2003 | 14634161 |
| mutational bias affects protein evolution in flowering plants. | amino acid sequences from several thousand homologous gene pairs were compared for two plant genomes, oryza sativa and arabidopsis thaliana. the arabidopsis genes all have similar g+c (guanine plus cytosine) contents, whereas their homologs in rice span a wide range of g+c levels. the results show that those rice genes that display increased divergence in their nucleotide composition (specifically, increased g+c content) showed a corresponding, predictable change in the amino acid compositions o ... | 2004 | 14595101 |
| abundance of plastid dna insertions in nuclear genomes of rice and arabidopsis. | pairwise comparison of whole plastid and draft nuclear genomic sequences of arabidopsis thaliana and oryza sativa l. ssp. indica shows that rice nuclear genomic sequences contain homologs of plastid dna covering about 94 kb (83%) of plastid genome and including one or more full-length intact (without mutations resulting in premature stop codons) homologues of 26 known protein-coding (kpc) plastid genes. by contrast, only about 20 kb (16%) of chloroplast dna, including a single intact plastid-der ... | 2003 | 14558655 |
| lumenp--a neural network predictor for protein localization in the thylakoid lumen. | we report the development of lumenp, a new neural network-based predictor for the identification of proteins targeted to the thylakoid lumen of plant chloroplasts and prediction of their cleavage sites. when used together with the previously developed targetp predictor, lumenp reaches a significantly better performance than what has been recorded for previous attempts at predicting thylakoid lumen location, mostly due to a lower false positive rate. the combination of targetp and lumenp predicts ... | 2003 | 14500894 |
| genome-wide comparative phylogenetic analysis of the rice and arabidopsis dof gene families. | dof proteins are a family of plant-specific transcription factors that contain a particular class of zinc-finger dna-binding domain. members of this family have been found to play diverse roles in gene regulation of processes restricted to the plants. the completed genome sequences of rice and arabidopsis constitute a valuable resource for comparative genomic analyses, since they are representatives of the two major evolutionary lineages within the angiosperms. in this framework, the identificat ... | 2003 | 12877745 |
| genetic manipulation of glycine decarboxylation. | the glycine-serine interconversion, catalysed by glycine decarboxylase and serine hydroxymethyltransferase, is an important reaction of primary metabolism in all organisms including plants, by providing one-carbon units for many biosynthetic reactions. in plants, in addition, it is an integral part of the photorespiratory metabolic pathway and produces large amounts of photorespiratory co(2) within mitochondria. although controversial, there is significant evidence that this process, by the relo ... | 2003 | 12730263 |
| genomewide structural annotation and evolutionary analysis of the type i mads-box genes in plants. | the type i mads-box genes constitute a largely unexplored subfamily of the extensively studied mads-box gene family, well known for its role in flower development. genes of the type i mads-box subfamily possess the characteristic mads box but are distinguished from type ii mads-box genes by the absence of the keratin-like box. in this in silico study, we have structurally annotated all 47 members of the type i mads-box gene family in arabidopsis thaliana and exerted a thorough analysis of the c- ... | 2003 | 12698294 |
| identification, cdna cloning and possible roles of seed-specific rice asparaginyl endopeptidase, rep-2. | we previously showed that two major cysteine endopeptidases, rep-1 and rep-2, were present in germinated rice ( oryza sativa l.) seeds, and that rep-1 was the enzyme that digests seed storage proteins. the present study shows that rep-2 is an asparaginyl endopeptidase that acts as an activator of rep-1, and we separated it into two forms, rep-2alpha (39 kda) and rep-2beta (40 kda), using ion-exchange chromatography and gel filtration chromatography. although analysis of the amino terminals revea ... | 2003 | 12684786 |
| two genes encoding protein phosphatase 2a catalytic subunits are differentially expressed in rice. | type 2a serine/threonine protein phosphatase (pp2a) plays a variety of regulatory roles in metabolism and signal transduction. two closely related pp2a catalytic subunit (pp2ac) genes, ospp2a-1 and ospp2a-3, have been isolated from the monocot oryza sativa. both genes contain six exons and five introns which intervene at identical locations, suggesting they have descended from a recent duplication event. their encoded proteins share 97% sequence identity and are highly similar (94-96%) to a pp2a ... | 2003 | 12602862 |
| impact of genomics approaches on plant genetics and physiology. | comprehensive analysis of genetic information in higher plants is under way for several plants of biological and agronomical importance. among them, arabidopsis thaliana, a member of brassica family, and oryza sativa(rice) have been chosen as model plants most suitable for genome analysis. sequencing of the genome of a. thaliana was completed in december 2000, and rice genome sequencing is in progress. the accumulated genome sequences, together with the hundreds of thousands of ests from several ... | 2002 | 12582730 |
| putative proteins related to group ii intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants. | the arabidopsis thaliana nuclear genome sequence revealed several open reading frames encoding proteins related to group ii intron-encoded reverse transcriptase/maturases. here, we show via sequence alignments that at least four such open reading frames are conserved in the nuclear genomes of a.thaliana and oryza sativa (rice) and that they encode putative proteins belonging to two different classes (nmat-1 and nmat-2), neither of which is associated with a group ii intron rna structure. the two ... | 2003 | 12527773 |
| the genome sequence and structure of rice chromosome 1. | the rice species oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. we summarize characteristics of the chromosome structure and the biological insight gained from the sequence. the analysis of 43.3 megabases (mb) of non-overlapping sequence reveals 6,756 protein codin ... | 2002 | 12447438 |
| family business: the multidrug-resistance related protein (mrp) abc transporter genes in arabidopsis thaliana. | despite the completion of the sequencing of the entire genome of arabidopsis thaliana (l.) heynh., the exact determination of each single gene and its function remains an open question. this is especially true for multigene families. an approach that combines analysis of genomic structure, expression data and functional genomics to ascertain the role of the members of the multidrug-resistance-related protein ( mrp) gene family, a subfamily of the atp-binding cassette (abc) transporters from arab ... | 2002 | 12430019 |
| the 5' leader of plant pgic has an intron: the leader shows both the loss and maintenance of constraints compared with introns and exons in the coding region. | pgic, a complex gene with 23 coding exons and 22 intervening introns, encodes the cytosolic isozyme of phosphoglucose isomerase (ec 5.3.1.9) in higher plants. here, we report rna ligase-mediated rapid amplification of cdna ends experiments that showed that pgic in clarkia (onagraceae) and arabidopsis thaliana has an intron in the 5' leader. comparison of the embl accessions of the cdna and genomic sequences showed that this is also the case in rice (oryza sativa), suggesting that a leader intron ... | 2002 | 12200488 |
| the novel rice (oryza sativa l.) gene ossbf1 encodes a putative member of the na+/bile acid symporter family. | pcr-based differential screening was used to identify ethylene-induced genes in deep-water rice (oryza sativa l.). one of the isolated cdnas represented a novel protein, ossbf1, with high homology to mammalian na+/bile acid transporters and to sodium-dependent transporters from bacteria. one highly homologous protein and three less conserved homologues were identified in arabidopsis thaliana indicating that sbf proteins exist in monocot and dicot plant species. expression of ossbf1 in deep-water ... | 2002 | 12177140 |
| trends in comparative genetics and their potential impacts on wheat and barley research. | we review some general points about comparative mapping, the evolution of gene families and recent advances in the understanding of angiosperm phylogeny. these are considered in relation to studies of large-genome cereals, particularly barley (hordeum vulgare) and wheat (triticum aestivum), with reference to methods of gene isolation. the relative merits of direct map-based cloning in barley and wheat, utilization of the smaller genome of rice (oryza sativa) and gene homology methods that utiliz ... | 2006 | 11999846 |
| a draft sequence of the rice genome (oryza sativa l. ssp. indica). | we have produced a draft sequence of the rice genome for the most widely cultivated subspecies in china, oryza sativa l. ssp. indica, by whole-genome shotgun sequencing. the genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. functional coverage in the assembled sequences was 92.0%. about 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. although 80.6% of predicted arabidopsis thalian ... | 2002 | 11935017 |
| brassinosteroid signaling in plants. | in animals and humans, steroid hormones (shs) regulate gene transcription via the binding of nuclear receptors. in addition, rapid nongenomic effects of steroids occur and appear to be mediated by plasma-membrane receptors. plants also use steroids as signaling molecules. these brassinosteroids (brs) show structural similarity to the shs of vertebrates and insects. plant mutants defective in brassinosteroid biosynthesis or perception exhibit dwarfism and reduced fertility, and reveal the need fo ... | 2001 | 11595541 |
| growth regulation mechanisms in higher plants under microgravity conditions - changes in cell wall metabolism. | during space shuttle sts-95 mission, we cultivated seedlings of rice (oryza sativa l. cv. koshihikari and cv. tan-ginbozu) and arabidopsis (arabidopsis thaliana l. cv. columbia and cv. etr1-1) for 68.5, 91.5, and 136 hr on board, and then analyzed changes in the nature of their cell walls, growth, and morphogenesis under microgravity conditions. in space, elongation growth of both rice coleoptiles and arabidopsis hypocotyls was stimulated. also, the increase in the cell wall extensibility, espec ... | 2000 | 11543424 |
| constancy of nitrogen turnover kinetics in the plant cell: insights into the integration of subcellular n fluxes. | compartmental analysis with 13n was used to determine cytosolic nitrate (no3-) pools, and their turnover rates, in roots of intact barley (hordeum vulgare l. cv klondike) seedlings. influx, efflux, flux to the vacuole and assimilation, and flux to the xylem, varied as much as 300-fold over a wide range of external no3- conditions. by contrast, the kinetic constant kc describing cytosolic no3- turnover varied by less than 4% from a mean value of 0.0407 min(-1). accordingly, cytosolic no3- pools v ... | 2001 | 11469581 |
| distinct patterns of expression but similar biochemical properties of protein l-isoaspartyl methyltransferase in higher plants. | protein l-isoaspartyl methyltransferase is a widely distributed repair enzyme that initiates the conversion of abnormal l-isoaspartyl residues to their normal l-aspartyl forms. here we show that this activity is expressed in developing corn (zea mays) and carrot (daucus carota var. danvers half long) plants in patterns distinct from those previously seen in winter wheat (triticum aestivum cv augusta) and thale cress (arabidopsis thaliana), whereas the pattern of expression observed in rice (oryz ... | 2001 | 11161058 |
| the blast algorithms: practical application in molecular cloning, marker-assisted selection (mas) and introgression of wheat. | blast (basic local alignment search) analyses of hordeum chilense rapd markers have shown dna sequence similarities with several plant genes. biologically significant hits were scored for: plastocianin (hordeum vulgare), alpha-gliadin (triticum aestivum), grandel-6 retrotransposon (zea diploperennis), retrofit (gag/pol) copia-like, transposon-like element (oryza longistaminata), copia-like retrotransposon hopscotch polyprotein (gag/pol) (zea mays) and several retrotransposons/retroelements from ... | 2000 | 11092750 |
| molecular cloning and characterization of a cdna and a gene for subtilisin-like serine proteases from rice (oryza sativa l.) and arabidopsis thaliana. | the complete nucleotide sequences of a cdna (rsp1) that encodes a subtilisin-like serine protease (subtilase) of rice (oryza sativa l.) and a gene (asp48) for arabidopsis subtilase were analyzed. the rspi cdna and asp48 dna encoded 736- and 757-residue pre-pro-polypeptides including a signal peptide with molecular masses of 78,668 da and 79,414 da, respectively. rsp1 is the first known serine protease in rice, and asp48 is a gene for ara12 cdna. sequence comparison and phylogenetic analysis show ... | 2000 | 11055401 |
| molecular analysis of the nac gene family in rice. | genes that encode products containing a nac domain, such as no apical meristem (nam) in petunia, cup-shaped cotyledon2 (cuc2) and nap in arabidopsis thaliana, have crucial functions in plant development. we describe here molecular aspects of the osnac genes that encode proteins with nac domains in rice (oryza sativa l.). sequence analysis revealed that the nac genes in plants can be divided into several subfamilies, such as the nam, ataf, and osnac3 subfamilies. in rice, osnac1 and osnac2 are cl ... | 2000 | 10660065 |
| rire2, a novel gypsy-type retrotransposon from rice. | the 441-bp dna segment in a pcr-amplified fragment from oryza sativa cv. ir36 was found to have a sequence with features characteristic of ltrs of retroelements, which was named rire2 (rice retroelement #2) and further analyzed. cloning and sequencing analyses of the dna segments connected to ltr-like sequence showed that rire2 has a long internal region almost 10 kb long that is flanked by ltr-like sequences. this internal region carries a primer binding site (pbs) and polypurine tract (ppt) wh ... | 1999 | 10586517 |
| dna sequence comparison considering both amino acid and nucleotide insertions/deletions because of evolution and experimental error. | amino acid similarity often needs to be considered in dna sequence comparison to elucidate gene functions. we propose a smith-waterman-like algorithm which considers amino acid similarity and insertions/deletions in sequences at the dna level and at the protein level in a hybrid manner. the algorithm is applied to cdna sequences of oryza sativa and those of arabidopsis thaliana. the results are compared with the results of application of ncbi's tblastx program (which compares the sequences in th ... | 1999 | 10201112 |
| non-ltr retrotransposons (lines) as ubiquitous components of plant genomes. | during the course of work aimed at isolating a rice gene from oryza australiensis by pcr, the oligonucleotide primers used were found to generate a fragment that showed sequence homology to the endonuclease (en) region of the maize non-ltr retrotransposon (line) cin4. we carried out further pcrs using oligonucleotide primers that hybridized to these sequences, and found that they amplified several fragments, each with homology to the en regions, from oryza sativa cv. nipponbare as well as o. aus ... | 1999 | 10071212 |
| characterization of the gene for delta1-pyrroline-5-carboxylate synthetase and correlation between the expression of the gene and salt tolerance in oryza sativa l. | a cdna for delta1-pyrroline-5-carboxylate (p5c) synthetase (cosp5cs), an enzyme involved in the biosynthesis of proline, was isolated and characterized from a cdna library prepared from 14-day-old seedlings of oryza sativa cv. akibare. the deduced amino acid sequence of the p5cs protein (osp5cs) from o. sativa exhibited 74.2% and 75.5% homology to that of the p5cs from arabidopsis thaliana and vigna aconitifolia, respectively. northern blot analysis revealed that the gene for p5cs (osp5cs) was i ... | 1997 | 9106509 |
| a computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. | several recent reports indicate that mobile elements are frequently found in and flanking many wild-type plant genes. to determine the extent of this association, we performed computer-based systematic searches to identify mobile elements in the genes of two "model" plants, oryza sativa (domesticated rice) and arabidopsis thaliana. whereas 32 common sequences belonging to nine putative mobile element families were found in the noncoding regions of rice genes, none were found in arabidopsis genes ... | 1996 | 8710903 |
| two-dimensional electrophoresis of plant proteins and standardization of gel patterns. | proteins of two plants, arabidopsis thaliana and rice (oryza sativa) were subjected to two-dimensional electrophoresis analysis with two modifications: (i) comigration of external standard marker proteins with resultant horizontal and vertical stripes in the gel, and (ii) deblocking with a vapor of aqueous heptafluorobutyric acid for n-acetylserine. approximately 5000 protein spots were separated from both the five tissues of arabidopsis and the nine tissues of rice. over one hundred spots were ... | 1996 | 8964270 |
| oxidative stress and responses in arabidopsis thaliana and oryza sativa subjected to chilling and salinity stress. | | 1996 | 8736786 |
| a wound- and methyl jasmonate-inducible transcript coding for a myrosinase-associated protein with similarities to an early nodulin. | myrosinase is regarded as a defense-related enzyme in the brassicaceae and is capable of hydrolyzing glucosinolates into various compounds, some of which are toxic. several myrosinase isoenzymes exist, and some of them have been found in association with nonmyrosinase proteins. one of these associated proteins, myrosinase-associated protein (myap), was purified from seeds of brassica napus both in complexes with myrosinase and in a free form. myap is a glycosylated, 40-kd protein with at least o ... | 1996 | 8742330 |
| molecular cloning and structural analysis of cdnas that encode 3 small gtp-binding proteins from sugar beet. | isolation of homologous ras-related genes from sugar beet has never been reported. screening cdna library from beta vulgaris l. hilma resulted in the isolation of 3 ras-homologous clones. two of these genes (rab1bv and rab2bv) belong to the rab/ypt group. the deduced polypeptidic sequences from them show strong homologies to ara3 (93% with rab1bv) of arabidopsis thaliana and rgp2 (97% with rab2bv) of oryza sativa. the third gene (rho1bv) belongs to the rho family. the homology of rho1bv protein ... | 1996 | 8680960 |
| mutations associated with floral organ number in rice. | how floral organ number is specified is an interesting subject and has been intensively studied in arabidopsis thaliana. in rice (oryza sativa l.), mutations associated with floral organ number have been identified. in three mutants of rice, floral organ number 1 (fon1) and the two alleles, floral organ number 2-1 (fon2-1) and floral organ number 2-2 (fon2-2), the floral organs were increased in number centripetally. lodicules, homologous to petals, were rarely affected, and stamens were frequen ... | 1996 | 28321674 |
| molecular cloning and characterization of a cdna for the alpha subunit of a g protein from rice. | we report the isolation of a cdna for the alpha subunit of a g protein from rice (oryza sativa l. cv. nipponbare). the cdna contained an open reading frame that encoded a protein of 380 amino acid residues with a mol wt of 44,204. we designated this polypeptide rga1 (rice g protein alpha subunit 1). the amino acid sequence of rga1 was 77% and 86% identical to the sequences of alpha subunits from arabidopsis thaliana and tomato (products of gpa1 and tga1), respectively, and 42% to 69% identical t ... | 1995 | 7767602 |
| the metabolism of gibberellin a20 to gibberellin a1 by tall and dwarf mutants of oryza sativa and arabidopsis thaliana. | the purpose of this study was to demonstrate the metabolism of gibberellin a20 (ga20) to gibberellin a1 (ga1) by tall and mutant shoots of rice (oryza sativa l.) and arabidopsis thaliana (l.) heynh. the data show that the tall and dx mutant of rice and the tall and ga5 mutant of arabidopsis metabolize ga20 to ga1. the data also show that the dy mutant of rice and the ga4 mutant of arabidopsis block the metabolism of ga20 to ga1. [17-13c,3h]ga20 was fed to tall and the dwarf mutants, dx and dy, o ... | 1994 | 12232414 |
| metabolism and biological activity of gibberellin a4 in vegetative shoots of zea mays, oryza sativa, and arabidopsis thaliana. | [17-13c,3h]gibberellin a4 (ga4) was injected into the shoots of tall (w23/l317), dwarf-1 (d1), and dwarf-5 (d5) zea mays l. (maize); tall (cv nipponbare), dwarf-x (dx), and dwarf-y (dy) oryza sativa l. (rice); and tall (ecotype landsberg erecta), ga4, and ga5 arabidopsis thaliana (l.) heynh. [13c]ga4 and its metabolites were identified from the shoots by full-scan gas chromatography-mass spectrometry and kovats retention indices. ga4 was metabolized to ga1 in all nine genotypes. ga4 was also met ... | 1993 | 12231829 |
| computer analysis of phytochrome sequences from five species: implications for the mechanism of action. | the amino acid sequences of phytochrome from avena sativa, oryza sativa, curcurbita pepo, pisum sativum and arabidopsis thaliana have been analyzed with a variety of computer programs, with a view to identifying areas of the protein which contribute to the properties of this photoreceptor. a region at the c-terminus has been shown to be amphiphilic, and by analogy with surface-seeking peptides, may be responsible for interaction of phytochrome with lipid bilayers. possible targeting sequences in ... | 2009 | 2291773 |
| characterization of the rice (oryza sativa) actin gene family. | four rice (oryza sativa) genomic actin genes have been characterized. the rice actin genes show a conservation of intron number and position that is characteristic of plant actins. sequence comparisons revealed that the plant actins generally have a high degree of inter- and intraspecific sequence heterogeneity. however, one rice actin gene has a much higher degree of nucleotide sequence identity to a previously isolated actin sequence from arabidopsis thaliana than to any other plant actin gene ... | 1990 | 2103449 |
| segregation of nod-containing and nod-deficient bradyrhizobia as endosymbionts of arachis hypogaea and as endophytes of oryza sativa in intercropped fields of bengal basin, india. | bradyrhizobial invasion in dalbergoid legumes like arachis hypogaea and endophytic bacterial invasions in non-legumes like oryza sativa occur through epidermal cracks. here, we show that there is no overlap between the bradyrhizobial consortia that endosymbiotically and endophytically colonise these plants. to minimise contrast due to phylogeographic isolation, strains were collected from arachis/oryza intercropped fields and a total of 17 bradyrhizobia from arachis (wbah) and 13 from oryza (wbo ... | 2016 | 27102878 |
| association of commercial rice varieties with weedy rice accessions (oryza sativa complex) in pulau pinang's rice granary area. | weedy rice (wr) is the most significant weed in direct-seeded fields. it has morphological characteristics similar to those of cultivated rice varieties. wr is more difficult to control than other weeds. we collected wr accessions from four sites within the pulau pinang rice growing areas. thirty six different accessions were collected from each site: b, the northern site; p, the central site; a, the southern site; and n, the southwestern site. wild rice (oryza rufipogon), which grows in the sam ... | 2011 | 24575213 |
| morphological study of the relationships between weedy rice accessions (oryza sativa complex) and commercial rice varieties in pulau pinang rice granary area. | weedy rice (wr) is found in many direct-seeded rice fields. wr possesses morphological characteristics that are similar to cultivated rice varieties in the early stage of growth, making them more difficult to control than other weeds. a comparative morphological study was conducted by collecting wr accessions from four sites within the pulau pinang rice growing areas. the objective of the study was to characterise wr accessions of the pulau pinang rice granary by comparing their morphological ch ... | 2010 | 24575197 |
| resilience of rice (oryza spp.) pollen germination and tube growth to temperature stress. | resilience of rice cropping systems to potential global climate change will partly depend on the temperature tolerance of pollen germination (pg) and tube growth (ptg). pollen germination of high temperature-susceptible oryza glaberrima steud. (cv. cg14) and oryza sativa l. ssp. indica (cv. ir64) and high temperature-tolerant o. sativa ssp. aus (cv. n22), was assessed on a 5.6-45.4 °c temperature gradient system. mean maximum pg was 85% at 27 °c with 1488 μm ptg at 25 °c. the hypothesis that in ... | 2016 | 25346255 |
| phytosulfokine-alpha, a sulfated pentapeptide, stimulates the proliferation of rice cells by means of specific high- and low-affinity binding sites. | peptide growth factors were isolated from conditioned medium derived from rice (oryza sativa l.) suspension cultures and identified to be a sulfated pentapeptide [h-tyr(so3h)-ile-tyr(so3h)-thr-gln-oh] and its c-terminal-truncated tetrapeptide [h-tyr(so3h)-ile-tyr(so3h)-thr-oh]. these structures were identical to the phytosulfokines originally found in asparagus (asparagus officinalis l.) mesophyll cultures. the pentapeptide [phytosulfokine-alpha (psk-alpha)] very strongly stimulated colony forma ... | 1997 | 9371850 |
| effects of winter cover crops straws incorporation on ch4 and n2o emission from double-cropping paddy fields in southern china. | residue management in cropping systems is believed to improve soil quality. however, the effects of residue management on methane (ch4) and nitrous oxide (n2o) emissions from paddy field in southern china have not been well researched. the emissions of ch4 and n2o were investigated in double cropping rice (oryza sativa l.) systems with straw returning of different winter cover crops by using the static chamber-gas chromatography technique. a randomized block experiment with three replications wa ... | 2014 | 25271923 |
| effects of winter cover crops residue returning on soil enzyme activities and soil microbial community in double-cropping rice fields. | residue management in cropping systems is useful to improve soil quality. however, the studies on the effects of residue management on the enzyme activities and microbial community of soils in south china are few. therefore, the effects of incorporating winter cover crop residue with a double-cropping rice (oryza sativa l.) system on soil enzyme activities and microbial community in southern china fields were studied. the experiment has conducted at the experimental station of the institute of s ... | 2014 | 24956152 |
| multifunctionalised benzoxazinones in the systems oryza sativa-echinochloa crus-galli and triticum aestivum-avena fatua as natural-product-based herbicide leads. | fifteen novel derivatives of d-diboa, including aromatic ring modifications and the addition of side chains in positions c-2 and n-4, had previously been synthesised and their phytotoxicity on standard target species (sts) evaluated. this strategy combined steric, electronic, solubility and lipophilicity requirements to achieve the maximum phytotoxic activity. an evaluation of the bioactivity of these compounds on the systems oryza sativa-echinochloa crus-galli and triticum aestivum-avena fatua ... | 2010 | 20628996 |
| rflp mapping of a hordeum bulbosum gene highly expressed in pistils and its relationship to homoeologous loci in other gramineae species. | a cdna sequence (hbc8-2) isolated from pistils of the self-incompatible species hordeum bulbosum was analysed for expression pattern and genetic map location. hbc8-2 was expressed just prior to anthesis in mature pistils, and expression was maintained at a high level throughout anthesis. the same expression pattern was found in self-incompatible rye ( secale cereale), but no expression was detected in the self-compatible cereals wheat ( triticum aestivum) or barley ( hordeum vulgare) at comparab ... | 2002 | 12582529 |
| pyricularia graminis-tritici, a new pyricularia species causing wheat blast. | pyricularia oryzae is a species complex that causes blast disease on more than 50 species of poaceous plants. pyricularia oryzae has a worldwide distribution as a rice pathogen and in the last 30 years emerged as an important wheat pathogen in southern brazil. we conducted phylogenetic analyses using 10 housekeeping loci for 128 isolates of p. oryzae sampled from sympatric populations of wheat, rice, and grasses growing in or near wheat fields. phylogenetic analyses grouped the isolates into thr ... | 2016 | 28232765 |
| quantitative profiling of feruloylated arabinoxylan side-chains from graminaceous cell walls. | graminaceous arabinoxylans are distinguished by decoration with feruloylated monosaccharidic and oligosaccharidic side-chains. although it is hypothesized that structural complexity and abundance of these feruloylated arabinoxylan side-chains may contribute, among other factors, to resistance of plant cell walls to enzymatic degradation, quantitative profiling approaches for these structural units in plant cell wall materials have not been described yet. here we report the development and applic ... | 2015 | 26834763 |
| physiological role of a multigrain diet in metabolic regulations of lipid and antioxidant profiles in hypercholesteremic rats: multigrain diet in hyperlipemia. | the objective of the present study was to investigate the lipid and the antioxidant regulatory potential of a multigrain diet in laboratory animals with reference to lipid profiles, tissue lipid peroxidation and antioxidant status. | 2014 | 25780697 |
| in silico analysis of dreb transcription factor genes and proteins in grasses. | plants are exposed to various environmental stresses, including drought, salinity, low temperature, etc. dehydration responsive element binding (dreb) genes, the members of ap2/erf transcription factor family, regulate the biological processes against cold and dehydration stresses. in this study, we analyzed a total of 19 dreb transcription factor genes and proteins from 14 grass species by using bioinformatic approaches, including their physiochemical properties, conserved motif structures, hom ... | 2014 | 25104001 |
| effect of feeding different cereal-based diets on the performance and gut health of weaned piglets with or without previous access to creep feed during lactation. | a trial was conducted to evaluate the effect of different cereals on the performance, gut mucosa, and microbiota of weanling pigs with or without previous access to creep feed during lactation. a total of 108 newly weaned pigs (7.4 kg bw; 26 d of age; half with and half without creep feed) were used. piglets were distributed by bw into 36 pens according to a 2 × 6 factorial arrangement of treatments with previous access to creep feed (with or without) and cereal source in the experimental diet [ ... | 2012 | 23365275 |
| effect of feeding piglets with different extruded and nonextruded cereals on the gut mucosa and microbiota during the first postweaning week. | two trials were conducted to evaluate the effect of different cereals in piglet diets on the jejunal mucosa and the ileal and cecal microbiota during the first postweaning days. in trial 1, 48 newly weaned pigs (7.95 kg bw; 26 d of age) were individually housed and distributed among 3 experimental diets containing white rice (oryza sativa), naked oats (avena sativa), or barley (hordeum vulgare) as the cereal source. at the start of the trial (weaning; day 0), 12 piglets were slaughtered and samp ... | 2012 | 23365267 |
| duplication and diversification of the leafy hull sterile1 and oryza sativa mads5 sepallata lineages in graminoid poales. | gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. the leafy hull sterile1 (lhs1) sepallata (sep) genes have been linked with the origin and diversification of the grass spikelet, but it is uncertain 1) when the duplication event that produced the lhs1 clade and its paralogous lineage oryza sativa mads5 (osm5) occurred, and 2) how chan ... | 2012 | 22340849 |
| soluble sugar availability of aerobically germinated barley, oat and rice coleoptiles in anoxia. | physiological and metabolic responses to anoxia were compared for aerobically germinated seedlings of barley (hordeum vulgare), oat (avena sativa) and rice (oryza sativa). coleoptile growth of barley, oat and rice seedlings was suppressed by a 24 h-anoxic stress, but the growth of the rice coleoptiles was much greater than that of the barley and oat coleoptiles. atp concentration in the anoxic rice coleoptiles was greater than that in the anoxic barley and oat coleoptiles. concentrations of etha ... | 2010 | 20727618 |
| contents of phenolic acids, alkyl- and alkenylresorcinols, and avenanthramides in commercial grain products. | the contents of free and total phenolic acids and alk(en)ylresorcinols were analyzed in commercial products of eight grains: oat (avena sativa), wheat (triticum spp.), rye (secale cerale), barley (hordeum vulgare), buckwheat (fagopyrum esculentum), millet (panicum miliaceum), rice (oryza sativa), and corn (zea mays). avenanthramides were determined in three oat products. free phenolic acids, alk(en)ylresorcinols, and avenanthramides were extracted with methanolic acetic acid, 100% methanol, and ... | 2005 | 16218677 |
| chromosomal rearrangements differentiating the ryegrass genome from the triticeae, oat, and rice genomes using common heterologous rflp probes. | an restriction fragment length polymorphism (rflp)-based genetic map of ryegrass (lolium) was constructed for comparative mapping with other poaceae species using heterologous anchor probes. the genetic map contained 120 rflp markers from cdna clones of barley (hordeum vulgare l.), oat (avena sativa l.), and rice (oryza sativa l.), covering 664 cm on seven linkage groups (lgs). the genome comparisons of ryegrass relative to the triticeae, oat, and rice extended the syntenic relationships among t ... | 2005 | 15742203 |
| reduction in the endogenous arginine decarboxylase transcript levels in rice leads to depletion of the putrescine and spermidine pools with no concomitant changes in the expression of downstream genes in the polyamine biosynthetic pathway. | we investigated whether down-regulation of arginine decarboxylase (adc) activity and concomitant changes in polyamine levels result in changes in the expression of downstream genes in the polyamine pathway. we generated transgenic rice (oryza sativa l.) plants in which the rice adc gene was down-regulated by expression of its antisense oat (avena sativa l.) ortholog. plants expressed the oat mrna adc transcript at different levels. the endogenous transcript was down-regulated in five out of eigh ... | 2003 | 12898254 |
| growth promotion and an increase in cell wall extensibility by silicon in rice and some other poaceae seedlings. | the effect of silicon on organ growth and its mechanisms of action were studied in rice ( oryza sativa l. cv. koshihikari), oat ( avena sativa l. cv. victory), and wheat ( triticum aestivum l. cv. daichino-minori) seedlings grown in the dark. applying silicon in the form of silicic acid to these seedlings via culture solution resulted in growth promotion of third (rice) or second (oat and wheat) leaves. the optimal concentration of silicon was 5-10 mm. no growth promotion was observed in early o ... | 2002 | 12884045 |
| gramene, a tool for grass genomics. | gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (oryza sativa). it combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. gramene curators read and extract detailed information from published sources, summarize that information in a stru ... | 2002 | 12481044 |
| ethanol sensitivity of rice and oat coleoptiles. | the ability to avoid the ethanol-induced injury was evaluated in rice (oryza sativa l.) and oat (avena sativa l.) coleoptiles. the growth of the rice and oat coleoptiles was inhibited by ethanol exogenously applied at concentrations greater than 200 and 30 mm, respectively. at 300 mm ethanol, oat coleoptiles were brown and flaccid but rice coleoptiles did not show any visible symptoms of toxicity. the acetaldehyde level in rice and oat coleoptiles was increased by exogenously applied ethanol and ... | 2002 | 12010475 |
| active retrotransposons are a common feature of grass genomes. | a large fraction of the genomes of grasses, members of the family graminae, is composed of retrotransposons. these elements resemble animal retroviruses in their structure and possess a life cycle similar to theirs that includes transcription, translation, and integration of daughter copies. we have investigated if retrotransposons are generally transcribed in the grasses and other plants, and whether the various families of elements are translationally and integrationally active in multiple gra ... | 2001 | 11244109 |
| suppression of gravitropic response of primary roots by submergence. | primary roots of six plant species were placed horizontally either in humid air or under water, and their growth and gravitropic responses were examined. in air, all the roots showed a normal gravitropic curvature. under water without aeration, roots of rice (oryza sativa l.), oat (avena sativa l.), azuki bean (vigna angularis ohwi et ohashi), and cress (lepidium sativum l.) curved downward at almost same rate as in air, whereas the curvature of roots of maize (zea mays l.) and pea (pisum sativu ... | 1996 | 11540722 |
| allelopathy of oats. ii. allelochemical effect ofl-tryptophan and its concentration in oat root exudates. | l-tryptophan caused growth inhibition of roots and hypocotyls (or coleoptiles) of cockscomb (amaranthus caudatus l.), lettuce (lactuca sativa l.), cress (lepidium sativum l.), timothy (phleum pratense l.), rice (oryza sativa l.), wheat (triticum aestivum l.), and oat (avena sativa l.), increasing the dose ofl-tryptophan increased the inhibition. the concentrations for 50% inhibition of the root growth were 0.14, 0.15, 0.21, 0.79, 0.95, 1.7, and 2.4 mm for cockscomb, cress, lettuce, timothy, rice ... | 1994 | 24242057 |
| rapid elicitation of second messengers by nanomolar doses of triacontanol and octacosanol. | triacontanol (tria) increases the dry weight and alters the metabolism of rice (oryza sativa l.) seedlings within 10 min of application to either the shoots or roots. this activity is prevented if octacosanol (octa, c28 primary alcohol) is applied with the tria on the roots or shoots. triacontanol activity is also stopped if the octa is applied at least 1 min before the tria on the opposite part of the seedling.triacontanol rapidly elicits a second messenger that moves rapidly throughout the pla ... | 1988 | 24226183 |
| reversible redistribution of phytochrome within the cell upon conversion to its physiologically active form. | the intracellular localization of phytochrome was seen in dark-grown oat (avena sativa l., cv. garry) and rice (oryza sativa l., cv. unknown) shoots after various light treatments using an indirect peroxidase-antiperoxidase antibody labeling method. phytochrome is generally distributed throughout the cytoplasm in cells of tissue that had not been exposed to light prior to fixation. within, at most, 8 min after the onset of saturating red irradiation, phytochrome, now present in the far-red-absor ... | 1975 | 1093170 |