Publications

conservation and divergence of light-regulated genome expression patterns during seedling development in rice and arabidopsis.	genome-wide 70-mer oligonucleotide microarrays of rice (oryza sativa) and arabidopsis thaliana were used to profile genome expression changes during light-regulated seedling development. we estimate that the expression of approximately 20% of the genome in both rice and arabidopsis seedlings is regulated by white light. qualitatively similar expression profiles from seedlings grown under different light qualities were observed in both species; however, a quantitatively weaker effect on genome ex ...	2005	16284311
computational detection of micrornas targeting transcription factor genes in arabidopsis thaliana.	micrornas, an abundant class of tiny non-coding rnas, have emerged as negative regulators for translational repression or cleavage of target mrnas by the manner of complementary base paring in plants and animals. recent studies have demonstrated that many known micrornas have a remarkable propensity to target genes involved in development, particularly those of transcription factor genes. therefore, an overall detection of arabidopsis thaliana micrornas targeting transcription factor genes will ...	2005	16221572
comparative plant genomics resources at plantgdb.	plantgdb (http://www.plantgdb.org/) is a database of plant molecular sequences. expressed sequence tag (est) sequences are assembled into contigs that represent tentative unique genes. est contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. tentative gene ontology terms are assigned to match those of the similar sequences identified. genome survey sequences are assembled similarly. the resulting ge ...	2005	16219921
the dark side of green fluorescent protein.	here, severe interference of chlorophyll with green fluorescent protein (gfp) fluorescence is described for medicago (medicago truncatula), rice (oryza sativa) and arabidopsis (arabidopsis thaliana). this interference disrupts the proportional relationship between gfp content and fluorescence that is intrinsic to its use as a quantitative reporter. the involvement of chlorophyll in the loss of gfp fluorescence with leaf age was shown in vivo, by the removal of chlorophyll through etiolation or b ...	2005	16219071
transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots.	it is not known how representative the arabidopsis thaliana complement of transcription factors (tfs) is of other plants. the availability of rice (oryza sativa) genome sequences makes possible a comparative analysis of tfs between monocots and eudicots, the two major monophyletic groups of angiosperms. here, we identified 1611 tf genes that belong to 37 gene families in rice, comparable to the 1510 in arabidopsis. several gene subfamilies, but no families, were found to be lineage-specific. phy ...	2005	16217612
genomic research in eucalyptus.	eucalyptus l'hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. with the sequencing of the genomes of arabidopsis thaliana and oryza sativa and the recent completion of the first tree genome sequence, populus trichocarpa, attention has turned to the current status of genomic research in eucalyptus. for sev ...	2005	16175457
plant photoreceptors: phylogenetic overview.	plants possess photoreceptors to perceive light which controls most aspects of their lives. three photoreceptor families are well characterized: cryptochromes (crys), phototropins (phots), and phytochromes (phys). two putative families have been identified more recently: zeitlupes (ztls) and uv-b photoreceptors (uli). using arabidopsis thaliana and oryza sativa photoreceptor sequences as references, we have searched for photoreceptor encoding genes in the major phyla of plant kingdom. for each p ...	2005	16170454
wheat cultivar-specific proteins in grain revealed by 2-de and their application to cultivar identification of flour.	wheat flour proteins were studied to identify the cultivar-specific proteins and use them to identify cultivars in flours. proteins extracted from flours of japanese wheat (cultivars hokushin, horoshirikomugi, kitanokaori and kachikei 33) and canadian wheat (canada western red spring wheat no. 1; 1cw) were analyzed by 2-de with ief gels over three ph ranges: ph 4-7, ph 5-8, and ph 6-11. this system enabled detection of more than 1600 protein spots. we recognized that among 50 protein spots showi ...	2005	16152659
the wp mutation of glycine max carries a gene-fragment-rich transposon of the cacta superfamily.	we used soybean (glycine max) cdna microarrays to identify candidate genes for a stable mutation at the wp locus in soybean, which changed a purple-flowered phenotype to pink, and found that flavanone 3-hydroxylase cdnas were overexpressed in purple flower buds relative to the pink. restriction fragment length polymorphism analysis and rna gel blots of purple and pink flower isolines, as well as the presence of a 5.7-kb transposon insertion in the wp mutant allele, have unequivocally shown that ...	2005	16141454
the genomic view of genes responsive to the antagonistic phytohormones, abscisic acid, and gibberellin.	we now have the various genomics tools for monocot (oryza sativa) and a dicot (arabidopsis thaliana) plant. plant is not only a very important agricultural resource but also a model organism for biological research. it is important that the interaction between aba and ga is investigated for controlling the transition from embryogenesis to germination in seeds using genomics tools. these studies have investigated the relationship between dormancy and germination using genomics tools. genomics too ...	2005	16492467
genome-wide comparative analysis of the iqd gene families in arabidopsis thaliana and oryza sativa.	calcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. stimulus-specific generation of intracellular calcium transients, decoding of calcium signatures, and transformation of the signal into cellular responses are integral modules of the transduction process. several hundred proteins with functions in calcium signaling circuits have been identified, and the number of downstream targets of calcium sensors is ...	2005	16368012
structure and architecture of the maize genome.	maize (zea mays or corn) plays many varied and important roles in society. it is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. in this study we report the systematic analysis of contiguous sequences of the maize genome. we selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. this ...	2005	16339807
genome-wide identification of potential plant e2f target genes.	entry into the s phase of the cell cycle is controlled by e2f transcription factors that induce the transcription of genes required for cell cycle progression and dna replication. although the e2f pathway is highly conserved in higher eukaryotes, only a few e2f target genes have been experimentally validated in plants. we have combined microarray analysis and bioinformatics tools to identify plant e2f-responsive genes. promoter regions of genes that were induced at the transcriptional level in a ...	2005	16126853
green sperm. identification of male gamete promoters in arabidopsis.	previously, in an effort to better understand the male contribution to fertilization, we completed a maize (zea mays) sperm expressed sequence tag project. here, we used this resource to identify promoters that would direct gene expression in sperm cells. we used reverse transcription-polymerase chain reaction to identify probable sperm-specific transcripts in maize and then identified their best sequence matches in the arabidopsis (arabidopsis thaliana) genome. we tested five different arabidop ...	2005	16055690
[isolation, characterization and expression analysis of male sterility gene homology sequence in wheat].	one 134 bp fragment was amplified in anthers of male sterile and fertile wheat using one pair of degenerated primer designed based on the conserved domain of ms2 gene in arabidopsis thaliana and oryza sativa, and one 1604 bp male sterility gene homology sequence was extended by in silico cloning based on the 134 bp fragment. the amino acids encoded by the male sterility gene homology sequence include a 200 amino acid conserved domain of male sterility, and this sequence expressed only in wheat m ...	2005	16018182
systematic spatial analysis of gene expression during wheat caryopsis development.	the cereal caryopsis is a complex tissue in which maternal and endosperm tissues follow distinct but coordinated developmental programs. because of the hexaploid genome in wheat (triticum aestivum), the identification of genes involved in key developmental processes by genetic approaches has been difficult. to bypass this limitation, we surveyed 888 genes that are expressed during caryopsis development using a novel high-throughput mrna in situ hybridization method. this survey revealed novel di ...	2005	16006577
mustang is a novel family of domesticated transposase genes found in diverse angiosperms.	while transposons have traditionally been viewed as genomic parasites or "junk dna," the discovery of transposon-derived host genes has fueled an ongoing debate over the evolutionary role of transposons. in particular, while mobility-related open reading frames have been known to acquire host functions, the contribution of these types of events to the evolution of genes is not well understood. here we report that genome-wide searches for mutator transposase-derived host genes in arabidopsis thal ...	2005	15987878
mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes.	transfers of organelle dna to the nucleus established several thousand functional genes in eukaryotic chromosomes over evolutionary time. recent transfers have also contributed nonfunctional plastid (pt)- and mitochondrion (mt)-derived dna (termed nupts and numts, respectively) to plant nuclear genomes. the two largest transferred organelle genome copies are 131-kb nuptdna in rice (oryza sativa) and 262-kb numtdna in arabidopsis (arabidopsis thaliana). these transferred copies were compared in d ...	2005	15951485
effects of free proline accumulation in petunias under drought stress.	petunias (petunia hybrida cv. 'mitchell') accumulate free proline (pro) under drought-stress conditions. it is therefore believed that pro acts as an osmoprotectant in plants subjected to drought conditions. petunia plants were transformed by delta(1)-pyrroline-5-carboxylate synthetase genes (atp5cs from arabidopsis thaliana l. or osp5cs from oryza sativa l.). the transgenic plants accumulated pro and their drought tolerance was tested. the pro content amounted to 0.57-1.01% of the total amino a ...	2005	15928013
mutations in the arabidopsis phosphoinositide phosphatase gene sac9 lead to overaccumulation of ptdins(4,5)p2 and constitutive expression of the stress-response pathway.	phosphoinositides (pis) are signaling molecules that regulate cellular events including vesicle targeting and interactions between membrane and cytoskeleton. phosphatidylinositol (ptdins)(4,5)p(2) is one of the best characterized pis; studies in which ptdins(4,5)p(2) localization or concentration is altered lead to defects in the actin cytoskeleton and exocytosis. ptdins(4,5)p(2) and its derivative ins(1,4,5)p(3) accumulate in salt, cold, and osmotically stressed plants. ptdins(4,5)p(2) signalin ...	2005	15923324
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
imidazolinone-tolerant crops: history, current status and future.	imidazolinone herbicides, which include imazapyr, imazapic, imazethapyr, imazamox, imazamethabenz and imazaquin, control weeds by inhibiting the enzyme acetohydroxyacid synthase (ahas), also called acetolactate synthase (als). ahas is a critical enzyme for the biosynthesis of branched-chain amino acids in plants. several variant ahas genes conferring imidazolinone tolerance were discovered in plants through mutagenesis and selection, and were used to create imidazolinone-tolerant maize (zea mays ...	2005	15627242
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
molecular and biochemical markers associated with leaffolder (cnaphalocrocis medinalis g.) resistance in rice (oryza sativa l.).	association of molecular markers namely isozymes and simple sequence repeats (ssrs) and various biochemical markers to leaffolder (cnaphalocrocis medinalis g., a predominant insect pest of rice) resistance were studied in rice (oryza sativa l.). recombinant inbred lines (rils) of f8 generation obtained by crossing ir36 (susceptible parent) and tnaulfr831311 (moderately resistant parent) were used in this study. soluble protein content, protein profile, and peroxidase and phenylalanine ammonia ly ...	2005	23923546
destination-selective long-distance movement of phloem proteins.	the phloem macromolecular transport system plays a pivotal role in plant growth and development. however, little information is available regarding whether the long-distance trafficking of macromolecules is a controlled process or passive movement. here, we demonstrate the destination-selective long-distance trafficking of phloem proteins. direct introduction, into rice (oryza sativa), of phloem proteins from pumpkin (cucurbita maxima) was used to screen for the capacity of specific proteins to ...	2005	15863519
the evolutionary fate of mule-mediated duplications of host gene fragments in rice.	dna transposons are known to frequently capture duplicated fragments of host genes. the evolutionary impact of this phenomenon depends on how frequently the fragments retain protein-coding function as opposed to becoming pseudogenes. gene fragment duplication by mutator-like elements (mules) has previously been documented in maize, arabidopsis, and rice. here we present a rigorous genome-wide analysis of mules in the model plant oryza sativa (domesticated rice). we identify 8274 mules with intac ...	2005	16140995
the sireviruses, a plant-specific lineage of the ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain 8.	plant genomes are rich in long terminal repeat retrotransposons, and here we describe a plant-specific lineage of ty1/copia elements called the sireviruses. the sireviruses vary greatly in their genomic organization, and many have acquired additional coding information in the form of an envelope-like open reading frame and an extended gag gene. two-hybrid screens were conducted with the novel domain of gag (the gag extension) encoded by a representative sirevirus from maize (zea mays) called hop ...	2005	16183843
determination of antagonism between cyhalofop-butyl and other rice (oryza sativa) herbicides in barnyardgrass (echinochloa crus-galli).	herbicide antagonism is defined as the reduction of control of certain weeds as the result of applying mixtures of two or more herbicides. cyhalofop-butyl, a graminicide used for postemergence grass weed control in rice, is antagonized by some rice herbicides when applied simultaneously. the result of this type of antagonism usually results in decreased control of grass weeds. research has shown that herbicide antagonism between graminicides and other herbicides may be caused by different mechan ...	2005	15884840
weed control in rice with metham-sodium.	metam-sodium is a soil fumigant with herbicidal properties. a field experiment was conducted in 2000 at copiano (pavia, italy) to determine the efficacy of three rates of metam-sodium (300, 450 and 600 l/ha) at three different planting times (5, 12 and 18 days after chemical treatments) for the control of weeds in rice cultivation. the study mainly focused on the control of red rice (oryza sativa var. selvatica), a weed which is worldwide distributed in rice fields and difficult to eradicate tes ...	2006	17390826
[allelopathic potential and physiological mechanism of oryza sativa l. under phosphorus deficiency stress].	in this paper, allelopathic rice pi312777 (pi) and non-allelopahtic rice lemont (le) were grown in the nutrient solution with two levels of phosphorus (p) supply, and their allelopathic effects on echinochloa crus-galli l. were studied. the results showed that under phosphorous deficiency stress, the inhibitory effect of pi on e. crus-galli root growth had an obvious increase. after growing in the nutrient solution with low p supply (0.5 mg x l(-1)) for 5, 10 and 15 days, the inhibitory rate of ...	2006	17269328
bioactive steroids from oryza sativa l.	rice is one of the most interesting crops in the world from both the social and the economic point of views. the monoculture practices along with the heavy use of herbicides are characteristic of modern agriculture and are inducing the appearance of tolerant and/or herbicide resistant weed biotypes. this is the case the world's main weed of rice barnyardgrass (echinochloa crus-galli). alternative strategies for weed suppression consist of the use of chemicals from rice due to necessity of obtain ...	2006	16620896
evaluation of allelopathic potential and quantification of momilactone a,b from rice hull extracts and assessment of inhibitory bioactivity on paddy field weeds.	rice (oryza sativa l.) hull extracts were used in a bioassay to evaluate the allelopathic potential of rice on the germination and growth of barnyard grass (echinochloa crus-galli p. beauv. var. oryzicola ohwi), to quantify momilactone a and b levels in rice hull germplasm and to assess the inhibitory bioactivity of momilactone a and b as a potential natural source of herbicide for weed control in paddy fields. four varieties of weeds including e. crus-galli p. beauv. var. oryzicola ohwi, monoch ...	2006	16569039
genetic dissection of silicon uptake ability in rice (oryza sativa l.).	the adequate presence of silicon (si) in rice plants can enhance their yield and improve their tolerance to various biotic and abiotic stresses. in this study si uptake abilities were compared between the japonica rice cultivar (cv.) kinmaze and the indica rice cv. dv85 under three si concentrations (0.16, 0.4, and 1.6mm) at different time points from 1 to 12h. the results showed that the phenotypic values of two traits-si uptake by individual plants (sp, si uptake by all roots of a plant) and s ...	2006	25193641
a database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation.	simple sequence repeats (ssrs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. in this paper, the ssr distributions within ests from the legumes soybean (glycine max, representing 135.86 mb), medicago (medicago truncatula, 121.1 mb) and lotus (lotus japonicus, 45.4 mb) have been studied relative to the distributions in cereals such as sorghum (sorghum bicolor, 98.9 mb), rice (oryza sativa, 143.9 mb) and maize (zea mays, 183.7 mb ...	2006	17518768
efficient delivery of small interfering rna to plant cells by a nanosecond pulsed laser-induced stress wave for posttranscriptional gene silencing.	small interfering rna (sirna) induced posttranscriptional gene silencing (ptgs) has been an efficient method for genetic and molecular analysis of certain developmental and physiological processes and represented a potential strategy for both controlling virus replication and developing therapeutic products. however, there are limitations for the methods currently used to deliver sirna into cells. we report here, to our knowledge, the first efficient delivery of sirna to plant cells by a nanosec ...	2006	22980207
the transposable element landscape of the model legume lotus japonicus.	the largest component of plant and animal genomes characterized to date is transposable elements (tes). the availability of a significant amount of lotus japonicus genome sequence has permitted for the first time a comprehensive study of the te landscape in a legume species. here we report the results of a combined computer-assisted and experimental analysis of the tes in the 32.4 mb of finished tac clones. while computer-assisted analysis facilitated a determination of te abundance and diversit ...	2006	17028332
investigation of the endosperm-specific sucrose synthase promoter from rice using transient expression of reporter genes in guar seed tissue.	we report the investigation of an endosperm-specific promoter from the rsus3 gene from rice (oryza sativa). the promoter was characterized by deletion analysis and transient expression in guar (cyamopsis tetragonoloba) seed-tissue. transient expression was monitored by histochemical gus assay, and quantitative dual reporter assays comprising firefly luciferase as a test reporter, and renilla luciferase and gus as reference reporters. these revealed high expression levels of the reporter genes di ...	2006	16670901
resistance to stem borers (lepidoptera: crambidae) among texas rice cultivars.	a 4-yr field study was conducted to assess the resistance of rice, oryza sativa l., cultivars to injury from the sugarcane borer, diatraea saccharalis (f.), and the mexican rice borer, eoreuma loftini (dyar) (both lepidoptera: crambidae). several cultivars showed reduced levels of injury ('clxl8', 'xl8', 'wells', 'cheniere', and 'xp710' in 2003; clxl8, xp723, cheniere, and 'cl161' in 2004) and lower stem borer yield loss (clxl8 in 2004) than the more susceptible 'priscilla'. the resistant clxl8 ...	2006	17066824
synthesis and herbicidal activity of n,n-diethyl-3-(arylselenonyl)-1h-1,2,4-triazole-1-carboxamide.	based on the carbamoyl triazole herbicide cafenstrole, 12 novel selenium-containing compounds were designed and synthesized. all of the compounds were characterized and confirmed by ir, 1h nmr, and high-resolution mass spectroscopy. the bioassay tests showed that some of the compounds (c2, c4, c(7-8), and c12) exhibited good inhibitory activity against cucumber (cucumis sativus l.) and semen euphorbiae (leptochloa chinensis n.). especially, compound c6 inhibited the growth of cucumber and semen ...	2006	17002445
molecular cloning of indian jujube (zizyphus mauritiana) allergen ziz m 1 with sequence similarity to plant class iii chitinases.	indian jujube (zizyphus mauritiana) is a sweet fruit that is abundantly cultivated in taiwan. we have previously identified 42 and 30 kda allergens that are cross-reactive with latex allergen from crude indian jujube extract. this study aimed to clone the 30 kda ziz m 1 z. mauritiana allergen. the ziz m 1 encoding cdna was isolated from a zapii cdna library constructed from z. mauritiana mrna, sequenced and expressed in pichia pastoris. the protein predicted from the cdna sequence has 330 amino ...	2006	16122801
conservation and diversification of meristem maintenance mechanism in oryza sativa: function of the floral organ number2 gene.	to elucidate the genetic mechanism that regulates meristem maintenance in monocots, here we have examined the function of the gene floral organ number2 (fon2) in oryza sativa (rice). mutations in fon2 cause enlargement of the floral meristem, resulting in an increase in the number of floral organs, although the vegetative and inflorescence meristems are largely normal. molecular cloning reveals that fon2 encodes a small secreted protein, containing a cle domain, that is closely related to clavat ...	2006	17056620
prediction of trans-antisense transcripts in arabidopsis thaliana.	natural antisense transcripts (nats) are coding or non-coding rnas with sequence complementarity to other transcripts (sense transcripts). these rnas could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level. experimental and computational methods have demonstrated the widespread occurrence of nats in eukaryotes. however, most previous studies only focused on cis-nats with little attention being paid to nats that originate in ...	2006	17040561
the gh3 family in plants: genome wide analysis in rice and evolutionary history based on est analysis.	the gh3 gene family in arabidopsis, implicated in hormonal homeostasis through the conjugation of indolacetic and jasmonic acids to amino acids, is involved in a broad range of plant growth and development processes. in this work, the analysis of the gh3 family in the genome of oryza sativa identified 13 hypothetical orfs. est analysis and rt-pcr assays demonstrated that 12 of them were active genes. an extensive est analysis of the gh3 family performed on 26 plant species was used to estimate t ...	2006	16488558
genome histories clarify evolution of the expansin superfamily: new insights from the poplar genome and pine ests.	expansins comprise a superfamily of plant cell wall-loosening proteins that has been divided into four distinct families, expa, expb, exla and exlb. in a recent analysis of arabidopsis thaliana and oryza sativa expansins, we proposed a further subdivision of the families into 17 clades, representing independent lineages in the last common ancestor of monocots and eudicots. this division was based on both traditional sequence-based phylogenetic trees and on position-based trees, in which genomic ...	2006	16411016
orthologid: automation of genome-scale ortholog identification within a parsimony framework.	the determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. until now, most researchers use pairwise distance comparisons algorithms, such as blast, cog, rbh, rsd and inparanoid, to determine gene orthology. in contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and ...	2006	16410324
the role of osbri1 and its homologous genes, osbrl1 and osbrl3, in rice.	since first identifying two alleles of a rice (oryza sativa) brassinosteroid (br)-insensitive mutant, d61, that were also defective in an orthologous gene in arabidopsis (arabidopsis thaliana) brassinosteroid insensitive1 (bri1), we have isolated eight additional alleles, including null mutations, of the rice bri1 gene osbri1. the most severe mutant, d61-4, exhibited severe dwarfism and twisted leaves, although pattern formation and differentiation were normal. this severe shoot phenotype was ca ...	2006	16407447
genome-wide analysis of the erf gene family in arabidopsis and rice.	genes in the erf family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. in this study, a comprehensive computational analysis identified 122 and 139 erf family genes in arabidopsis (arabidopsis thaliana) and rice (oryza sativa l. subsp. japonica), respectively. a complete overview of this gene family in arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. ...	2006	16407444
ramosa2 encodes a lateral organ boundary domain protein that determines the fate of stem cells in branch meristems of maize.	genetic control of grass inflorescence architecture is critical given that cereal seeds provide most of the world's food. seeds are borne on axillary branches, which arise from groups of stem cells in axils of leaves and whose branching patterns dictate most of the variation in plant form. normal maize (zea mays) ears are unbranched, and tassels have long branches only at their base. the ramosa2 (ra2) mutant of maize has increased branching with short branches replaced by long, indeterminate one ...	2006	16399802
genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and arabidopsis.	the basic/helix-loop-helix (bhlh) transcription factors and their homologs form a large family in plant and animal genomes. they are known to play important roles in the specification of tissue types in animals. on the other hand, few plant bhlh proteins have been studied functionally. recent completion of whole genome sequences of model plants arabidopsis (arabidopsis thaliana) and rice (oryza sativa) allows genome-wide analysis and comparison of the bhlh family in flowering plants. we have ide ...	2006	16896230
cross genome comparisons of serine proteases in arabidopsis and rice.	serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. the availability of arabidopsis thaliana and rice (oryza sativa) genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species.	2006	16895613
whole-genome analysis of oryza sativa reveals similar architecture of two-component signaling machinery with arabidopsis.	the two-component system (tcs), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. employing the tools of bioinformatics, we have characterized tcs signaling candidate genes in the genome of oryza sativa l. subsp. japonica. we present a complete overview of tcs gene families in o. sativa, including gene structures, ...	2006	16891544
rna interference-based gene silencing as an efficient tool for functional genomics in hexaploid bread wheat.	insertional mutagenesis and gene silencing are efficient tools for the determination of gene function. in contrast to gain- or loss-of-function approaches, rna interference (rnai)-induced gene silencing can possibly silence multigene families and homoeologous genes in polyploids. this is of great importance for functional studies in hexaploid wheat (triticum aestivum), where most of the genes are present in at least three homoeologous copies and conventional insertional mutagenesis is not effect ...	2006	16861570
genome-wide comparative analyses of domain organisation of repertoires of protein kinases of arabidopsis thaliana and oryza sativa.	a comparative analysis on protein kinases encoded in the completely sequenced genomes of two plant species, namely arabidopsis thaliana and oryza sativa spp japonica cv. nipponbare is reported in the current study. we have analysed 836 and 1386 kinases identified from a. thaliana and the o. sativa genomes respectively. their classification into known subfamilies reveals selective expansions of the plant receptor kinase subfamily comprising of ser/thr receptor kinases. the presence of calcium dep ...	2006	16843620
isolation and characterization of a new na+/h+ antiporter gene osnha1 from rice (oryza sativa l.).	the full-length cdna (3612 bp) of osnha1 was cloned by rt-pcr approach from rice (oryza sativa l.), which encodes a putative plasma membrane na+/h+ antiporter. its deduced protein, osnha1, has 11 transmembrane domains and a significant similarity to a plasma membrane na+/h+ antiporter atnha1 from arabidopsis thaliana. phylogenetic analysis showed that the osnha1 clusters with the plasma membrane na+/h+ antiporters from various organisms. the semi-quantitative rt-pcr assay revealed that the expre ...	2006	16753814
genome-wide analysis of plant glutaredoxin systems.	the recent release of the first tree genome (populus trichocarpa) has allowed a comparison to be made of the multigenic glutaredoxin (grx) and glutathione reductase (gr) families of this tree with those of other sequenced organisms and especially of the two other fully sequenced plant species, arabidopsis thaliana and oryza sativa. grxs are small proteins involved in disulphide bridge or protein-glutathione adduct reduction, and they are maintained in a reduced form using glutathione and an nadp ...	2006	16720602
the atl gene family from arabidopsis thaliana and oryza sativa comprises a large number of putative ubiquitin ligases of the ring-h2 type.	ubiquitin ligases play an important regulatory role in the control of protein degradation processes via the ubiquitin/26s proteasome pathway in eukaryotes. these enzymes participate in substrate specification and mediate the transfer of ubiquitin to target proteins. a large number of ubiquitin ligases are predicted in the eukaryotes whose genomes have been sequenced; in arabidopsis thaliana more than 1300 genes are thought to encode ubiquitin ligases. at least three classes of ubiquitin ligases ...	2006	16557337
rice hydroperoxide lyases with unique expression patterns generate distinct aldehyde signatures in arabidopsis.	hydroperoxide lyase (hpl) genes encode enzymes that catalyze the cleavage of fatty acid hydroperoxides into aldehydes and oxoacids. there are three hpls in rice (oryza sativa), designated oshpl1 through oshpl3. to explore the possibility of differential functional activities among these genes, we have examined their expression patterns and biochemical properties of their encoded products. transcript analysis indicates that these genes have distinct patterns and levels of expression. oshpl1 is ub ...	2006	16531481
plastid cues posttranscriptionally regulate the accumulation of key enzymes of the methylerythritol phosphate pathway in arabidopsis.	plastid isoprenoids (including hormones and photosynthetic pigments) are essential for plant growth and development, but relatively little is known of how the production of their metabolic precursors via the recently elucidated methylerythritol phosphate (mep) pathway is regulated. we have identified an arabidopsis (arabidopsis thaliana) mutant that survives an otherwise lethal block of the mep pathway with fosmidomycin (fsm). in rif10 (resistant to inhibition with fsm 10) plants, the accumulati ...	2006	16531478
survey of conserved alternative splicing events of mrnas encoding sr proteins in land plants.	the serine/arginine-rich (sr) protein family plays an important role in constitutive and alternative splicing (as). these proteins regulate as in a tissue-specific and stress-responsive manner. pre-mrnas encoding sr proteins are often alternatively spliced, and these as events may be important for the regulation of as events of other pre-mrnas. in this study, we analyzed as events of sr proteins in arabidopsis thaliana and oryza sativa (rice). we found three sets of as events conserved between a ...	2006	16520337
plant methionine sulfoxide reductase a and b multigenic families.	methionine oxidation to methionine sulfoxide (metso), which results in modification of activity and conformation for many proteins, is reversed by an enzyme present in most organisms and termed as methionine sulfoxide reductase (msr). on the basis of substrate stereospecificity, two types of msr, a and b, that do not share any sequence similarity, have been identified. in the present review, we first compare the multigenic msr families in the three plant species for which the genome is fully seq ...	2006	17031545
the floral organ number4 gene encoding a putative ortholog of arabidopsis clavata3 regulates apical meristem size in rice.	to understand the molecular mechanism regulating meristem development in the monocot rice (oryza sativa), we describe here the isolation and characterization of three floral organ number4 (fon4) alleles and the cloning of the fon4 gene. the fon4 mutants showed abnormal enlargement of the embryonic and vegetative shoot apical meristems (sams) and the inflorescence and floral meristems. likely due to enlarged sams, fon4 mutants produced thick culms (stems) and increased numbers of both primary rac ...	2006	17012407
the reactive oxygen species network pathways:an essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants.	availability of complete arabidopsis (arabidopsis thaliana) and rice (oryza sativa) genome sequences, together with molecular recourses of functional genomics and proteomics have revolutionized our understanding of reactive oxygen species (ros) signalling network mediating disease resistance in plants. so far, ros have been associated with aging, cellular and molecular alteration in animal and plant cells. recently,concluding evidences suggest that ros network is essential to induce disease resi ...	2006	17006022
the arabidopsis unannotated secreted peptide database, a resource for plant peptidomics.	in the era of genomics, if a gene is not annotated, it is not investigated. due to their small size, genes encoding peptides are often missed in genome annotations. secreted peptides are important regulators of plant growth, development, and physiology. identification of additional peptide signals by sequence homology searches has had limited success due to sequence heterogeneity. a bioinformatics approach was taken to find unannotated arabidopsis (arabidopsis thaliana) peptides. arabidopsis chr ...	2006	16998087
plant proteome analysis: a 2004-2006 update.	since the appearance of the review entitled "plant proteome analysis" in proteomics in february 2004 (cánovas, f. m., dumas-gaudot, e., recorbert, g., jorrín, j. et al., proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. these papers concern the proteome of at least 35 plant s ...	2006	16991197
divergence of the dof gene families in poplar, arabidopsis, and rice suggests multiple modes of gene evolution after duplication.	it is widely accepted that gene duplication is a primary source of genetic novelty. however, the evolutionary fate of duplicated genes remains largely unresolved. the classical ohno's duplication-retention-non/neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. duplicated genes are also affected by epigenetic c ...	2006	16980566
identification of a new family of plant proteins loosely related to glutaredoxins with four cxxc motives.	the annotation of the recently released populus trichocarpa genome, has allowed us to characterize extensively the multigenic families of the redoxin proteins. proteins with two cysteines separated by two amino acids (cxxc motif) are often involved in redox reactions by promoting the formation, reduction or isomerization of disulfide bonds or by binding prosthetic groups or metals. we report here the presence of a new protein family in higher plants, constituted of 19 members in populus trichoca ...	2006	16915354
light-regulated overexpression of an arabidopsis phytochrome a gene in rice alters plant architecture and increases grain yield.	the phytochromes are a family of red/far-red light absorbing photoreceptors that control plant developmental and metabolic processes in response to changes in the light environment. we report here the overexpression of arabidopsis thaliana phytochrome a (phya) gene in a commercially important indica rice variety (oryza sativa l. pusa basmati-1). the expression of the transgene was driven by the light-regulated and tissue-specific rice rbcs promoter. several independent homozygous sixth generatio ...	2006	16136335
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
importance of plant species and external silicon concentration to active silicon uptake and transport.	here, we characterized silicon (si) uptake and xylem loading in oryza sativa, zea mays, helianthus annuus and benincase hispida in a series of hydroponic experiments. both active and passive si-uptake components co-exist in all the plants tested. the active component is the major mechanism responsible for si uptake in o. sativa and z. mays. by contrast, passive uptake prevails in h. annuus and b. hispida at a higher external si concentration (0.85 mm), while the active component constantly exist ...	2006	16945089
fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between oryza sativa and oryza rufipogon.	a quantitative trait locus (qtl) for grain weight (gw) was detected near ssr marker rm210 on chromosome 8 in backcross populations derived from a cross between the korean japonica cultivar hwaseongbyeo and oryza rufipogon (irgc 105491). the o. rufipogon allele increased gw in the hwaseongbyeo background despite the fact that o. rufipogon was the small-seeded parent. using sister bc(3)f(3) near-isogenic lines (nils), gw8.1 was validated and mapped to a 6.1 cm region in the interval between rm42 a ...	2006	16850315
caught red-handed: rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice.	rc is a domestication-related gene required for red pericarp in rice (oryza sativa). the red grain color is ubiquitous among the wild ancestors of o. sativa, in which it is closely associated with seed shattering and dormancy. rc encodes a basic helix-loop-helix (bhlh) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between oryza rufipogon (red pericarp) and o. sativa cv jefferson (white pericarp). sequencing of the alleles from both mapping parents as well a ...	2006	16399804
molecular characterization of mature pollen-specific genes encoding novel small cysteine-rich proteins in rice (oryza sativa l.).	in our previous cdna microarray analysis, we identified 53 mature anther-specific genes, whose function was unknown, in rice. we reanalyzed these genes from the viewpoint of the specific amino acid motif. out of 53 genes, three genes, os-26, os-32, and os-169 (renamed as osscp1, osscp2, and osscp3), encoded cysteine-rich motif (cys-x3-cys-x13-cys-x3-cys), indicating that they were novel small cysteine-rich proteins. from the search of specific elements in promoter regions, several pollen-specifi ...	2006	16397782
rice ascorbate peroxidase gene family encodes functionally diverse isoforms localized in different subcellular compartments.	aerobic organisms evolved a complex antioxidant system, which protect the cells against oxidative damage caused by partially reduced oxygen intermediates, also known as reactive oxygen species. in plants, ascorbate peroxidases (ec, 1.11.1.11) catalyze the conversion of h(2)o(2) to h(2)o, using ascorbate as the specific electron donor in this enzymatic reaction. previously, eight apx genes were identified in the rice (oryza sativa l.) genome through in silico analysis: two cytosolic isoforms, two ...	2006	16397796
elongated uppermost internode encodes a cytochrome p450 monooxygenase that epoxidizes gibberellins in a novel deactivation reaction in rice.	the recessive tall rice (oryza sativa) mutant elongated uppermost internode (eui) is morphologically normal until its final internode elongates drastically at the heading stage. the stage-specific developmental effect of the eui mutation has been used in the breeding of hybrid rice to improve the performance of heading in male sterile cultivars. we found that the eui mutant accumulated exceptionally large amounts of biologically active gibberellins (gas) in the uppermost internode. map-based clo ...	2006	16399803
pair2 is essential for homologous chromosome synapsis in rice meiosis i.	the pair2 gene is required for homologous chromosome synapsis at meiosis i in rice (oryza sativa l.) and encodes a horma-domain protein that is homologous to saccharomyces cerevisiae hop1 and arabidopsis asy1. immunocytological and electron microscopic analyses indicate that pair2 proteins associate with axial elements (aes) at leptotene and zygotene, and is removed from the aes of arm regions when homologous chromosomes have been synapsed. immunocytology against a centromeric histone h3 variant ...	2006	16410547
rice plants take up iron as an fe3+-phytosiderophore and as fe2+.	only graminaceous monocots possess the strategy ii iron (fe)-uptake system in which fe is absorbed by roots as an fe3+-phytosiderophore. in spite of being a strategy ii plant, however, rice (oryza sativa) contains the previously identified fe2+ transporter osirt1. in this study, we isolated the osirt2 gene from rice, which is highly homologous to osirt1. real-time pcr analysis revealed that osirt1 and osirt2 are expressed predominantly in roots, and these transporters are induced by low-fe condi ...	2006	16412081
an endornavirus from a hypovirulent strain of the violet root rot fungus, helicobasidium mompa.	we determined the complete nucleotide (nt) sequence (16,614 nt) of a large double-stranded (ds) rna (referred to as l1 dsrna), previously identified as the hypovirulence factor from strain v670 of the violet root rot fungus, helicobasidium mompa. the positive-strand of l1 dsrna contained a long open reading frame (orf) potentially encoding a protein of 5,373 amino acids (molecular mass 603,080 da) with conserved motifs characteristic of rna-dependent rna polymerase (rdrp) and helicase. the orf i ...	2006	16417937
a higher plant has three different types of rpa heterotrimeric complex.	replication protein a (rpa) is a protein complex composed of three subunits known as rpa70, rpa32, and rpa14. generally, only one version of each of the three rpa genes is present in animals and yeast (with the exception of the human rpa32 ortholog). in rice (oryza sativa l.), however, two paralogs of rpa70 have been reported. we screened the rice genome for rpa subunit genes, and identified three osrpa70 (osrpa70a, osrpa70b and osrpa70c), three osrpa32 (osrpa32-1, osrpa32-2 and osrpa32-3), and ...	2006	16428324
genome-wide analysis of cyclin family in rice (oryza sativa l.).	the cyclins together with highly conserved cyclin-dependent kinases regulate cell cycle progression in plants. although extensive and systematic study on cell cycle mechanisms and cyclin functions in yeasts and animals has been carried out, only a small number of plant cyclins have been characterized and classified functionally and phylogenetically. we identified several types of cyclin genes in the rice genome and characterized them by phylogenetic, tandem and segmental duplications analyses. o ...	2006	16435118
molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress.	we isolated and identified four rice genes, osbierf1 to osbierf4 (oryza sativa benzothiadiazole (bth)-induced ethylene responsive transcriptional factors (erf)) and analyzed their expressions in rice disease resistance response and under various abiotic stress conditions. the osbierf1-4 proteins contain conserved erf domains, but are categorized into different classes of the previously characterized erf proteins based on their structural organizations. osbierf3 and osbierf2 belong to classes i a ...	2006	16436304
gold hull and internode2 encodes a primarily multifunctional cinnamyl-alcohol dehydrogenase in rice.	lignin content and composition are two important agronomic traits for the utilization of agricultural residues. rice (oryza sativa) gold hull and internode phenotype is a classical morphological marker trait that has long been applied to breeding and genetics study. in this study, we have cloned the gold hull and internode2 (gh2) gene in rice using a map-based cloning approach. the result shows that the gh2 mutant is a lignin-deficient mutant, and gh2 encodes a cinnamyl-alcohol dehydrogenase (ca ...	2006	16443696
isolation and identification of natural endophytic rhizobia from rice (oryza sativa l.) through rdna pcr-rflp and sequence analysis.	three novel endophytic rhizobial strains (rre3, rre5, and rre6) were isolated from naturally growing surface sterilized rice roots. these isolates had the ability to nodulate common bean (phaseolus vulgaris). polymerase chain reaction-restriction fragment length polymorphism and sequencing of 16s rdna of these isolates revealed that rre3 and rre5 are phylogenetically very close to burkholderia cepacia complex, whereas rre6 has affinity with rhizobium leguminosarum bv. phaseoli. plant infection t ...	2006	16450073
substitution mapping of dth1.1, a flowering-time quantitative trait locus (qtl) associated with transgressive variation in rice, reveals multiple sub-qtl.	a quantitative trait locus (qtl), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the oryza sativa variety jefferson and an accession of the wild rice relative oryza rufipogon. a series of near-isogenic lines (nils) containing different o. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. in contrast to the late-flowering o. rufipogon parent, o. rufipogon allele ...	2006	16452146
cholic acid, a bile acid elicitor of hypersensitive cell death, pathogenesis-related protein synthesis, and phytoalexin accumulation in rice.	when plants interact with certain pathogens, they protect themselves by generating various defense responses. these defense responses are induced by molecules called elicitors. since long ago, composts fermented by animal feces have been used as a fertilizer in plant cultivation, and recently, have been known to provide suppression of plant disease. therefore, we hypothesized that the compounds from animal feces may function as elicitors of plant defense responses. as a result of examination of ...	2006	16461384
diversity of centromeric repeats in two closely related wild rice species, oryza officinalis and oryza rhizomatis.	oryza officinalis (cc, 2n = 24) and oryza rhizomatis (cc, 2n = 24) belong to the oryza genus, which contains more than 20 identified wild rice species. although much has been known about the molecular composition and organization of centromeres in oryza sativa, relatively little is known of its wild relatives. in the present study, we isolated and characterized a 126-bp centromeric satellite (cento-c) from three bacterial artificial chromosomes of o. officinalis. in addition to cento-c, low abun ...	2006	16463049
cyanobacterial chemotaxis to extracts of host and nonhost plants.	chemotaxis may be important when forming cyanobacterial symbioses. however, knowledge of cyanobacterial attraction towards plants and factors affecting chemotaxis is limited. chemo-attraction was observed in nostoc strains 8964:3 and pcc 73102 towards exudate or crushed extract of the natural hosts gunnera manicata, cycas revoluta and blasia pusilla, and the nonhost plants trifolium repens, arabidopsis thaliana and oryza sativa. as all tested plant extracts generated chemotaxis, the possibility ...	2006	16466377
the telomerase inhibitor telomestatin induces telomere shortening and cell death in arabidopsis.	the cellular response to telomere dysfunction in plants was investigated with the use of telomestatin, an inhibitor of human telomerase activity. telomestatin bound to plant telomeric repeat sequence, and inhibited telomerase activity in suspension-cultured cells of arabidopsis thaliana and oryza sativa (rice) in a dose-dependent manner. the inhibitor did not affect transcript level of the tert gene, which encodes the catalytic subunit of telomerase, in the plant cells. inhibition of telomerase ...	2006	16473138
exploring the escrting machinery in eukaryotes.	the profile of protein sorting into multivesicular bodies (mvbs) has risen recently with the identification of three heteromeric complexes known as escrt-i,-ii,-iii (endosomal sorting complex required for transport). genetic analyses in yeast have identified up to 15 soluble class e vps (vacuolar protein sorting) proteins that have been assigned to the escrt machinery and function in cargo recognition and sorting, complex assembly, vesicle formation and dissociation. despite their functional imp ...	2006	16488176
arbuscular mycorrhizal fungi can alleviate the adverse effects of chlorothalonil on oryza sativa l.	a glasshouse pot experiment was conducted to investigate the effect of the fungicide chlorothalonil on the growth of upland rice, in the absence or presence of the arbuscular mycorrhizal fungus (amf) glomus mosseae (nm and gm treatments). the plants were grown with three concentrations of chlorothalonil (0, 50 and 100 mg kg(-1) soil). mycorrhizal colonization decreased significantly with increasing chlorothalonil concentrations. plant biomass decreases were smaller in gm plants than in non-mycor ...	2006	16499948
functional characterization of osppt1, which encodes p-hydroxybenzoate polyprenyltransferase involved in ubiquinone biosynthesis in oryza sativa.	prenylation of the aromatic intermediate p-hydroxybenzoate (phb) is a critical step in ubiquinone (uq) biosynthesis. the enzyme that catalyzes this prenylation reaction is p-hydroxybenzoate polyprenyltransferase (ppt), which substitutes an aromatic proton at the m-position of phb with a prenyl chain provided by polyprenyl diphosphate synthase. the rice genome contains three ppt candidates that share significant similarity with the yeast ppt (coq2 gene), and the rice gene showing the highest simi ...	2006	16501255
identification of a mitochondrial atp synthase small subunit gene (rmtatp6) expressed in response to salts and osmotic stresses in rice (oryza sativa l.).	large areas of northern china have alkaline soil due to the accumulation of sodium carbonates (nahco3, na2co3). to understand better how plants can tolerate alkaline soil, a cdna library was prepared from rice (oryza sativa l.) roots grown in the presence of nahco3 stress. a cdna clone isolated from this library was identified by a homology search as a mitochondrial atp synthase 6 kda subunit gene (rmtatp6; genbank accession nos ab055076, bab21526). in transformed yeast and tobacco protoplasts, ...	2006	16317034