Publications

gene content and virtual gene order of barley chromosome 1h.	chromosome 1h (approximately 622 mb) of barley (hordeum vulgare) was isolated by flow sorting and shotgun sequenced by gsflx pyrosequencing to 1.3-fold coverage. fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1h fraction. sequence comparison against the reference genomes of rice (oryza sativa) and sorghum (sorghum bicolor) and against wheat (triticum aestivum) and barley expressed sequence ...	2009	19692534
premature tapetum degeneration: a major cause of abortive pollen development in photoperiod sensitive genic male sterility in rice.	photoperiod-sensitive genic male-sterile (psgms) rice (oryza sativa l.), a natural mutant found in the rice cultivar nongken 58, is very useful for the development of hybrid rice cultivars. despite its widespread use in breeding programs, the initial stage of the abortive development of psgms rice and the possible cytological mechanisms of pollen abortion have not been determined. in the present study, a systematic cytological comparison of the anther development of psgms rice with its normal fe ...	2009	19686374
proteomic analysis of cytoskeleton-associated rna binding proteins in developing rice seed.	in eukaryotes, rna binding proteins (rbps) play an integral role not only in rna processing within the nucleus, but also in the cytoplasmic events of rna transport, localization, translation, storage and degradation. while many studies have been done, relatively little is known about rbps in plants. as part of our continuing efforts to understand cytoplasmic gene expression events in developing rice seed (oryza sativa l.), a proteomics approach was used to identify cytoplasmic-localized, cytoske ...	2009	19685898
computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize.	the architecture of grass genomes varies on multiple levels. large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. to characterize the organization and distribution of repeat clusters and gene islands across ...	2009	19675151
er membrane-localized oxidoreductase ero1 is required for disulfide bond formation in the rice endosperm.	the developing endosperm of rice (oryza sativa, os) synthesizes a large amount of storage proteins on the rough (r)er. the major storage proteins, glutelins and prolamins, contain either intra or intermolecular disulfide bonds, and oxidative protein folding is necessary for the sorting of the proteins to the protein bodies. here, we investigated an electron transfer pathway for the formation of protein disulfide bonds in the rer of the rice endosperm, focusing on the roles of the thiol-disulfide ...	2009	19666483
hydroxyiminodisuccinic acid (hids): a novel biodegradable chelating ligand for the increase of iron bioavailability and arsenic phytoextraction.	the influence of biodegradable chelating ligands on arsenic and iron uptake by hydroponically grown rice seedlings (oryza sativa l.) was investigated. even though the growth solution contained sufficient fe, the growth of rice seedlings gradually decreased up to 76% with the increase of ph of the solution from 7 to 11. iron forms insoluble ferric hydroxide complexes at neutral or alkaline ph in oxic condition. chelating ligands produce soluble 'fe-ligand complex' which assist fe uptake in plants ...	2009	19665755
heterotrimeric g protein signaling is required for epidermal cell death in rice.	in rice (oryza sativa) adventitious root primordia are formed at the nodes as part of normal development. upon submergence of rice plants, adventitious roots emerge from the nodes preceded by death of epidermal cells above the root primordia. cell death is induced by ethylene and mediated by hydrogen peroxide (h(2)o(2)). pharmacological experiments indicated that epidermal cell death was dependent on signaling through g proteins. treatment with gtp-gamma-s induced epidermal cell death, whereas g ...	2009	19656904
brassinosteroid upregulated1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice.	brassinosteroids (brs) are involved in many developmental processes and regulate many subsets of downstream genes throughout the plant kingdom. however, little is known about the br signal transduction and response network in monocots. to identify novel br-related genes in rice (oryza sativa), we monitored the transcriptomic response of the brassinosteroid deficient1 (brd1) mutant, with a defective br biosynthetic gene, to brassinolide treatment. here, we describe a novel br-induced rice gene br ...	2009	19648232
neck leaf 1, a gata type transcription factor, modulates organogenesis by regulating the expression of multiple regulatory genes during reproductive development in rice.	in the monocot rice species oryza sativa l., one of the most striking morphological processes during reproductive development is the concurrence of panicle development with the sequential elongation of upper internodes (upis). to elucidate the underlying molecular mechanisms, we cloned the rice gene neck leaf 1 (nl1), which when mutated results in delays in flowering time, smaller panicles with overgrown bracts and abnormal upi elongation patterns. the nl1 gene encodes a gata-type transcription ...	2009	19337211
genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups.	completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. with the objective of developing genic but non-coding microsatellite (gnms) markers for the rice (oryza sativa l.) genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences.	2009	19335879
pcr marker-based evaluation of the eating quality of japonica rice ( oryza sativa l.).	evaluation of eating quality in early breeding generations of rice is critical to developing varieties with better palatability. this paper reports dna markers associated with eating quality of temperate japonica rice and an evaluation method aided by multiple regression analysis. a total of 30 markers comprising stss, snps, and ssrs were tested for their association with palatability using 22 temperate japonica varieties with different palatability values. eating quality-related traits of the 2 ...	2009	19334756
genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice.	heat shock proteins (hsps) are molecular chaperons, which function in protein folding and assembly, protein intracellular localization and secretion, and degradation of misfolded and truncated proteins. heat shock factors (hsfs) are the transcriptional activators of hsps. it has been reported that hsps and hsfs are widely involved in response to various abiotic stresses such as heat, drought, salinity and cold. to elucidate the function and regulation of rice hsp and hsf genes, we examined a glo ...	2009	26493149
establishment of a high efficiency agrobacterium-mediated transformation system of rice (oryza sativa l.).	technologies for transformation of rice have been developed to meet the requirements of functional genomics in order to enable the production of transgenic rice plants with useful agricultural characters. however, many rice varieties are not efficiently transformed by agrobacterium. we have succeeded in establishing a highly efficient transformation system in rice by co-cultivating rice calli with agrobacterium on three filter papers moistened with enriched n6 or dkn media instead of using solid ...	2009	26493142
isolation and expression analysis of ospme1, encoding for a putative pectin methyl esterase from oryza sativa (subsp. indica).	pectin methyl esterases (pmes) play an essential role during plant development by affecting the mechanical properties of the plant cell walls. recent studies indicated that pmes play important role in pollen tube development. in this study, we isolated a 1.3 kb cdna clone from rice panicle cdna library. it contained a 1038 bp of open reading frame (orf) encoding for a putative pectin methyl esterase of 345 aminoacids with a 20 aminoacid signal peptide and was hence designated as ospme1 (oryza sa ...	2009	23572921
international collaborative study of the endogenous reference gene, sucrose phosphate synthase (sps), used for qualitative and quantitative analysis of genetically modified rice.	one rice ( oryza sativa ) gene, sucrose phosphate synthase (sps), has been proven to be a suitable endogenous reference gene for genetically modified (gm) rice detection in a previous study. herein are the reported results of an international collaborative ring trial for validation of the sps gene as an endogenous reference gene and its optimized qualitative and quantitative polymerase chain reaction (pcr) systems. a total of 12 genetically modified organism (gmo) detection laboratories from sev ...	2009	19326953
characterization of glossy1-homologous genes in rice involved in leaf wax accumulation and drought resistance.	the outermost surfaces of plants are covered with an epicuticular wax layer that provides a primary waterproof barrier and protection against different environmental stresses. glossy 1 (gl1) is one of the reported genes controlling wax synthesis. this study analyzed gl1-homologous genes in oryza sativa and characterized the key members of this family involved in wax synthesis and stress resistance. sequence analysis revealed 11 homologous genes of gl1 in rice, designated osgl1-1 to osgl1-11. osg ...	2009	19322663
dehydration-responsive nuclear proteome of rice (oryza sativa l.) illustrates protein network, novel regulators of cellular adaptation, and evolutionary perspective.	water deficit or dehydration is the most crucial environmental constraint on plant growth and development and crop productivity. it has been postulated that plants respond and adapt to dehydration by altering their cellular metabolism and by activating various defense machineries. the nucleus, the regulatory hub of the eukaryotic cell, is a dynamic system and a repository of various macromolecules that serve as modulators of cell signaling dictating the cell fate decision. to better understand t ...	2009	19321431
a major quantitative trait locus controlling cadmium translocation in rice (oryza sativa).	the trait of low cadmium (cd) accumulation in brown rice (oryza sativa) is important for food safety. an effective way to reduce cd accumulation in the grain is to control cd transfer from the roots to the shoots. here, we investigated genotypic variation in the shoot cd concentration among 146 accessions from a rice core collection and performed a quantitative trait locus (qtl) analysis to determine the loci controlling shoot cd accumulation. furthermore, we physiologically characterized the tw ...	2009	19309445
molecular evolution and functional divergence of hak potassium transporter gene family in rice (oryza sativa l.).	the high-affinity k(+) (hak) transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. in the present study, we identified 27 members of this family in rice genome. the phylogenetic tree divided the land plant hak transporter proteins into 6 distinct groups. although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members ...	2009	19302972
efficiency of experimental rice (oryza sativa l.) fields in mitigating diazinon runoff toxicity to hyalella azteca.	this study assessed the viability of using planted, mature rice fields in mitigating diazinon (an organophosphate insecticide) runoff toxicity using aqueous 48 h hyalella azteca whole effluent toxicity bioassays. rice fields decreased diazinon concentrations 80.1%-99.9% compared with 10.8% in the unvegetated field control. h. azteca survival responses coincided with observed diazinon concentrations. estimated lc50 effects dilutions (%) ranged from 1.15 to 1.47 for inflow samples and 1.66 (unvege ...	2009	19290453
osdeg10 encoding a small rna-binding protein is involved in abiotic stress signaling.	excessive light can be harmful to photosynthetic apparatus since it causes photoinhibition and photooxidation, and plants often encounter hypoxic or anoxic environments when they become submerged by heavy rain or an ensuing flood. in this study, oryza sativa differentially expressed genes (osdegs) from rice under photooxidation and anoxia conditions were isolated using dd-pcr. among them, osdeg10 is predicted to encode a small rna-binding protein (rbp) and the transcript levels of osdeg10 strong ...	2009	19285007
a comparative cytogenetic study of the rice (oryza sativa l.) autotetraploid restorers and hybrids.	we studied pollen fertility, seed set and cytogenetic characteristics of restorer lines and f1 hybrids of autotetraploid rice. t4002, t4063, t461a x t4002 and t461a x t4063 showed significantly higher pollen fertility and seed set than t4132 and t461a x t4132. meiotic pairing configurations of t4002, t4063, t4132, t461a x t4002, t461a x t4063 and t461a x t4132 were 0.051 + 19.96ii (9.89 rod + 10.07 ring) + 0.01iii + + 2.00iv, 0.11i + 19.17ii (8.90 rod + 10.37 ring) + 0.09iii + 2.26iv + 0.01vi, 1 ...	2009	19824543
adaptive evolution of chloroplast genomes in ancestral grasses.	the grass family, poaceae, is one of the most successful families among angiosperms. although it has long been suggested that the chloroplast genomes of the poaceae have undergone an elevated evolutionary rate compared to other angiosperms, little was known about the details of this phenomenon. by using chloroplast genome data from 31 seed plants species, we recently showed that episodic rate acceleration occurred in the common ancestral branch of the core poaceae (a clade formed by rice oryza s ...	2009	19820316
a new genetic factor for root gravitropism in rice (oryza sativa l.).	root gravitropism is one of the important factors to determine root architecture. to understand the mechanism underlying root gravitropism, we isolated a rice (xiushui63) mutant defective in root gravitropism, designated as gls1. vertical sections of root caps revealed that gls1 mutant displayed normal distribution of amyloplast in the columella cells compared with the wild type. the gls1 mutant was less sensitive to 2,4-dichlorophenoxyacetic acid (2,4-d) and alpha-naphthaleneacetic acid (naa) t ...	2009	19817003
[dynamic changes of rice (oryza sativa l.) tiller angle under effects of photoperiod and effective accumulated temperature].	using rice variety di508 as test material, a field experiment of different seeding dates and a test with plant growth chamber were conducted to study the dynamic changes of rice tiller angle under effects of different photoperiod and effective accumulated temperature. under field condition, the tiller angle of di508 plants changed gradually into erect after 10-15 days of photoperiod becoming shorter (since the summer solstice on 21st june), irrespective of seeding dates (4th april, 5th may, and ...	2009	19803166
genetic analysis and gene mapping of a new rolled-leaf mutant in rice (oryza sativa l.).	to understand the development of rice leaf blades, we identified a new rolled-leaf mutant, w32, from indica cultivar ir64 through ems mutagenesis. the mutant showed a stable rolled-leaf phenotype throughout the life cycle. two f2 populations were developed by crossing w32 to cultivar ir24 and pa64. genetic analysis showed that the rolled-leaf phenotype was controlled by a single recessive gene. to determine the location of the gene, bulked segregant analysis was carried out using mutant and wild ...	2009	19802748
rice microrna effector complexes and targets.	micrornas (mirnas) are small silencing rnas with regulatory roles in gene expression. mirnas interact with argonaute (ago) proteins to form effector complexes that cleave target mrnas or repress translation. rice (oryza sativa) encodes four ago1 homologs (ago1a, ago1b, ago1c, and ago1d). we used rna interference (rnai) to knock down the four ago1s. the rnai lines displayed pleiotropic developmental phenotypes and had increased accumulation of mirna targets. ago1a, ago1b, and ago1c complexes were ...	2009	19903869
substrate selectivity of glycerol-3-phosphate acyl transferase in rice.	substrate selectivity of glycerol-3-phosphate acyltransferase (ec 2. 3. 1. 15) of rice (oryza sativa l.) was explored in a comparative study of acyltransferases from seven plant species. in vitro labeling of acyl carrier protein (acp) with (14)c or (3)h showed that acyltransferase from chill-sensitive plants, such as rice that uses either oleic (18:1) or palmitic acid (16:0) as acyl donor at comparable rates, displays lower selectivity than the enzyme from chill-resistant plants, such as spinach ...	2009	19903225
overexpression of rice (oryza sativa l.) oscdr1 leads to constitutive activation of defense responses in rice and arabidopsis.	plant aspartic proteases (ap) play key roles in the regulation of biological processes, such as the recognition of pathogens and pests and the induction of effective defense responses. a large number of ap (>400) have been identified in silico in the rice genome. none have previously been isolated and functionally characterized for their involvement in disease resistance. we describe here the isolation and characterization of a gene (oscdr1) from rice which encodes a predicted aspartate protease ...	2009	19888828
diversity of the ty-1 copia retrotransposon tos17 in rice (oryza sativa l.) and the aa genome of the oryza genus.	retrotransposons are mobile genetic elements, ubiquitous in eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. we investigate here the diversity of the ty1-copia retrotransposon tos17 in the cultivated rice of asian origin (oryza sativa l.) and related aa genome species of the oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element ...	2009	19856189
structure and expression of osubp6, an ubiquitin-specific protease 6 homolog in rice (oryza sativa l.).	although the possible cellular roles of several ubiquitin-specific proteases (ubps) were identified in arabidopsis, almost nothing is known about ubp homologs in rice, a monocot model plant. in this report, we searched the rice genome database ( http://signal.salk.edu/cgi-bin/ricege ) and identified 21 putative ubp family members (osubps) in the rice genome. these osubp genes each contain a ubiquitin carboxyl-terminal hydrolase (uch) domain with highly conserved cys and his boxes and were subdiv ...	2009	19855938
osbadh1 is possibly involved in acetaldehyde oxidation in rice plant peroxisomes.	although rice (oryza sativa l.) produces little glycine betaine (gb), it has two betaine aldehyde dehydrogenase (badh; ec 1.2.1.8) gene homologs (osbadh1 and osbadh2). we found that osbadh1 catalyzes the oxidation of acetaldehyde efficiently, while the activity of osbadh2 is extremely low. the accumulation of osbadh1 mrna decreases following submergence treatment, but quickly recovers after re-aeration. we confirmed that osbadh1 localizes in peroxisomes. in this paper, a possible physiological f ...	2009	19850038
multiple gene loci affecting genetic background-controlled disease resistance conferred by r gene xa3/xa26 in rice.	the function of bacterial-blight resistance gene xa3/xa26 in rice is influenced by genetic background; the oryza sativa l. ssp. japonica background can increase xa3/xa26 expression, resulting in an enhanced resistance. to identify whether xa3/xa26 transcript level is the only factor contributing to genetic background-controlled resistance, we screened an f(2) population that was developed from a cross between oryza sativa l. ssp. indica and japonica rice lines and was segregating for xa3/xa26, a ...	2009	19826775
expression of pin genes in rice (oryza sativa l.): tissue specificity and regulation by hormones.	twelve genes of the pin family in rice were analyzed for gene and protein structures and an evolutionary relationship with reported atpins in arabidopsis. four members of pin1 (designated as ospin1a-d), one gene paired with atpin2 (ospin2), three members of pin5 (ospin5a-c), one gene paired with atpin8 (ospin8), and three monocot-specific pins (ospin9, ospin10a, and b) were identified from the phylogenetic analysis. tissue-specific expression patterns of nine pin genes among them were investigat ...	2009	19825657
do genetic recombination and gene density shape the pattern of dna elimination in rice long terminal repeat retrotransposons?	in flowering plants, the accumulation of small deletions through unequal homologous recombination (ur) and illegitimate recombination (ir) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (ltr-rts). however, the full suite of evolutionary forces that govern the gain or loss of transposable elements (tes) and their distribution within a genome remains unclear. here, we investigated ...	2009	19789376
rice cytosine dna methyltransferases - gene expression profiling during reproductive development and abiotic stress.	dna methylation affects important developmental processes in both plants and animals. the process of methylation of cytosines at c-5 is catalysed by dna methyltransferases (mtases), which are highly conserved, both structurally and functionally, in eukaryotes. in this study, we identified and characterized cytosine dna mtase genes that are activated with the onset of reproductive development in rice. the rice genome (oryza sativa l. subsp. japonica) encodes a total of 10 genes that contain the h ...	2009	19788421
high frequency plant regeneration from embryogenic callus of a popular indica rice (oryza sativa l.).	the aim of the study is to establish a routine procedure for high frequency plant regeneration from in vitro raised embryogenic callus of abiotic salt sensitive indica rice (oryza sativa l.) cultivar adt 43. the effect of synthetic auxin 2,4-d on callus induction was optimized to achieve high frequency plant regeneration from fresh embryogenic callus without further subculture. friable, nodular and creamish-white embryogenic callus cultures were raised from mature rice seeds on ls medium supplem ...	2009	23572948
gas exchange variability and water use efficiency of thirty landraces of rice still under cultivation in kumaun region of the indian central himalaya.	gas exchange characteristics of thirty landraces of rice (oryza sativa l.) along with an introduced variety vl-206 (recommended high yielding variety for rainfed uplands of the indian central himalaya, ich), grown in earthen pots and kept in the open at the institute nursery at kosi (1150m amsl, 79°38'10″e and 29°38'15″n) were studied. the photosynthetic rate (pn) and other related parameters were found to vary considerably among landraces. based on the comparison of pn of landraces with that of ...	2009	23572940
in silico analysis of motifs in promoters of differentially expressed genes in rice (oryza sativa l.) under anoxia.	the aim of this study was to characterise the molecular mechanisms of transcriptional regulation of differentially expressed genes (degs) in rice coleoptiles under anoxia by identifying motifs that are common in the promoter region of co-regulated genes. un-changed degs (<2 fold and >-2), up-regulated degs (>or=2 fold) and down-regulated degs (<or=-2 fold) were separated in three different data sets. their gene promoters were extracted from eukaryotic promoter database. statistically significant ...	2009	19778868
differential ozone sensitivity of rice cultivars as indicated by visible injury and grain yield.	surface ozone pollution may cause reductions in rice (oryza sativa l.) yield. ozone sensitivity in rice cultivars is often evaluated based on visible leaf injury at an early growth stage. however, it is not clear whether reduction in grain yield is related to visible injury. therefore, visible damage and grain yield reduction were examined in japanese and asian rice cultivars exposed to ozone. in experiment 1, 3-week-old rice seedlings were exposed to ozone (min.: 20 nl.l(-1), max.:120 nl.l(-1)) ...	2009	19778370
rice cellulose synthase-like d4 is essential for normal cell-wall biosynthesis and plant growth.	cellulose synthase-like (csl) proteins of glycosyltransferase family 2 (gt2) are believed to be involved in the biosynthesis of cell-wall polymers. the csl d sub-family (csld) is common to all plants, but the functions of cslds remain to be elucidated. we report here an in-depth characterization of a narrow leaf and dwarf1 (nd1) rice mutant that shows significant reduction in plant growth due to retarded cell division. map-based cloning revealed that nd1 encodes oscsld4, one of five members of t ...	2009	19765235
apoplastic barriers effectively block oxygen permeability across outer cell layers of rice roots under deoxygenated conditions: roles of apoplastic pores and of respiration.	despite the importance of the barrier to oxygen losses of the roots of hygrophytes growing in wet environments devoid of oxygen, there are few data available on permeability coefficients for o(2) across outer root cell layers (p(opr)) and how they may change in response to low o(2). a gas perfusion technique was used to measure the p(opr) of rice (oryza sativa) plants grown in either aerated or deoxygenated solution. the contributions of the apoplast and of living cells to the overall p(opr) w ...	2009	19765231
identification and characterization of a novel waxy allele from a yunnan rice landrace.	low amylose content (ac) is a desirable trait for rice (oryza sativa l.) cooking quality and is selected in soft rice breeding. to gain a better understanding of the molecular mechanism controlling ac formation, we screened 83 yunnan rice landraces in china and identified a rice variety, haopi, with low ac. genetic analyses and transgenic experiments revealed that low ac in haopi was controlled by a novel allele of the wx locus, wx(hp), encoding a granule-bound starch synthase (gbssi). sequence ...	2009	19760367
structural characterization and expression analysis of the serk/serl gene family in rice (oryza sativa).	somatic embryogenesis (se) is the developmental restructuring of somatic cells towards the embryogenic pathway and forms the basis of cellular totipotency in angiosperms. with the availability of full-length cdna sequences from knowledge-based oryza molecular biological encylopedia (kome), we identified the leucine-rich repeat receptor-like kinase (lrr-rlk) genes from rice (oryza sativa), which also encompasses genes involved in regulating somatic embryogenesis. eight out of eleven of the rice s ...	2009	19756234
evolution of agl6-like mads box genes in grasses (poaceae): ovule expression is ancient and palea expression is new.	agamous-like6 (agl6) genes encode mikc-type mads box transcription factors and are closely related to sepallata and ap1/ful-like genes. here, we focus on the molecular evolution and expression of the agl6-like genes in grasses. we have found that agl6-like genes are expressed in ovules, lodicules (second whorl floral organs), paleas (putative first whorl floral organs), and floral meristems. each of these expression domains was acquired at a different time in evolution, indicating that each repr ...	2009	19749151
phytochrome-mediated growth inhibition of seminal roots in rice seedlings.	in rice (oryza sativa) seedlings, continuous white-light irradiation inhibited the growth of seminal roots but promoted the growth of crown roots. in this study, we examined the mechanisms of photoinhibition of seminal root growth. photoinhibition occurred in the absence of nitrogen but increased with increasing nitrogen concentrations. in the presence of nitrogen, photoinhibition was correlated with coiling of the root tips. the seminal roots were most photosensitive 48-72 h after germination d ...	2009	19744160
the rice transcription factor idef1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes.	higher plants maintain iron homeostasis by regulating the expression of iron (fe)-related genes in accordance with fe availability. the transcription factor idef1 regulates the response to fe deficiency in oryza sativa (rice) by recognizing catgc sequences within the fe deficiency-responsive cis-acting element ide1. to investigate the function of idef1 in detail, we analyzed the response to fe deficiency in transgenic rice plants exhibiting induced or repressed idef1 expression. fe-deficiency tr ...	2009	19737364
resistance mechanism in rice to the midge orseolia oryzae (diptera: cecidomyiidae).	the midge orseolia oryzae (wood-mason) (diptera: cecidomyiidae) is a major and endemic pest throughout asia. the pest is difficult to manage in view of a mixture of biotypes co-occurring in the same location and showing variable response to cultivated rice, oryza sativa l., varieties and differentials. to develop an understanding of the resistance mechanism(s), studies were initiated during wet 2005 and 2006 in coastal karnataka. antibiosis was the predominant resistance category. the maggots su ...	2009	19736778
spectral response of rice (oryza sativa l.) leaves to fe(2+) stress.	in the management of lake eutrophication, the regulation effect of fe is considered, in addition to the controlling nitrogen- and phosphorus input. based on the "fe hypothesis", this paper tentatively applied plant spectral response to the remote sensing early-warning mechanism of lake eutrophication. a laboratory water culture experiment with rice (oryza sativa l.) was conducted to study fe uptake by plants and the chlorophyll concentration and visible-near infrared spectrum of vegetable leaves ...	2009	19727593
correlation and quantitative trait loci analyses of total chlorophyll content and photosynthetic rate of rice (oryza sativa) under water stress and well-watered conditions.	in order to explore the relevant molecular genetic mechanisms of photosynthetic rate (pr) and chlorophyll content (cc) in rice (oryza sativa l.), we conducted a series of related experiments using a population of recombinant inbred lines (zhenshan97b x irat109). we found a significant correlation between cc and pr (r= 0.19**) in well-watered conditions, but no significant correlation during water stress (r= 0.08). we detected 13 main quantitative trait loci (qtls) located on chromosomes 1, 2, 3, ...	2009	19723247
differences in expression of the rbcs multigene family and rubisco protein content in various rice plant tissues at different growth stages.	four out of five members of the rbcs multigene family (osrbcs2-osrbcs5) were highly expressed in leaf blades of rice (oryza sativa l.) irrespective of plant growth stage, whereas accumulation of all rbcs mrnas in leaf sheaths, roots and developing spikelets was quite low. a highly positive correlation was observed between total rbcs and rbcl mrna levels and rubisco content at their maxima, irrespective of tissue and growth stage. the results indicate that the total rbcs mrna level may be a prima ...	2009	19720627
phytochromes are the sole photoreceptors for perceiving red/far-red light in rice.	phytochromes are believed to be solely responsible for red and far-red light perception, but this has never been definitively tested. to directly address this hypothesis, a phytochrome triple mutant (phyaphybphyc) was generated in rice (oryza sativa l. cv. nipponbare) and its responses to red and far-red light were monitored. since rice only has three phytochrome genes (phya, phyb and phyc), this mutant is completely lacking any phytochrome. rice seedlings grown in the dark develop long coleopti ...	2009	19706555
the origin and evolution of fragrance in rice (oryza sativa l.).	fragrance in the grain is one of the most highly valued grain quality traits in rice, yet the origin and evolution of the betaine aldehyde dehydrogenase gene (badh2) underlying this trait remains unclear. in this study, we identify eight putatively nonfunctional alleles of the badh2 gene and show that these alleles have distinct geographic and genetic origins. despite multiple origins of the fragrance trait, a single allele, badh2.1, is the predominant allele in virtually all fragrant rice varie ...	2009	19706531
[application of competitive pcr for screening selectable marker-free xa21 transgenic rice].	polymerase chain reaction (pcr) is a simple, quick and highly sensitive method. however the accuracy of the conventional pcr assay was often affected by false positives and false negatives. in this study, a protocol competitive pcr was used to reduce the false results in screening for selectable marker-free (smf) xa2l transgenic rice plants. the competitive template of xa21 was the endogenous xa2l homologous sequence located on chromosome 11. the competitive template of the selectable marker gen ...	2009	19637639
exogenous nitric oxide enhances cadmium tolerance of rice by increasing pectin and hemicellulose contents in root cell wall.	to study the mechanisms of exogenous no contribution to alleviate the cadmium (cd) toxicity in rice (oryza sativa), rice plantlets subjected to 0.2-mm cdcl(2) exposure were treated with different concentrations of sodium nitroprusside (snp, a no donor), and cd toxicity was evaluated by the decreases in plant length, biomass production and chlorophyll content. the results indicated that 0.1 mm snp alleviated cd toxicity most obviously. atomic absorption spectrometry and fluorescence localization ...	2009	19626338
amyloplast division progresses simultaneously at multiple sites in the endosperm of rice.	the amyloplast, a form of differentiated plastid, proliferates in sink tissues, where it synthesizes and stores starch granules. little is known about the molecular mechanism for amyloplast division and development. the rice (oryza sativa) endosperm provides an excellent model system for studying molecular mechanisms involved in amyloplast division and starch synthesis. we compared amyloplast division processes in the endosperm of wild type and a mutant of arc5, a member of the dynamin superfami ...	2009	19622530
comprehensive metabolite profiling of phya phyb phyc triple mutants to reveal their associated metabolic phenotype in rice leaves.	the phytochrome photoreceptors regulate plant growth and development throughout their life cycle. rice (oryza sativa) possesses three phytochromes, phya, phyb, and phyc. physiological, genetic, and biochemical analyses of null mutants of each phytochrome have revealed the function of each in rice. however, few studies have investigated the relationship between phytochrome signaling and metabolism. in the present study, non-targeted metabolite analysis by gas chromatography time-of-flight mass sp ...	2009	19619864
identification and characterization of pseudogenes in the rice gene complement.	the osa1 genome annotation of rice (oryza sativa l. ssp. japonica cv. nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes. as such, it is likely to mis-annotate pseudogenes as functional genes. a total of 22,033 gene models within the osa1 release 5 were investigated as potential pseudogenes as these genes exhibit at least one feature potentially indicative of pseudogenes: lack of transcript support, short coding region, long untranslated region, ...	2009	19607679
physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings.	the antagonistic interaction between iron (fe) and phosphorus (p) has been noted in the area of plant nutrition. to understand the physiology and molecular mechanisms of this interaction, we studied the growth performance, nutrient concentration, and gene expression profiles of root and shoot segments derived from 10-d-old rice (oryza sativa) seedlings under four different nutrient conditions: (1) full strength of fe and p (+fe+p); (2) full strength of p and no fe (-fe+p); (3) full strength of f ...	2009	19605549
effects of active silicon uptake by rice on 29si fractionation in various plant parts.	rice (oryza sativa l.) accumulates large amounts of silicon which improves its growth and health due to enhanced resistance to biotic and abiotic stresses. silicon uptake and loading to xylem in rice are predominantly active processes performed by transporters encoded by the recently identified genes lsi1 (si influx transporter gene) and lsi2 (si efflux transporter gene). silicon deposition in rice during translocation to upper plant tissues is known to discriminate against the heavier isotopes ...	2009	19603477
dwarf 88, a novel putative esterase gene affecting architecture of rice plant.	rice architecture is an important agronomic trait that affects grain yield. we characterized a tillering dwarf mutant d88 derived from oryza sativa ssp. japonica cultivar lansheng treated with ems. the mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. a reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant. the d88 gene w ...	2009	19603144
[substitution mapping of qtl for panicle exertion using cssl in rice (oryza sativa l.)].	panicle exertion, the distance between the leaf cushion of flag and the neck-panicle node, is an important morphological trait, which has significant impact on hybrid seed production of rice. in this study, 94 chromosome segment substitution lines (cssl), derived from 9311/nipponbare with 9311 as the recurrent parent, were used to analyze quantitative trait loci (qtl) controlling the panicle exertion. the results showed that 17 cssl contained qtl for the panicle exertion. using substitution mapp ...	2009	19586880
[genetic analysis and mapping of high-tillering and dwarf mutant htd1-2 in rice].	tillering is one of the most important agronomic traits of rice. in order to explore the molecular mechanism of rice tillering, a high-tillering dwarf 1-2 (htd1-2) mutant was isolated from the offspring of the indica rice (oryza sativa l. ssp. indica) variety 9311 treated with 350gy 60co gamma-radiation. genetic analysis showed that both high tillering and dwarf phenotypes of htd1-2 were controlled by a single recessive nuclear gene. by means of molecular marker technique, the high-tillering dwa ...	2009	19586849
the effect of salinity on morphological characteristics of seven rice (oryza sativa) genotypes differing in salt tolerance.	the effect of salinity on morphological characters of salt tolerant genotypes pvsb9, pvsb19, pnr381, pnr519, iratom24 and salt sensitive genotype ns15 along with one standard check salt tolerant rice cultivar pokkali were assessed in two factors completely randomized design with four replications. seven rice genotypes in combination with six levels of salinity (0, 3, 6, 9, 12 and 15 ds m(-1)) were randomly assigned in 168 experimental plastic pots. the different morphological characters studied ...	2009	19579979
defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings.	analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. this may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. in order to dissect out these responses, the effect of the presen ...	2009	19571305
regulation of osspx1 and osspx3 on expression of osspx domain genes and pi-starvation signaling in rice.	the rice (oryza sativa l.) genome contains at least six genes exclusively with an spx (syg1/pho81/xpr1) domain at the n-terminal, designated as osspx1-6. here we report the diverse expression patterns of the osspx genes in different tissues and their responses to pi-starvation. among them, five genes, osspx1, 2, 3, 5 and 6 are responsive to pi-starvation in shoots and/or in roots. the subcellular localization analysis indicates that osspx1 and osspx2 is exclusively located in nucleus, osspx3 in ...	2009	19566645
nitrate assimilatory enzymes of spirulina (arthospira) platensis are more thermotolerant than those of rice.	in order to assess the potential of spirulina (arthospira) platensis as a source of abundant, thermostable nitrate assimilatory enzymes, the specific activities and thermal tolerance of nitrate reductase (nr), nitrite reductase (nir) and glutamine synthetase (gs) were compared with those of rice in crude extracts in vitro. the results show that spirulina enzymes have relatively higher thermotolerance. when the extracts were pre-exposed to 80 °c for 1 hr, spirulina enzymes retained higher activit ...	2009	23572937
dynamic bridges--a calponin-domain kinesin from rice links actin filaments and microtubules in both cycling and non-cycling cells.	interaction and cross-talk between microtubules and actin microfilaments are important for the cell axis and polarity during plant cell growth and development, but little is known about the molecular components of this interaction. plant kinesins with a calponin-homology domain (kchs) were recently identified and associated with a putative role in microtubule-microfilament cross-linking. kchs belong to a distinct branch of the minus end-directed kinesin subfamily and so far have only been identi ...	2009	19561334
a novel carotenoid derivative, lutein 3-acetate, accumulates in senescent leaves of rice.	the biosynthetic pathway of lutein, the most abundant carotenoid in leaves, has been extensively studied, while its degradation pathway during senescence is poorly understood. we found that a novel carotenoid derivative, lutein 3-acetate, accumulates in senescent leaves of rice (oryza sativa l.). the change in contents of lutein and lutein 3-acetate suggests that lutein is converted to lutein 3-acetate during senescence. analysis of mutants involved in light-harvesting complex ii (lhcii) accumul ...	2009	19561331
oshal3 mediates a new pathway in the light-regulated growth of rice.	plants show distinct morphologies in different light conditions through a process called photomorphogenesis. a predominant feature of photomorphogenesis is the reduced growth of seedlings under light conditions compared with darkness. for this adaptive event, the most well-known molecular mechanism involves photoreceptor-mediated inhibition of cell elongation. however, it is not known whether additional pathways exist. here, we describe a newly discovered pathway of light-modulated plant growth ...	2009	19543273
transcriptional regulation of wheat ver2 promoter in rice in response to abscisic acid, jasmonate, and light.	ver2 is a key gene associated with vernalization process in winter wheat. the expression of ver2 can be induced by low temperature treatment. to further understand how the expression of this gene is mediated by various external and internal factors, different lengths of the ver2 promoter region have been transcriptionally fused with a reporter gene, green fluorescence protein (gfp), and transformed into the model plant, rice (oryza sativa l.). using confocal and western blot analyses, we determi ...	2009	19539247
comparative analysis of anoxic coleoptile elongation in rice varieties: relationship between coleoptile length and carbohydrate levels, fermentative metabolism and anaerobic gene expression.	rice (oryza sativa l.) seeds can germinate under anoxia and can show coleoptile elongation. the anoxic coleoptile is usually longer than aerobic coleoptiles. although several hypotheses have been proposed to explain the ability of rice to elongate coleoptiles under anoxia, conclusive experimental evidence explaining this physiological trait is lacking. in order to investigate whether metabolic and molecular markers correlate with anoxic coleoptile length, we screened 141 italian and 23 sri lanka ...	2009	19538394
gene flow from weedy red rice (oryza sativa l.) to cultivated rice and fitness of hybrids.	gene transfer from weeds to crops could produce weedy individuals that might impact upon the evolutionary dynamics of weedy populations, the persistence of escaped genes in agroecosystems and approaches to weed management and containment of transgenic crops. the present aim was to quantify the gene flowrate from weedy red rice to cultivated rice, and evaluate the morphology, phenology and fecundity of resulting hybrids. field experiments were conducted at stuttgart and rohwer, arkansas, usa. twe ...	2009	19530257
evaluation of seven function-known candidate genes for their effects on improving drought resistance of transgenic rice under field conditions.	many stress responsive genes have been reported with an effect on improving stress resistance in model plants under greenhouse conditions. towards identification of genes for drought resistance breeding, seven well documented genes (cbf3, sos2, nced2, npk1, los5, zat10, and nhx1) in stress resistance were selected in this study and transformed into rice cultivar zhonghua 11 under the control of constitutive promoter actin1 and stress-inducible promoter of a rice hva22 homolog, and transgenic ric ...	2009	19529831
new changes in the plasma-membrane-associated proteome of rice roots under salt stress.	to gain a better understanding of salt stress responses in plants, we used a proteomic approach to investigate changes in rice (oryza sativa) root plasma-membrane-associated proteins following treatment with 150 mmol/l nacl. with or without a 48 h salt treatment, plasma membrane fractions from root tip cells of a salt-sensitive rice cultivar, wuyunjing 8, were purified by peg aqueous two-phase partitioning, and plasma-membrane-associated proteins were separated by ief/sds-page using an optimized ...	2009	19526560
sequence and expression analysis of the c3hc4-type ring finger gene family in rice.	c3hc4-type ring finger genes comprise a large family in the plant kingdom and play important roles in various physiologic processes of plant life. in this study, we identified 29 c3hc4-type ring finger family genes in rice (oryza sativa) by database search. motif analysis revealed the presence of three conserved motifs with unknown functions within the predicted proteins. promoter analysis found 196 cis-elements in the 2-kb upstream regions of these genes, including a stress-responsive element, ...	2009	19523506
host manipulation by the orange leafhopper cicadulina bipunctata: gall induction on distant leaves by dose-dependent stimulation.	the evolution of the gall-inducing ability in insects and the adaptive significance of the galling habit have been addressed by many studies. cicadulina bipunctata, the maize orange leafhopper, is an ideal study organism for evaluating these topics because it can be mass-reared and it feeds on model plants such as rice (oryza sativa) and maize (zea mays). to reveal differences between gall inductions by c. bipunctata and other gall inducers, we conducted four experiments concerning (a) the relat ...	2009	19513593
identification of cis-localization elements of the maize 10-kda delta-zein and their use in targeting rnas to specific cortical endoplasmic reticulum subdomains.	the rnas for the storage proteins of rice (oryza sativa), prolamines and glutelins, which are stored as inclusions in the lumen of the endoplasmic reticulum (er) and storage vacuoles, respectively, are targeted by specific cis-localization elements to distinct subdomains of the cortical er. glutelin rna has one or more cis-localization elements (zip codes) at the 3' end of the rna, whereas prolamine has two cis-elements; one located in the 5' end of the coding sequence and a second residing in t ...	2009	19508424
identification of quantitative trait loci for rice quality in a population of chromosome segment substitution lines.	the demand for high quality rice represents a major issue in rice production. the primary components of rice grain quality include appearance, eating, cooking, physico-chemical, milling and nutritional qualities. most of these traits are complex and controlled by quantitative trait loci (qtls), so the genetic characterization of these traits is more difficult than that of traits controlled by a single gene. the detection and genetic identification of qtls can provide insights into the genetic me ...	2009	19508361
elemental content in brown rice by inductively coupled plasma atomic emission spectroscopy reveals the evolution of asian cultivated rice.	the phylogenetic relationship for classification traits and eight mineral elements in brown rice (oryza sativa l.) from yunnan province in china was carried out using microwave assisted digestion followed by inductively coupled plasma atomic emission spectroscopy, and the analytical procedures were carefully controlled and validated. in general, the results show that the mean levels of k, ca, mg, fe and cu in brown rice for 789 accessions of rice landraces was distinctly lower than that of impro ...	2009	19508358
evolutionary history of gs3, a gene conferring grain length in rice.	unlike maize and wheat, where artificial selection is associated with an almost uniform increase in seed or grain size, domesticated rice exhibits dramatic phenotypic diversity for grain size and shape. here we clone and characterize gs3, an evolutionarily important gene controlling grain size in rice. we show that gs3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering, and we use genetic transformation to de ...	2009	19506305
identification of a novel gene ef7 conferring an extremely long basic vegetative growth phase in rice.	a late heading-time mutant line, hs276, which was induced by gamma-irradiation of seeds of the japonica rice (oryza sativa l.) variety gimbozu, exhibits an extremely long basic vegetative growth phase (bvp). a genetic analysis using the f(2) population from the cross between hs276 and gimbozu revealed that the late heading of hs276 is governed by a single recessive mutant gene. the subsequent analysis on heading responses of hs276 and gimbozu to four photoperiods (12, 13, 14, and 15 h) and to th ...	2009	19495721
molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability.	inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. it remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked.	2009	19476655
compensation and interaction between risbz1 and rpbf during grain filling in rice.	the rice (oryza sativa l.) basic leucine zipper factor risbz1 and rice prolamin box binding factor (rpbf) are transcriptional activators of rice seed storage protein (ssp) genes in vivo. to ascertain the functions of these trans-activators in seed development, knock-down (kd) transgenic rice plants were generated in which the accumulation of risbz1 and rpbf was reduced in an endosperm-specific manner by co-suppression (kd-risbz1 and kd-rpbf). the accumulation of most ssps changed little between ...	2009	19473328
crystal structure of a class xib phospholipase a2 (pla2): rice (oryza sativa) isoform-2 pla2 and an octanoate complex.	phospholipase a(2) catalyzes the specific hydrolysis of the sn-2 acyl bond of various glycerophospholipids, producing fatty acids and lysophospholipids. phospholipase a(2)s (pla(2)s) constitute a large superfamily of enzymes whose products are important for a multitude of signal transduction processes, lipid mediator release, lipid metabolism, development, plant stress responses, and host defense. the crystal structure of rice (oryza sativa) isoform 2 phospholipase a(2) has been determined to 2. ...	2009	19457861
g-string slippage turns white rice red.	the mutations that convey the white pericarp phenotype to rice (oryza sativa subsp. japonica) are in a regulatory gene, rc. we have identified a genetic difference between the cultivar 'perla' and its natural red rice mutant 'perla rosso' in the rc gene. the deletion of a g base restores the reading frame for the rc gene, lost by the original 14 bp deletion that gave rise to white rice.	2009	19448729
effect of physical desiccation on plant regeneration efficiency in rice (oryza sativa l.) variety super basmati.	this experiment assessed the effect of partial physical desiccation on plant regeneration efficiency in scutellum-derived embryogenic calluses of rice (oryza sativa l.) variety super basmati. a number of callusing cultures were developed, and efficient callus induction was observed on ms (murashige and skoog) basal medium supplemented with 2.0mg/l 2,4-dichlorophenoxy acetic acid. the calluses were proliferated on the same medium for 3 weeks and then shifted to dehydration desiccation treatment f ...	2009	19446363
functional and chemical comparison of apoplastic barriers to radial oxygen loss in roots of rice (oryza sativa l.) grown in aerated or deoxygenated solution.	radial oxygen loss (rol) and root porosity of rice (oryza sativa l.) plants grown in either aerated or deoxygenated (stagnant) conditions were combined for the first time with extensive histochemical and biochemical studies of the apoplastic barriers in the roots' peripheral cell layers. growth in stagnant solution significantly affected structural and, consequently, the physiological features of rice roots. it increased adventitious root porosity by about 20% and decreased the rol towards the b ...	2009	19443620
na(+) but not cl(-) or osmotic stress is involved in nacl-induced expression of glutathione reductase in roots of rice seedlings.	glutathione reductase (gr, ec 1,6.4.2) is an important reactive oxygen species-scavenging enzyme. the present study examined the relative importance of na(+), cl(-), and the osmotic component in nacl-induced expression of oryza sativa glutathione reductase (osgr) genes in rice roots. semi-quantitative rt-pcr was used to quantify the mrna levels for one cytosolic (osgr2) and two chloroplastic (osgr1 and osgr3) isoforms of gr identified in the rice genome. the expression of osgr2 and osgr3 but not ...	2009	19423186
qtl detection of rice grain quality traits by microsatellite markers using an indica rice (oryza sativa l.) combination.		2009	19417548
unintended consequence of plant transformation: biolistic transformation caused transpositional activation of an endogenous retrotransposon tos17 in rice ssp. japonica cv. matsumae.	genetic instability could be provoked as an unintended consequence of genetic engineering in plants. here, we report that the rice endogenous long terminal repeat (ltr) retrotransposon tos17 was transpositionally activated only in transgenic calli and their regenerated plants produced by biolistic transformation in rice (oryza sativa l.) ssp. japonica cv. matsumae. moreover, the transpositional activity of tos17 was sustained after plant regeneration in the t0 generation, and produced new germin ...	2009	19415284
how large is the metabolome? a critical analysis of data exchange practices in chemistry.	calculating the metabolome size of species by genome-guided reconstruction of metabolic pathways misses all products from orphan genes and from enzymes lacking annotated genes. hence, metabolomes need to be determined experimentally. annotations by mass spectrometry would greatly benefit if peer-reviewed public databases could be queried to compile target lists of structures that already have been reported for a given species. we detail current obstacles to compile such a knowledge base of metab ...	2009	19415114
aspartic proteases gene family in rice: gene structure and expression, predicted protein features and phylogenetic relation.	aspartic proteases constitute a large family in eukaryotes, which play fundamental roles in protein processing, maturation and degradation. in this study, we identified 96 osap genes in rice (oryza sativa l.), the model plant for monocots, by a reiterative database search. the analysis of the complete set of osap genes is presented, including chromosomal location, phylogenetic relationships, classification and gene structure. moreover, a comprehensive expression analysis of osap family genes was ...	2009	19409457
identification and characterization of the erect-pose panicle gene ep conferring high grain yield in rice (oryza sativa l.).	the breeding of japonica varieties with erect-pose panicle (ep) has recently progressed in the northern part of china, because these varieties exhibit a far higher grain yield than the varieties with normal-pose panicle (np). a genetic analysis using the f(2) population from the cross between liaojing5, the first japonica ep variety in china, and the japanese japonica np variety toyonishiki revealed that ep is governed by a single dominant gene ep. based on previous studies, map-based cloning of ...	2009	19407986
rslpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information.	the attainment of complete map-based sequence for rice (oryza sativa) is clearly a major milestone for the research community. identifying the localization of encoded proteins is the key to understanding their functional characteristics and facilitating their purification. our proposed method, rslpred, is an effort in this direction for genome-scale subcellular prediction of encoded rice proteins. first, the support vector machine (svm)-based modules have been developed using traditional amino a ...	2009	19402042
the effect of sucrose and abscisic acid interaction on sucrose synthase and its relationship to grain filling of rice (oryza sativa l.).	rice grain filling is a process of conversion of sucrose into starch catalysed by a series of enzymes. sucrose synthase (sus) is considered as a key enzyme regulating this process. this study investigated the possible roles of sucrose and abscisic acid (aba) in mediating the activity and expression of sus protein of grains during grain filling in rice (oryza sativa). field-grown rice plants and detached cultured panicles were used as experimental materials. several treatments, including spikelet ...	2009	19401410
ultra low-dose radiation: stress responses and impacts using rice as a grass model.	we report molecular changes in leaves of rice plants (oryza sativa l. - reference crop plant and grass model) exposed to ultra low-dose ionizing radiation, first using contaminated soil from the exclusion zone around chernobyl reactor site. results revealed induction of stress-related marker genes (northern blot) and secondary metabolites (lc-ms/ms) in irradiated leaf segments over appropriate control. second, employing the same in vitro model system, we replicated results of the first experimen ...	2009	19399245
light-saturated photosynthetic rate in high-nitrogen rice (oryza sativa l.) leaves is related to chloroplastic co2 concentration.	to identify the effect of nitrogen (n) nutrition on photosynthetic efficiency and mesophyll conductance of rice seedlings (oryza sativa l., cv. 'shanyou 63' hybrid indica china), hydroponic experiments with different concentrations of n were conducted in a greenhouse. although leaf n concentration on a dry mass basis increased with increasing supply of n, no significant differences in seedling biomass were observed. a higher light-saturated co(2) assimilation rate (a) with a high concentration o ...	2009	19395387
ectopic expression of a cold-responsive osasr1 cdna gives enhanced cold tolerance in transgenic rice plants.	the osasrt cdna clone was isolated from a cdna library prepared from developing seed coats of rice (oryza sativa l.). low-temperature stress increased mrna levels of osasr1 in both vegetative and reproductive organs. in situ analysis showed that osasr1 transcript was preferentially accumulated in the leaf mesophyll tissues and parenchyma cells of the palea and lemma. for transgenic rice plants that over-expressed full-length osasr1 cdna in the sense orientation, the fv/fm values for photosynthet ...	2009	19390826
highly sensitive and high-throughput analysis of plant hormones using ms-probe modification and liquid chromatography-tandem mass spectrometry: an application for hormone profiling in oryza sativa.	we have developed a highly sensitive and high-throughput method for the simultaneous analysis of 43 molecular species of cytokinins, auxins, aba and gibberellins. this method consists of an automatic liquid handling system for solid phase extraction and ultra-performance liquid chromatography (uplc) coupled with a tandem quadrupole mass spectrometer (qms/ms) equipped with an electrospray interface (esi; uplc-esi-qms/ms). in order to improve the detection limit of negatively charged compounds, su ...	2009	19369275