Publications

the central element protein zep1 of the synaptonemal complex regulates the number of crossovers during meiosis in rice.	zep1, a transverse filament (tf) protein, is the rice (oryza sativa) homolog of arabidopsis thaliana zyp1. in the tos17-insertional zep1 mutants, homologous chromosomes align along the entire length of the chromosome, but the synaptonemal complex is not assembled in early prophase i. crossovers are well formed, and 12 bivalents could be detected from diakinesis to metaphase i, which leads to equal chromosomal segregation in anaphase i. moreover, the number of crossovers has a tendency to be incr ...	2010	20154151
the role of the rice aquaporin lsi1 in arsenite efflux from roots.	when supplied with arsenate (as(v)), plant roots extrude a substantial amount of arsenite (as(iii)) to the external medium through as yet unidentified pathways. the rice (oryza sativa) silicon transporter lsi1 (osnip2;1, an aquaporin channel) is the major entry route of arsenite into rice roots. whether lsi1 also mediates arsenite efflux was investigated. expression of lsi1 in xenopus laevis oocytes enhanced arsenite efflux, indicating that lsi1 facilitates arsenite transport bidirectionally. ...	2010	20163552
variations in heavy metal accumulation, growth and yield of rice plants grown at different sewage sludge amendment rates.	use of sewage sludge in agriculture is an alternative disposal technique for this waste. the present field study was conducted to assess the suitability of sewage sludge amendment in soil for rice (oryza sativa l. cv. pusa sugandha 3) by evaluating the heavy metal accumulation, growth, biomass and yield responses of plants grown at 0, 3, 4.5, 6, 9, 12 kgm(-2) sewage sludge amendment (ssa) rate. sewage sludge amendment modified the physico-chemical properties of soil, thus increasing the availabi ...	2010	20163857
massive gene losses in asian cultivated rice unveiled by comparative genome analysis.	rice is one of the most important food crops in the world. with increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. wild rice is expected to provide useful genetic resources that could improve the present cultivated species. however, the quantity and quality of these unexplored resources remain unclear. recent accumulation of the genomic information of both cultivated and wild ...	2010	20167122
contribution of momilactone a and b to rice allelopathy.	eight cultivars of rice (oryza sativa l.) inhibited shoot and root growth of echinochloa crus-galli when co-cultured with rice seedlings in a bioassay medium. momilactone a and b were found in the bioassay medium of all rice cultivars, and concentrations of momilactone a and b in the medium were 0.21-1.5 and 0.66-3.8 micromol/l, respectively, indicating that all rice cultivars may secrete momilactone a and b into the medium. exogenously applied momilactone a and b inhibited the growth of shoots ...	2010	20170980
activation of gibberellin 2-oxidase 6 decreases active gibberellin levels and creates a dominant semi-dwarf phenotype in rice (oryza sativa l.).	gibberellin (ga) 2-oxidase plays a key role in the ga catabolic pathway through 2beta-hydroxylation. in the present study, we isolated a camv 35s-enhancer activation tagged mutant, h032. this mutant exhibited a dominant dwarf and ga-deficient phenotype, with a final stature that was less than half of its wild-type counterpart. the endogenous bioactive gas are markedly decreased in the h032 mutant, and application of bioactive gas (ga(3) or ga(4)) can reverse the dwarf phenotype. the integrated t ...	2010	20171575
codon usage biases of transposable elements and host nuclear genes in arabidopsis thaliana and oryza sativa.	transposable elements (tes) are mobile genetic entities ubiquitously distributed in nearly all genomes. high frequency of codons ending in a/t in tes has been previously observed in some species. in this study, the biases in nucleotide composition and codon usage of te transposases and host nuclear genes were investigated in the at-rich genome of arabidopsis thaliana and the gc-rich genome of oryza sativa. codons ending in a/t are more frequently used by tes compared with their host nuclear gene ...	2009	20172490
tracing cadmium from culture to spikelet: noninvasive imaging and quantitative characterization of absorption, transport, and accumulation of cadmium in an intact rice plant.	we characterized the absorption and short-term translocation of cadmium (cd) in rice (oryza sativa 'nipponbare') quantitatively using serial images observed with a positron-emitting tracer imaging system. we fed a positron-emitting 107cd (half-life of 6.5 h) tracer to the hydroponic culture solution and noninvasively obtained serial images of cd distribution in intact rice plants at the vegetative stage and at the grain-filling stage every 4 min for 36 h. the rates of absorption of cd by the roo ...	2010	20172965
identification of shared single copy nuclear genes in arabidopsis, populus, vitis and oryza and their phylogenetic utility across various taxonomic levels.	although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. using the gene clustering algorithm mcl-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of arabidopsis thaliana, populus trichocarpa, vitis vin ...	2010	20181251
rnase t2 genes from rice and the evolution of secretory ribonucleases in plants.	the plant rnase t2 family is divided into two different subfamilies. s-rnases are involved in rejection of self-pollen during the establishment of self-incompatibility in three plant families. s-like rnases, on the other hand, are not involved in self-incompatibility, and although gene expression studies point to a role in plant defense and phosphate recycling, their biological roles are less well understood. although s-rnases have been subjects of many phylogenetic studies, few have included an ...	2010	20182746
functional role of rice germin-like protein1 in regulation of plant height and disease resistance.	the functional role of rice (oryza sativa) germin-like protein1 (osglp1) was elucidated through development of transgenic plants involving endogenous gene silencing in rice and heterologous gene expression in tobacco. usually, the single copy osglp1 gene in rice plant was found to be expressed predominantly in green vegetative tissues. the transgenic rice lines showed significant reduction in endogenous osglp1 expression due to 26nt sirna-mediated gene silencing, displayed semi-dwarfism and were ...	2010	20188068
cell cycle-mediated regulation of plant infection by the rice blast fungus.	to gain entry to plants, many pathogenic fungi develop specialized infection structures called appressoria. here, we demonstrate that appressorium morphogenesis in the rice blast fungus magnaporthe oryzae is tightly regulated by the cell cycle. shortly after a fungus spore lands on the rice (oryza sativa) leaf surface, a single round of mitosis always occurs in the germ tube. we found that initiation of infection structure development is regulated by a dna replication-dependent checkpoint. genet ...	2010	20190078
arsenic as a food chain contaminant: mechanisms of plant uptake and metabolism and mitigation strategies.	arsenic (as) is an environmental and food chain contaminant. excessive accumulation of as, particularly inorganic arsenic (as(i)), in rice (oryza sativa) poses a potential health risk to populations with high rice consumption. rice is efficient at as accumulation owing to flooded paddy cultivation that leads to arsenite mobilization, and the inadvertent yet efficient uptake of arsenite through the silicon transport pathway. iron, phosphorus, sulfur, and silicon interact strongly with as during i ...	2010	20192735
an unedited 1.1 kb mitochondrial orfb gene transcript in the wild abortive cytoplasmic male sterility (wa-cms) system of oryza sativa l. subsp. indica.	the application of hybrid rice technology has significantly increased global rice production during the last three decades. approximately 90% of the commercially cultivated rice hybrids have been derived through three-line breeding involving the use of wa-cms lines. it is believed that during the 21st century, hybrid rice technology will make significant contributions to ensure global food security. this study examined the poorly understood molecular basis of the wa-cms system in rice.	2010	20193092
phosphoenolpyruvate carboxylase intrinsically located in the chloroplast of rice plays a crucial role in ammonium assimilation.	phosphoenolpyruvate carboxylase (pepc) is a key enzyme of primary metabolism in bacteria, algae, and vascular plants, and is believed to be cytosolic. here we show that rice (oryza sativa l.) has a plant-type pepc, osppc4, that is targeted to the chloroplast. osppc4 was expressed in all organs tested and showed high expression in the leaves. its expression in the leaves was confined to mesophyll cells, and osppc4 accounted for approximately one-third of total pepc protein in the leaf blade. reco ...	2010	20194759
identification of a second major resistance gene to rice yellow mottle virus, rymv2, in the african cultivated rice species, o. glaberrima.	rice yellow mottle virus (rymv) is the most damaging rice-infecting virus in africa. however, few sources of high resistance and only a single major resistance gene, rymv1, are known to date. we screened a large representative collection of african cultivated rice (oryza glaberrima) for rymv resistance. whereas high resistance is known to be very rare in asian cultivated rice (oryza sativa), we identified 29 (8%) highly resistant accessions in o. glaberrima. the mif4g domain of rymv1 was sequenc ...	2010	20198467
expression analysis and functional characterization of the monosaccharide transporters, ostmts, involving vacuolar sugar transport in rice (oryza sativa).	in arabidopsis, the compartmentation of sugars into vacuoles is known to be facilitated by sugar transporters. however, vacuolar sugar transporters have not been studied in detail in other plant species. to characterize the rice (oryza sativa) tonoplast monosaccharide transporters, ostmt1 and ostmt2, we analysed their subcellular localization using green fluorescent protein (gfp) and expression patterns using reverse-transcription polymerase chain reaction (rt-pcr), performed histochemical beta- ...	2010	20202129
zebra-necrosis, a thylakoid-bound protein, is critical for the photoprotection of developing chloroplasts during early leaf development.	the zebra-necrosis (zn) mutant of rice (oryza sativa) produces transversely green/yellow-striped leaves. the mutant phenotype is formed by unequal impairment of chloroplast biogenesis before emergence from the leaf sheath under alternate light/dark or high/low temperatures (restrictive), but not under constant light and temperature (permissive) conditions. map-based cloning revealed that zn encodes a thylakoid-bound protein of unknown function. virus-induced gene silencing of a zn homolog in nic ...	2010	20202171
transcriptome-wide identification of microrna targets in rice.	microrna (mirna)-guided target rna expression is vital for a wide variety of biological processes in eukaryotes. currently, mirbase (version 13) lists 142 and 353 mirnas from arabidopsis and rice (oryza sativa), respectively. the integration of mirnas in diverse biological networks relies upon the confirmation of their rna targets. in contrast with the well-characterized mirna targets that are cleaved in arabidopsis, only a few such targets have been confirmed in rice. to identify small rna targ ...	2010	20202174
northern blotting techniques for small rnas.	in eukaryotes, rna silencing encompasses a range of biochemical processes mediated by approximately 20-25 nt small rnas (smrnas). this chapter describes northern blot hybridization techniques optimized for detection of such smrnas, whether extracted from plant or animal tissues. the basic protocol is described, and control blots illustrate the detection specificity and sensitivity of this method using dna oligonucleotide probes. known endogenous smrnas are analyzed in samples prepared from sever ...	2010	20204871
differential oxidative metabolism and 5-ketoclomazone accumulation are involved in echinochloa phyllopogon resistance to clomazone.	echinochloa phyllopogon (late watergrass) is a major weed of california rice (oryza sativa) that has evolved cytochrome p450-mediated metabolic resistance to different herbicides with multiple modes of action. e. phyllopogon populations from sacramento valley rice fields have also recently shown resistance to the herbicide clomazone. clomazone is a proherbicide that must be metabolized to 5-ketoclomazone, which is the active compound that inhibits deoxyxylulose 5-phosphate synthase, a key enzyme ...	2010	20207709
expression, purification, crystallization and preliminary x-ray analysis of rice (oryza sativa l.) os4bglu12 beta-glucosidase.	rice (oryza sativa l.) os4bglu12, a glycoside hydrolase family 1 beta-glucosidase (ec 3.2.1.21), was expressed as a fusion protein with an n-terminal thioredoxin/his(6) tag in escherichia coli strain origami b (de3) and purified with subsequent removal of the n-terminal tag. native os4bglu12 and its complex with 2,4-dinitrophenyl-2-deoxy-2-fluoro-beta-d-glucopyranoside (dnp2fg) were crystallized using 19% polyethylene glycol (3350 or 2000, respectively) in 0.1 m tris-hcl ph 8.5, 0.16 m nacl at 2 ...	2010	20208171
identification and organization of chloroplastic and cytosolic l-myo-inositol 1-phosphate synthase coding gene(s) in oryza sativa: comparison with the wild halophytic rice, porteresia coarctata.	the gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (mips; ec 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive approximately 60 kda chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic mips coded by osino1-1 gene. a possible chloroplastic transit peptide sequence was identified upstr ...	2010	20213122
identification of fe-excess-induced genes in rice shoots reveals a wrky transcription factor responsive to fe, drought and senescence.	fe participates in several important reactions in plant metabolism. however, fe homeostasis in plants is not completely understood, and molecular studies on fe-excess stress are scarce. rice (oryza sativa l. ssp. indica) is largely cultivated in submerged conditions, where the extremely reductive environment can lead to severe fe overload. in this work, we used representational difference analysis (rda) to isolate sequences up-regulated in rice shoots after exposure to fe-excess. we isolated 24 ...	2010	20217243
evaluation of the impacts of different nuclear dna content in the hull, endosperm, and embryo of rice seeds on gm rice quantification.	rice (oryza sativa) is a main staple food in the world, and several genetically modified (gm) rice events have been approved for commercialization. to accurately quantify gm contents in rice derived products, we have evaluated the variation of seed dna density and nuclear dna content in the hull, endosperm, and embryo of rice seeds from 19 cultivars, as well as their impacts on gm rice quantification. rice endosperm dna accounts for 73.71% of total seed dna, whereas the hull and embryo dnas acco ...	2010	20222712
tc-motifs at the tata-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.	the tata-box and tata-variants are regulatory elements involved in the formation of a transcription initiation complex. both have been conserved throughout evolution in a restricted region close to the transcription start site (tss). however, less than half of the genes in model organisms studied so far have been found to contain either one of these elements. indeed different core-promoter elements are involved in the recruitment of the tata-box-binding protein. here we assessed the possibility ...	2010	20222994
ele restrains empty glumes from developing into lemmas.	although there is evident homology among reproductive organs when comparing poaceae (grass) and eudicots, the identity of grass specific organs, such as lodicules, palea, lemma, and glumes has been the subject of a vast and largely inconclusive discussion. here we provide some direct evidence to support the idea that the empty glumes of rice (oryza sativa) are counterparts of lemmas. we show that the development of empty glumes is regulated by ele (elongated empty glume), which belongs to a plan ...	2010	20227044
the arbuscular mycorrhizal symbiosis enhances the photosynthetic efficiency and the antioxidative response of rice plants subjected to drought stress.	rice (oryza sativa) is the most important crop for human consumption, providing staple food for more than half of the world's population. rice is conventionally grown under flooded conditions for most of its growing cycle. however, about half of the rice area in the world does not have sufficient water to maintain optimal growing conditions and yield is reduced by drought. one possible way to increase rice production in order to meet the rice demand is to improve its drought tolerance by means o ...	2010	20227134
light-induced activation of class ii cyclobutane pyrimidine dimer photolyases.	light-induced activation of class ii cyclobutane pyrimidine dimer (cpd) photolyases of arabidopsis thaliana and oryza sativa has been examined by uv/vis and pulsed davies-type electron-nuclear double resonance (endor) spectroscopy, and the results compared with structure-known class i enzymes, cpd photolyase and (6-4) photolyase. by endor spectroscopy, the local environment of the flavin adenine dinucleotide (fad) cofactor is probed by virtue of proton hyperfine couplings that report on the elec ...	2010	20227927
glycine-rich rna-binding proteins are functionally conserved in arabidopsis thaliana and oryza sativa during cold adaptation process.	contrary to the increasing amount of knowledge regarding the functional roles of glycine-rich rna-binding proteins (grps) in arabidopsis thaliana in stress responses, the physiological functions of grps in rice (oryza sativa) currently remain largely unknown. in this study, the functional roles of six osgrps from rice on the growth of e. coli and plants under cold or freezing stress conditions have been evaluated. among the six osgrps investigated, osgrp1, osgrp4, and osgrp6 were shown to have t ...	2010	20231330
association mapping of stigma and spikelet characteristics in rice (oryza sativa l.).	stigma and spikelet characteristics play an essential role in hybrid seed production. a mini-core of 90 accessions developed from usda rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 dna markers, 108 ssrs plus an indel. three major clusters were built upon rogers' genetic distance, indicative of indicas, and temperate and tropical japonicas. a mixed linear model combining pc-matrix and k-matrix was adapted for mapping marker-trait ...	2009	20234878
physiological and proteomic characterization of manganese sensitivity and tolerance in rice (oryza sativa) in comparison with barley (hordeum vulgare).	research on manganese (mn) toxicity and tolerance indicates that mn toxicity develops apoplastically through increased peroxidase activities mediated by phenolics and mn, and mn tolerance could be conferred by sequestration of mn in inert cell compartments. this comparative study focuses on mn-sensitive barley (hordeum vulgare) and mn-tolerant rice (oryza sativa) as model organisms to unravel the mechanisms of mn toxicity and/or tolerance in monocots.	2010	20237113
genetic control of phenotypic plasticity in asian cultivated and wild rice in response to nutrient and density changes.	phenotypic plasticity is an adaptive mechanism adopted by plants in response to environmental heterogeneity. cultivated and wild species adapt in contrasting environments; however, it is not well understood how genetic changes responsible for phenotypic plasticity were involved in crop evolution. we investigated the genetic control of phenotypic plasticity in asian cultivated (oryza sativa) and wild rice (o. rufipogon) under 5 environmental conditions (2 nutrient and 3 density levels). quantitat ...	2010	20237598
wdbtf: an integrated database resource for studying wheat transcription factor families.	transcription factors (tfs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their dna-binding domains. genes coding for tfs have been identified in the sequences of model plant genomes. the rice (oryza sativa spp. japonica) genome contains 2,384 tf gene models, which represent the mrna transcript of a locus, classed into 63 families.	2010	20298594
diel time-courses of leaf growth in monocot and dicot species: endogenous rhythms and temperature effects.	diel (24 h) leaf growth patterns were differently affected by temperature variations and the circadian clock in several plant species. in the monocotyledon zea mays, leaf elongation rate closely followed changes in temperature. in the dicotyledons nicotiana tabacum, ricinus communis, and flaveria bidentis, the effect of temperature regimes was less obvious and leaf growth exhibited a clear circadian oscillation. these differences were related neither to primary metabolism nor to altered carbohyd ...	2010	20299442
a clomazone immunoassay to study the environmental fate of the herbicide in rice (oryza sativa) agriculture.	the environmental impact of rice agriculture is poorly studied in developing countries, mainly due to limitations of the analytical capacity. here, we report the development of a clomazone enzyme-linked immunosorbent assay as a fast and cost-effective tool to monitor the dissipation of this herbicide along the harvest. antibodies were prepared using different strategies of hapten conjugation, and the best hapten/antibody pair was selected. it proved to be a reliable tool to measure the herbicide ...	2010	20302341
atlas of rice grain filling-related metabolism under high temperature: joint analysis of metabolome and transcriptome demonstrated inhibition of starch accumulation and induction of amino acid accumulation.	high temperature impairs grain filling by inhibiting the deposition of storage materials such as starch and protein. to comprehend its impact on grain filling metabolism in rice (oryza sativa), levels of metabolites and transcripts related to central pathways of metabolism were simultaneously determined in developing caryopses exposed to high temperature (33 degrees c/28 degrees c) and a control temperature (25 degrees c/20 degrees c) during the milky stage. a capillary electrophoresis-based met ...	2010	20304786
carbon starved anther encodes a myb domain protein that regulates sugar partitioning required for rice pollen development.	in flowering plants, sink tissues rely on transport of carbohydrates from photosynthetic tissues (sources) for nutrition and energy. however, how sugar partitioning in plants is regulated at the molecular level during development remains unknown. we have isolated and characterized a rice (oryza sativa) mutant, carbon starved anther (csa), that showed increased sugar contents in leaves and stems and reduced levels of sugars and starch in floral organs. in particular, the csa mutant had reduced le ...	2010	20305120
a conserved mechanism of bract suppression in the grass family.	suppression of inflorescence leaf, or bract, growth has evolved multiple times in diverse angiosperm lineages, including the poaceae and brassicaceae. studies of arabidopsis thaliana mutants have revealed several genes involved in bract suppression, but it is not known if these genes play a similar role in other plants with suppressed bracts. we identified maize (zea mays) tassel sheath (tsh) mutants, characterized by the loss of bract suppression, that comprise five loci (tsh1-tsh5). we used ma ...	2010	20305121
cop: a database for characterizing co-expressed gene modules with biological information in plants.	using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the cop database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. the confeito algorithm developed previously in our laboratory, which is suitable to calculate the interconnectivity between genes in co-expressed gene network, was applied to extract co-expressed gene modules. the database includes the gene ...	2010	20305269
characterization of rice nucleotide sugar transporters capable of transporting udp-galactose and udp-glucose.	using the basic local alignment search tool (blast) algorithm to search the oryza sativa (japanese rice) nucleotide sequence databases with the arabidopsis thaliana udp-galactose transporter sequences as queries, we found a number of sequences encoding putative o. sativa udp-galactose transporters. from these, we cloned four putative udp-galactose transporters, designated osugt1, 2, 3 and 4, which exhibited high sequence similarity with arabidopsis thaliana udp-galactose transporters. osugt1, 2, ...	2010	20305274
root-specific expression of osnac10 improves drought tolerance and grain yield in rice under field drought conditions.	drought poses a serious threat to the sustainability of rice (oryza sativa) yields in rain-fed agriculture. here, we report the results of a functional genomics approach that identified a rice nac (an acronym for nam [no apical meristem], ataf1-2, and cuc2 [cup-shaped cotyledon]) domain gene, osnac10, which improved performance of transgenic rice plants under field drought conditions. of the 140 osnac genes predicted in rice, 18 were identified to be induced by stress conditions. phylogenic anal ...	2010	20335401
plant twitter: ligands under 140 amino acids enforcing stomatal patterning.	stomata are an essential land plant innovation whose patterning and density are under genetic and environmental control. recently, several putative ligands have been discovered that influence stomatal density, and they all belong to the epidermal patterning factor-like family of secreted cysteine-rich peptides. two of these putative ligands, epf1 and epf2, are expressed exclusively in the stomatal lineage cells and negatively regulate stomatal density. a third, epfl6 or challah, is also a negati ...	2010	20336477
analysing lodging of the panicle bearing cereal teff (eragrostis tef).	lodging, the permanent displacement of crop plants from their vertical because of root or shoot failure, is a major yield constraint of the gluten free, panicle bearing cereal teff. the objective of this paper was to analyse the causes of lodging of teff by using, modifying and validating conventional biomechanical models. the model parameters were obtained from a field trial with two contrasting teff cultivars, using novel in situ and laboratory measurements under wet and dry conditions. cross- ...	2010	20345637
discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes.	plant mitochondrial genomes are known for their complexity, and there is abundant evidence demonstrating that this organelle is important for plant sexual reproduction. cytoplasmic male sterility (cms) is a phenomenon caused by incompatibility between the nucleus and mitochondria that has been discovered in various plant species. as the exact sequence of steps leading to cms has not yet been revealed, efforts should be made to elucidate the factors underlying the mechanism of this important trai ...	2010	20346185
heterologous expression and characterization of recombinant oscdr1, a rice aspartic proteinase involved in disease resistance.	the oryza sativa constitutive disease resistance 1 (oscdr1) gene product is an aspartic proteinase that has been implicated in disease resistance signaling. this apoplastic enzyme is a member of the group of 'atypical' plant aspartic proteinases. recombinant oscdr1 expressed in escherichia coli exhibited protease activity against succinylated-casein substrate. inactivating the enzyme through modification of an aspartate residue present in the deduced active site completely abolished its proteina ...	2010	20347986
alkylresorcinol synthases expressed in sorghum bicolor root hairs play an essential role in the biosynthesis of the allelopathic benzoquinone sorgoleone.	sorghum bicolor is considered to be an allelopathic crop species, producing phytotoxins such as the lipid benzoquinone sorgoleone, which likely accounts for many of the allelopathic properties of sorghum spp. current evidence suggests that sorgoleone biosynthesis occurs exclusively in root hair cells and involves the production of an alkylresorcinolic intermediate (5-[(z,z)-8',11',14'-pentadecatrienyl]resorcinol) derived from an unusual 16:3delta(9,12,15) fatty acyl-coa starter unit. this led to ...	2010	20348430
common genetic pathways regulate organ-specific infection-related development in the rice blast fungus.	magnaporthe oryzae is the most important fungal pathogen of rice (oryza sativa). under laboratory conditions, it is able to colonize both aerial and underground plant organs using different mechanisms. here, we characterize an infection-related development in m. oryzae produced on hydrophilic polystyrene (phil-ps) and on roots. we show that fungal spores develop preinvasive hyphae (pre-ih) from hyphopodia (root penetration structures) or germ tubes and that pre-ih also enter root cells. changes ...	2010	20348434
defining reference genes in oryza sativa using organ, development, biotic and abiotic transcriptome datasets.	reference genes are widely used to normalise transcript abundance data determined by quantitative rt-pcr and microarrays. however, the approaches taken to define reference genes can be variable. although oryza sativa (rice) is a widely used model plant and important crop specie, there has been no comprehensive analysis carried out to define superior reference genes.	2010	20353606
purification and properties of cysteine protease from rhizomes of curcuma longa (linn.).	turmeric rhizome (curcuma domestica linn.) contains proteases and has proteolytic activity. curcumin from turmeric rhizomes has been used for healing many ailments, including cancer. the purpose of this study was to purify turmeric protease and to research their biochemical characteristics [corrected].	2010	20355018
arabidopsis rap2.2: an ethylene response transcription factor that is important for hypoxia survival.	arabidopsis (arabidopsis thaliana) rap2.2 (at3g14230) is an apetala2/ethylene response factor-type transcription factor that belongs to the same subfamily as the rice (oryza sativa) submergence tolerance gene sub1a. rap2.2 is expressed at constitutively high levels in the roots and at lower levels in the shoots, where it is induced by darkness. effector studies and analysis of ethylene signal transduction mutants indicate that rap2.2 is induced in shoots by ethylene and functions in an ethylene- ...	2010	20357136
regulation of microbe-associated molecular pattern-induced hypersensitive cell death, phytoalexin production, and defense gene expression by calcineurin b-like protein-interacting protein kinases, oscipk14/15, in rice cultured cells.	although cytosolic free ca(2+) mobilization induced by microbe/pathogen-associated molecular patterns is postulated to play a pivotal role in innate immunity in plants, the molecular links between ca(2+) and downstream defense responses still remain largely unknown. calcineurin b-like proteins (cbls) act as ca(2+) sensors to activate specific protein kinases, cbl-interacting protein kinases (cipks). we here identified two cipks, oscipk14 and oscipk15, rapidly induced by microbe-associated molecu ...	2010	20357140
[effect of napthalene on the dna methylation patterns and level in rice (oryza sativa l.)].	in this study,two elite rice inbred lines, nipponbare and mastumae were selected and irrigated with naphthalene solution with different concentrations. epigenetic instabilities in the blade of the plants in tillering and heading stage were assessed by msap marks. the results showed that naphthalene exposure induced epigenetic variations in all the samples based on different levels and patterns of dna methylation. the changes of the percentage of 5-methylcytosine have no regulation. in total 1051 ...	2010	20358845
distribution patterns of inorganic mercury and methylmercury in tissues of rice (oryza sativa l.) plants and possible bioaccumulation pathways.	whole rice plants (oryza sativa l.) were collected at different typical mercury (hg) contaminated sites during regular harvest periods to investigate the distribution of inorganic mercury (ihg) and methylmercury (mehg) in tissues. the whole rice plants were divided into rice seed (brown rice), hull, root, stalk and leaf. elevated ihg and mehg concentrations were observed in rice plants cultivated in hg mining area compared to those obtained from the control site, which attributed to the hg conta ...	2010	20369851
identification of candidate genes for grain number in rice (oryza sativa l.).	large number of well-filled grains per panicle is an important yield component trait in rice. a combination of qtl mapping and transcriptome profiling was used to identify candidate genes for grain number. a framework linkage map was constructed using 166 ssr markers evenly distributed over the 12 rice chromosomes. qtl mapping using 3 years phenotyping data on a set of recombinant inbred lines derived from a cross between pusa 1266 (high grain number) and pusa basmati 1 (low grain number) identi ...	2010	20376514
characterization and fine mapping of the glabrous leaf and hull mutants (gl1) in rice (oryza sativa l.).	the glabrous leaf and hull (gl1) mutants were isolated from m(2) generation of indica cultivar 93-11. these mutants produced smooth leaves and hairless glumes under normal growth conditions. by analyzing through scanning electron microscope, it was revealed that the leaf trichomes, including macro and micro hairs, were deficient in these mutants. genetic analysis indicated that the mutation was controlled by a single recessive gene. using nine ssr markers and one indel marker, the gl1 gene was m ...	2010	20376671
identification and gene mapping of a novel mutant supernumerary lodicules (snl) in rice.	in order to gain a better understanding of rice flower development, a rice flower mutant supernumerary lodicules (snl), which was identified from ethyl methane sulfonate (ems)-treated jinhui10 (oryza sativa l. ssp. indica) was used in the present study. in the snl mutant, the palea obtained lemma identity, additional glume-like organs formed, lodicules increased and elongated, stamens decreased, and a few aberrant carpels formed. these phenotypes suggest that snl is involved in the entire rice f ...	2010	20377687
genomic organization of plant aminopropyl transferases.	aminopropyl transferases like spermidine synthase (spds; ec 2.5.1.16), spermine synthase and thermospermine synthase (spms, tspms; ec 2.5.1.22) belong to a class of widely distributed enzymes that use decarboxylated s-adenosylmethionine as an aminopropyl donor and putrescine or spermidine as an amino acceptor to form in that order spermidine, spermine or thermospermine. we describe the analysis of plant genomic sequences encoding spds, spms, tspms and pmt (putrescine n-methyltransferase; ec 2.1. ...	2010	20381365
dna methylation mediated by a microrna pathway.	in plants, the known micrornas (mirnas) are produced as approximately 21 nucleotide (nt) duplexes from their precursors by dicer-like 1 (dcl1). they are incorporated into argonaute 1 (ago1) protein to regulate target gene expression primarily through mrna cleavage. we report here the discovery of a class of mirnas in the model monocot rice (oryza sativa). these are 24 nt in length and require another member of the dicer family, dcl3, for their biogenesis. the 24 nt long mirnas (lmirnas) are load ...	2010	20381393
effect of three insecticides and two herbicides on rice (oryza sativa) seedling germination and growth.	rice (oryza sativa l.) is one of the most important food crops worldwide. however, it is also a valuable tool in assessing toxicity of organic and inorganic compounds. for more than 20 years, it has been an approved species for standardized phytotoxicity experiments. the objective of this study is to determine germination and radicle (root) and coleoptile (shoot) growth of rice seeds exposed to three insecticides and two herbicides, commonly used in the agricultural production landscape. althoug ...	2010	20387062
rice tillering and yield as affected by artificial and sugarcane borer (lepidoptera: crambidae) culm injury.	a 2-yr study was conducted to evaluate the tillering and yield response of rice, oryza sativa l., whose culms were injured artificially or by larval sugarcane borers, diatraea saccharalis (f.). artificially injured plants produced approximately 0.49 more tillers than uninjured plants, similar to what has previously been reported for larval injured plants. in contrast, artificial injury did not affect yield per tiller, whereas larval injury did. the proximity of larval injury to the panicle had a ...	2010	20388284
the sepallata-like gene osmads34 is required for rice inflorescence and spikelet development.	grass plants develop distinct inflorescences and spikelets that determine grain yields. however, the mechanisms underlying the specification of inflorescences and spikelets in grasses remain largely unknown. here, we report the biological role of one sepallata (sep)-like gene, osmads34, in controlling the development of inflorescences and spikelets in rice (oryza sativa). osmads34 encodes a mads box protein containing a short carboxyl terminus without transcriptional activation activity in yeast ...	2010	20395452
screening of ir50 x rathu heenati f7 rils and identification of ssr markers linked to brown planthopper (nilaparvata lugens stål) resistance in rice (oryza sativa l.).	brown planthopper (nilaparvata lugens stål) is one of the major insect pests of rice. a sri lankan indica rice cultivar rathu heenati was found to be resistant to all biotypes of the brown planthopper. in the present study, a total of 268 f(7) rils of ir50 and rathu heenati were phenotyped for their level of resistance against bph by the standard seedbox screening test (ssst) in the greenhouse. a total of 53 ssr primers mapped on the chromosome 3 were used to screen the polymorphism between the ...	2010	20396978
a new species of harpophora (magnaporthaceae) recovered from healthy wild rice (oryza granulata) roots, representing a novel member of a beneficial dark septate endophyte.	a survey of the endophytic fungal community of wild rice (oryza granulata) in china was conducted. two isolates recovered from healthy roots are assumed to be dark septate endophytes (dses). they are morphologically similar to species from the genus harpophora and are identified as a new species, harpophora oryzae, based on the molecular phylogeny and morphological characteristics. a neighbor-joining tree constructed from its-5.8s rrna gene regions reveals that h. oryzae forms a distinctive subc ...	2010	20402786
nonhost resistance to magnaporthe oryzae in arabidopsis thaliana.	rice blast, caused by magnaporthe oryzae, is a devastating disease of rice (oryza sativa). the mechanisms involved in resistance of rice to blast have been studied extensively and the rice--m. oryzae pathosystem has become a model for plant--microbe interaction studies. however, the mechanisms involved in nonhost resistance (nhr) of other plants to rice blast are still poorly understood. we have recently demonstrated that agb1 and pmr5 contribute to pen2-mediated preinvasion resistance to m. ory ...	2010	20404515
protocol: a simple gel-free method for snp genotyping using allele-specific primers in rice and other plant species.	abstract:	2010	20409329
ap2/erebp transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling.	to optimize acclimation responses to environmental growth conditions, plants integrate and weigh a diversity of input signals. signal integration within the signalling networks occurs at different sites including the level of transcription factor activation. accumulating evidence assigns a major and diversified role in environmental signal integration to the family of apetala 2/ethylene response element binding protein (ap2/erebp) transcription factors. presently, the plant transcription factor ...	2010	20411284
biochemical and physiological responses of rice (oryza sativa l.) grown on different sewage sludge amendments rates.	using sewage sludge, a biological residue from sewage treatment processes, in agriculture is an alternative disposal technique of waste. to study the biochemical and physiological responses of rice (oryza sativa l.) grown on different sewage sludge amendments (ssa) rates a field experiment was conducted by mixing sewage sludge at 0, 3, 4.5, 6, 9, 12 kg m(-2) rate to the agricultural soil. rate of photosynthesis and stomatal conductance increased in plants grown at different ssa rate. chlorophyll ...	2010	20414639
actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a thai jasmine rice plant.	the novel strain gmku 370(t) was isolated from roots of a thai jasmine rice plant (oryza sativa l. 'kdml 105') collected from pathum thani rice research center, pathum thani province, thailand. a phylogenetic analysis based on 16s rrna gene sequences indicated that strain gmku 370(t) formed a distinct clade within the genus actinoallomurus. strain gmku 370(t) contained meso-diaminopimelic acid and lysine in the cell-wall peptidoglycan and galactose and madurose as whole-cell sugars. no mycolic a ...	2011	20418407
comparative genomics of flowering time pathways using brachypodium distachyon as a model for the temperate grasses.	brachypodium distachyon (brachypodium) is a model for the temperate grasses which include important cereals such as barley, wheat and oats. comparison of the brachypodium genome (accession bd21) with those of the model dicot arabidopsis thaliana and the tropical cereal rice (oryza sativa) provides an opportunity to compare and contrast genetic pathways controlling important traits. we analysed the homologies of genes controlling the induction of flowering using pathways curated in arabidopsis re ...	2010	20419097
redox homeostasis, antioxidant defense, and methylglyoxal detoxification as markers for salt tolerance in pokkali rice.	to identify biochemical markers for salt tolerance, two contrasting cultivars of rice (oryza sativa l.) differing in salt tolerance were analyzed for various parameters. pokkali, a salt-tolerant cultivar, showed considerably lower level of h(2)o(2) as compared to ir64, a sensitive cultivar, and such a physiology may be ascribed to the higher activity of enzymes in pokkali, which either directly or indirectly are involved in the detoxification of h(2)o(2). enzyme activities and the isoenzyme patt ...	2010	20419461
two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in oryza sativa.	long chain prenyl diphosphates are crucial biosynthetic precursors of ubiquinone (uq) in many organisms, ranging from bacteria to humans, as well as precursors of plastoquinone in photosynthetic organisms. the cloning and characterization of two solanesyl diphosphate synthase genes, ossps1 and ossps2, in oryza sativa is reported here. ossps1 was highly expressed in root tissue whereas ossps2 was found to be high in both leaves and roots. enzymatic characterization using recombinant proteins show ...	2010	20421194
crop management techniques to enhance harvest index in rice.	a major challenge in rice (oryza sativa l.) production is to enhance water use efficiency (wue) and maintain or even increase grain yield. wue, if defined as the biomass accumulation over water consumed, may be fairly constant for a given species in given climate. wue can be enhanced by less irrigation. however, such enhancement is largely a trade-off against lower biomass production. if wue is defined as the grain production per unit amount of water irrigated, it would be possible to increase w ...	0	20421195
quality determination of nickel-loaded silica prepared from poaceous biomass.	klason lignin or preacid hydrolysate of a poaceous biomass such as rice husk, rice straw ( oryza sativa ), and wheat straw ( triticum aestivum ) became a good source of highly pure silica by simple calcinations in the testing process for application of high-boiling solvent (hbs) pulping of agricultural byproduct. especially, klason lignin or preacid hydrolysis residue of rice husks offered highly purified silica, which was converted to an excellent ni/sio(2) catalyst for methanation of carbon di ...	2010	20423088
genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (oryza sativa l.).	arabinogalactan proteins (agps) comprise a family of hydroxyproline-rich glycoproteins that are implicated in plant growth and development. in this study, 69 agps are identified from the rice genome, including 13 classical agps, 15 arabinogalactan (ag) peptides, three non-classical agps, three early nodulin-like agps (enod-like agps), eight non-specific lipid transfer protein-like agps (nsltp-like agps), and 27 fasciclin-like agps (flas). the results from expressed sequence tags, microarrays, an ...	2010	20423940
new regulator for energy signaling pathway in plants highlights conservation among species.	the "low-energy checkpoint" snf1-related protein kinases, which are conserved in all eukaryotes, play an important role in cellular metabolic adaptation to differences in energy and oxygen availability. although the signaling pathways involved in such metabolic adaptations are well understood in yeast and mammals, they have been poorly understood in plants. a recent study revealed that calcineurin b-like interacting protein kinase 15 (cipk15) acted as a global regulator of such adaptations, link ...	2010	20424261
identification and characterization of nagnag alternative splicing in the moss physcomitrella patens.	alternative splicing (as) involving tandem acceptors that are separated by three nucleotides (nagnag) is an evolutionarily widespread class of as, which is well studied in homo sapiens (human) and mus musculus (mouse). it has also been shown to be common in the model seed plants arabidopsis thaliana and oryza sativa (rice). in one of the first studies involving sequence-based prediction of as in plants, we performed a genome-wide identification and characterization of nagnag as in the model plan ...	2010	20426810
identification of extracellular matrix proteins of rice (oryza sativa l.) involved in dehydration-responsive network: a proteomic approach.	water-deficit or dehydration impairs almost all physiological processes and greatly influences the geographical distribution of many crop species. it has been postulated that higher plants rely mostly on induction mechanisms to maintain cellular integrity during stress conditions. plant cell wall or extracellular matrix (ecm) forms an important conduit for signal transduction between the apoplast and symplast and acts as front-line defense, thereby playing a key role in cell fate decision under ...	2010	20433195
amelioration of experimental autoimmune encephalitis by novel peptides: involvement of t regulatory cells.	the purpose of the present study was to develop a peptide for treatment of multiple sclerosis (ms). we have tested the effect of a novel anti-inflammatory peptide (kghyaervg, termed iiim1) on experimental autoimmune encephalitis (eae), an animal model of ms. our findings demonstrate significant reduction in neurological score following oral administration of iiim1. structural studies revealed that the entire peptide is required for activity. the peptide caused significant reduction in il17, inte ...	2010	20434883
translocation of magnaporthe oryzae effectors into rice cells and their subsequent cell-to-cell movement.	knowledge remains limited about how fungal pathogens that colonize living plant cells translocate effector proteins inside host cells to regulate cellular processes and neutralize defense responses. to cause the globally important rice blast disease, specialized invasive hyphae (ih) invade successive living rice (oryza sativa) cells while enclosed in host-derived extrainvasive hyphal membrane. using live-cell imaging, we identified a highly localized structure, the biotrophic interfacial complex ...	2010	20435900
overexpression and purification of pwl2d, a mutant of the effector protein pwl2 from magnaporthe grisea.	the rice blast disease caused by the ascomycete magnaporthe grisea continues to cause a tremendous impact in rice (oryza sativa) cultures around the world. elucidating the molecular basis of the fungus interactions with its host might help increase the general understanding of the pathogen-host relationship. at the moment of invasion, the fungus secretes effectors that modify host defenses and cellular processes as they successively invade living rice cells. pwl2, an effector protein, is a known ...	2010	20438845
identification and application of a rice senescence-associated promoter.	sag39 is a rice (oryza sativa) gene that encodes a cysteine protease. sag39 shares 55% homology with the arabidopsis (arabidopsis thaliana) senescence-associated protein sag12. the promoter for sag39 (p(sag39)) was isolated, and sag39 expression was determined to be relatively low in mature leaves, while not expressed in the endosperm. sag39 mrna levels increased as senescence progressed, with maximum accumulation of transcripts at late senescence stages. gel retardation assays indicated that tw ...	2010	20439547
changes in protein expression profiles between a low phytic acid rice ( oryza sativa l. ssp. japonica) line and its parental line: a proteomic and bioinformatic approach.	the seed proteome of a low phytic acid (lpa) rice line (os-lpa-xs110-1), developed as a novel food source, was compared to that of its parental line, xiushui 110 (xs-110). analysis by surfaced enhanced laser desorption ionization-time-of-flight mass spectrometry (seldi-tof ms) and two-dimensional gel electrophoresis (2-de) allowed the detection of a potential low molecular weight biomarker and identification of 23 differentially expressed proteins that include stress-related proteins, storage pr ...	2010	20441221
expression, purification, and characterization of recombinant human transferrin from rice (oryza sativa l.).	transferrin is an essential ingredient used in cell culture media due to its crucial role in regulating cellular iron uptake, transport, and utilization. it is also a promising drug carrier used to increase a drug's therapeutic index via the unique transferrin receptor-mediated endocytosis pathway. due to the high risk of contamination with blood-borne pathogens from the use of human or animal plasma-derived transferrin, recombinant transferrin is preferred for use as a replacement for native tr ...	2010	20447458
genetic diversity and evolutionary relationships in genus oryza revealed by using highly variable regions of chloroplast dna.	we studied the phylogeny of the genus oryza using chloroplast dna sequences. to identify regions containing sufficient variation for elucidating the relationship of closely related species with fine resolution and high reliability, we first compared the complete chloroplast sequences of oryza sativa japonica, o. sativa indica, and o. nivara, and identified regions containing many variant sites. nucleotide sequences of the variant regions were newly determined in 19 oryza species including 58 cul ...	2010	20450965
alkylresorcylic acid synthesis by type iii polyketide synthases from rice oryza sativa.	alkylresorcinols, produced by various plants, bacteria, and fungi, are bioactive compounds possessing beneficial activities for human health, such as anti-cancer activity. in rice, they accumulate in seedlings, contributing to protection against fungi. alkylresorcylic acids, which are carboxylated forms of alkylresorcinols, are unstable compounds and decarboxylate readily to yield alkylresorcinols. genome mining of the rice oryza sativa identified two type iii polyketide synthases, named aras1 ( ...	2010	20451227
structure, allelic diversity and selection of asr genes, candidate for drought tolerance, in oryza sativa l. and wild relatives.	asr (aba, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. to analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. the maintenance of six members of the asr gene family, which are the result of combination between tandem dup ...	2010	20454772
osnoa1/rif1 is a functional homolog of atnoa1/rif1: implication for a highly conserved plant cgtpase essential for chloroplast function.	the bacterial protein yqeh is a circularly permuted gtpase with homologs encoded by plant nuclear genomes. the rice homolog osnoa1/rif1 is encoded by the single-copy gene os02g01440. osnoa1/rif1 is expressed in different tissues and is light-inducible. the osnoa1/rif1-eyfp fusion protein was targeted to chloroplasts in transgenic arabidopsis plants. in addition, the rice homolog was able to rescue most of the growth phenotypes in an arabidopsis rif1 mutant. rice (oryza sativa) osnoa1/rif1 rnai ...	2010	20456051
a genetic model for the female sterility barrier between asian and african cultivated rice species.	s(1) is the most important locus acting as a reproductive barrier between oryza sativa and o. glaberrima. it is a complex locus, with factors that may affect male and female fertility separately. recently, the component causing the allelic elimination of pollen was fine mapped. however, the position and nature of the component causing female sterility remains unknown. to fine map the factor of the s(1) locus affecting female fertility, we developed a mapping approach based on the evaluation of t ...	2010	20457876
binding of 2ca1p (nocturnal inhibitor) to the active site of rubisco using genetic algorithm (ga).	ribulose-1, 5- bisphosphate carboxylase/ oxygenase (rubisco) catalyzes the first step in net photosynthetic assimilation and photorespiratory carbon oxidation. the activity of this enzyme is modulated in response to changes in light intensity as suggested in a number of early reports. several studies found that the natural inhibitor 2ca1p is involved in the inhibition of the enzyme under reduced light intensity in rice (oryza sativa). due to the lack of studies and information on the interaction ...	2009	20461160
fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley.	the barley mutant allele sdw3 confers a gibberellin-insensitive, semi-dwarf phenotype with potential for breeding of new semi-dwarfed barley cultivars. towards map-based cloning, sdw3 was delimited by high-resolution genetic mapping to a 0.04 cm interval in a "cold spot" of recombination of the proximal region of the short arm of barley chromosome 2h. extensive synteny between the barley sdw3 locus (hvu_sdw3) and the orthologous regions (osa_sdw3, sbi_sdw3, bsy_sdw3) of three other grass species ...	2010	20464438
ectopic expression of the rice lumazine synthase gene contributes to defense responses in transgenic tobacco.	lumazine synthase (ls) catalyzes the penultimate reaction in the multistep riboflavin biosynthesis pathway, which is involved in plant defenses. plant defenses are often subject to synergistic effects of jasmonic acid and ethylene whereas ls is a regulator of jasmonic acid signal transduction. however, little is known about whether the enzyme contributes to defense responses. to study the role of ls in plant pathogen defenses, we generated transgenic tobacco expressing the rice (oryza sativa) ls ...	2010	20465413
large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants.	knowledge of phosphorylation events and their regulation is crucial to understand the functional biology of plants. here, we report a large-scale phosphoproteome analysis in the model monocot rice (oryza sativa japonica 'nipponbare'), an economically important crop. using unfractionated whole-cell lysates of rice cells, we identified 6,919 phosphopeptides from 3,393 proteins. to investigate the conservation of phosphoproteomes between plant species, we developed a novel phosphorylation-site eval ...	2010	20466843
putrescine differently influences the effect of salt stress on polyamine metabolism and ethylene synthesis in rice cultivars differing in salt resistance.	effects of salt stress on polyamine metabolism and ethylene production were examined in two rice (oryza sativa l.) cultivars [i kong pao (ikp), salt sensitive; and pokkali, salt resistant] grown for 5 d and 12 d in nutrient solution in the presence or absence of putrescine (1 mm) and 0, 50, and 100 mm nacl. the salt-sensitive (ikp) and salt-resistant (pokkali) cultivars differ not only in their mean levels of putrescine, but also in the physiological functions assumed by this molecule in stresse ...	2010	20472577
genome-wide classification and evolutionary analysis of the bhlh family of transcription factors in arabidopsis, poplar, rice, moss, and algae.	basic helix-loop-helix proteins (bhlhs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. a growing number of bhlh proteins have been functionally characterized in plants. however, some of these have not been previously classified. we present here an updated and comprehensive classification of the bhlhs encoded by the whole sequenced genomes of arabidopsis (arabidopsis thaliana), populus trichocarpa, oryza sativa, physcomitrel ...	2010	20472752
bioaccumulation of methylmercury versus inorganic mercury in rice (oryza sativa l.) grain.	mercury (hg) bioaccumulation in aquatic food webs has been much studied, motivated from high hg levels found in many fish species important for human consumption. hg bioaccumulation in terrestrial food chains have received little attention and assumed to be of minor importance. however, recent studies showed that rice can be an important pathway of methylmercury (mehg) exposure to inhabitants in hg mining areas in china. in this study, 59 sampling sites (including 32 sites from "heavily polluted ...	2010	20476782
uptake, translocation, and remobilization of zinc absorbed at different growth stages by rice genotypes of different zn densities.	zinc (zn) is an essential micronutrient for humans, and increasing zn density in rice ( oryza sativa l.) grains is important for improving human nutrition. the characteristics of zn translocation and remobilization were investigated in high zn density genotype ir68144, in comparison with the low zn density genotype ir64. stable isotope tracer (68)zn was supplied at various growth stages, either to the roots in nutrient solution or to the flag leaves to investigate the contribution of (68)zn abso ...	2010	20481473
a simple optimization can improve the performance of single feature polymorphism detection by affymetrix expression arrays.	high-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. in small genome species (genome size: < approximately 300 mb), whole-genome dna hybridization to expression arrays has been used for various applications. in large genome species, transcript hybridization to expression arrays has been used for genotyping. although rice is a fully sequenced model plant of medium genome size (approximately 400 mb), there are a few examples of the use of rice oligon ...	2010	20482895
divinyl chlorophyll(ide) a can be converted to monovinyl chlorophyll(ide) a by a divinyl reductase in rice.	3,8-divinyl (proto)chlorophyll(ide) a 8-vinyl reductase (dvr) catalyzes the reduction of 8-vinyl group on the tetrapyrrole to an ethyl group, which is indispensable for monovinyl chlorophyll (chl) synthesis. so far, three 8-vinyl reductase genes (dvr, bcia, and slr1923) have been characterized from arabidopsis (arabidopsis thaliana), chlorobium tepidum, and synechocystis sp. pcc6803. however, no 8-vinyl reductase gene has yet been identified in monocotyledonous plants. in this study, we isolated ...	2010	20484022
genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (oryza sativa l.).	peptide transporter (ptr) family whose member can transport di-/tripeptides and nitrate is important for plant growth and development. although the rice (oryza sativa l.) genome has been sequenced for a few years, a genomic survey, characterization and expression profile analysis of the ptr family in this species has not been reported.	2010	20487558