Publications

ricearraynet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice.	microarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. however, there have been no reports, to date, of such a database being constructed for rice (oryza sativa). here, we describe the construction of such a database, called ricearraynet (ran; http://www.ggbio.com/arrayne ...	2009	19605550
full-size abc transporters from the abcg subfamily in medicago truncatula.	full-size atp-binding cassette (abc) transporters belonging to the abcg subfamily are unique for plants and fungi. there is growing evidence that certain of these proteins play a role in plant defense or signaling systems. as yet, a complete set of full-size abcg protein genes has been inventoried and classified in only two plants: arabidopsis thaliana and oryza sativa. recently, a domain-based clustering analysis has predicted the presence of at least 12 genes encoding such proteins in the lotu ...	2009	19589068
the spatial expression patterns of drooping leaf orthologs suggest a conserved function in grasses.	the drooping leaf (dl) gene regulates carpel specification in the flower and midrib formation in the leaf in oryza sativa (rice). loss-of-function mutations in the dl locus cause homeotic transformation of carpels into stamens and lack of midrib, resulting in the drooping leaf phenotype. dl is a member of the yabby gene family and is closely related to the crabs claw (crc) gene in arabidopsis thaliana. the function of arabidopsis crc, however, differs from that of rice dl: it is responsible for ...	2009	19556707
expansion mechanisms and functional annotations of hypothetical genes in the rice genome.	in each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. in the rice (oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the michigan state university rice genome annotation. we have implemented an integrative approach to analyze their duplication/expansion and function. the analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the ...	2009	19535473
posmed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants.	molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. a key step is forward genetics or positional cloning to identify the genes that confer useful functions. in order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed posmed-plus (positional medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal int ...	2009	19528193
refining the definition of plant mitochondrial presequences through analysis of sorting signals, n-terminal modifications, and cleavage motifs.	mitochondrial protein import is a complex multistep process from synthesis of proteins in the cytosol, recognition by receptors on the organelle surface, to translocation across one or both mitochondrial membranes and assembly after removal of the targeting signal, referred to as a presequence. in plants, import has to further discriminate between mitochondria and chloroplasts. in this study, we determined the precise cleavage sites in the presequences for arabidopsis (arabidopsis thaliana) and ...	2009	19474214
trifldb: a database of clustered full-length coding sequences from triticeae with applications to comparative grass genomics.	the triticeae full-length cds database (trifldb) contains available information regarding full-length coding sequences (cdss) of the triticeae crops wheat (triticum aestivum) and barley (hordeum vulgare) and includes functional annotations and comparative genomics features. trifldb provides a search interface using keywords for gene function and related gene ontology terms and a similarity search for dna and deduced translated amino acid sequences to access annotations of triticeae full-length c ...	2009	19448038
expression level of aberrant panicle organization1 determines rice inflorescence form through control of cell proliferation in the meristem.	two types of branches, rachis branches (i.e. nonfloral) and spikelets (i.e. floral), are produced during rice (oryza sativa) inflorescence development. we previously reported that the aberrant panicle organization1 (apo1) gene, encoding an f-box-containing protein orthologous to arabidopsis (arabidopsis thaliana) unusual floral organs, suppresses precocious conversion of rachis branch meristems to spikelets to ensure generation of certain number of spikelets. here, we identified four dominant mu ...	2009	19386809
comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome.	alternative splicing (as) is a widespread phenomenon in higher eukaryotes but the extent to which it leads to functional protein isoforms and to proteome expansion at large is still a matter of debate. in contrast to animal species, for which as has been studied extensively at the protein and functional level, protein-centered studies of as in plant species are scarce. here we investigate the functional impact of as in dicot and monocot plant species using a comparative approach.	2009	19358722
in silico analysis of promoter regions from cold-induced genes in rice (oryza sativa l.) and arabidopsis thaliana reveals the importance of combinatorial control.	cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. the dreb1/cbfs are transcription factors (tfs) that are prominent in the regulation of cold responses in arabidopsis thaliana, rice and many other crops. we investigated if the expression of dreb1/cbfs and co-expressed genes relies on combinatorial control by several tfs. our results support this notion and indicate that methods for studying the regulation of complex c ...	2009	19321735
genomic expression profiling of mature soybean (glycine max) pollen.	pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. the current knowledge of the pollen transcriptome is limited to the model plant systems arabidopsis thaliana and oryza sativa which have tri-cellular pollen grains at maturity. comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. in this study, we used ...	2009	19265555
meta-analysis of small rna-sequencing errors reveals ubiquitous post-transcriptional rna modifications.	recent advances in dna-sequencing technology have made it possible to obtain large datasets of small rna sequences. here we demonstrate that not all non-perfectly matched small rna sequences are simple technological sequencing errors, but many hold valuable biological information. analysis of three small rna datasets originating from oryza sativa and arabidopsis thaliana small rna-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous no ...	2009	19255090
the pentatricopeptide repeat (ppr) gene family, a tremendous resource for plant phylogenetic studies.	* despite the paramount importance of nuclear gene data in plant phylogenetics, the search for candidate loci is believed to be challenging and time-consuming. here we report that the pentatricopeptide repeat (ppr) gene family, containing hundreds of members in plant genomes, holds tremendous potential as nuclear gene markers. * we compiled a list of 127 ppr loci that are all intronless and have a single orthologue in both rice (oryza sativa) and arabidopsis thaliana. the uncorrected p-distances ...	2009	19192190
highly diversified molecular evolution of downstream transcription start sites in rice and arabidopsis.	alternative usage of transcription start sites (tsss) is one of the key mechanisms to generate gene variation in eukaryotes. here, we show diversified molecular evolution of tsss in remotely related flowering plants, rice (oryza sativa) and arabidopsis (arabidopsis thaliana), by comprehensive analyses of large collections of full-length cdnas and genome sequences. we determined 45,917 representative tsss within 23,445 loci of rice and 35,313 tsss within 16,964 loci of arabidopsis, about two tsss ...	2009	19118127
evaluating the microtubule cytoskeleton and its interacting proteins in monocots by mining the rice genome.	microtubules (mts) are assembled by heterodimers of alpha- and beta-tubulins, which provide tracks for directional transport and frameworks for the spindle apparatus and the phragmoplast. mt nucleation and dynamics are regulated by components such as the gamma-tubulin complex which are conserved among eukaryotes, and other components which are unique to plants. following remarkable progress made in the model plant arabidopsis thaliana toward revealing key components regulating mt activities, the ...	2009	19106179
the uniprotkb/swiss-prot knowledgebase and its plant proteome annotation program.	the uniprot knowledgebase, uniprotkb, is the main product of the uniprot consortium. it consists of two sections, uniprotkb/swiss-prot, the manually curated section, and uniprotkb/trembl, the computer translation of the embl/genbank/ddbj nucleotide sequence database. taken together, these two sections cover all the proteins characterized or inferred from all publicly available nucleotide sequences. the plant proteome annotation program (ppap) of uniprotkb/swiss-prot focuses on the manual annotat ...	2009	19084081
experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity.	mitochondria in rice (oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. we have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. quantitative comp ...	2009	19010998
integrating genes and phenotype: a wheat-arabidopsis-rice glycosyltransferase database for candidate gene analyses.	glycosyltransferases (gts) constitute a very large multi-gene superfamily, containing several thousand members identified in sequenced organisms especially in plants. gts are key enzymes involved in various biological processes such as cell wall formation, storage polysaccharides biosynthesis, and glycosylation of various metabolites. gts have been identified in rice (oryza sativa) and arabidopsis thaliana, but their precise function has been demonstrated biochemically for only a few. in this wo ...	2009	19005709
involvement of osspx1 in phosphate homeostasis in rice.	arabidopsis thaliana spx (syg/pho81/xpr1) domain genes have recently been shown to be involved in the phosphate (pi) signaling pathway. we show here that a rice (oryza sativa) spx gene, osspx1, is specifically induced by pi starvation in roots. suppression of osspx1 by rna interference resulted in severe signs of toxicity caused by the over-accumulation of pi, similar to that found in osphr2 (phosphate starvation response transcription factor 2) overexpressors and pho2 (phosphate-responsive muta ...	2009	19000161
rice blast fungus (magnaporthe oryzae) infects arabidopsis via a mechanism distinct from that required for the infection of rice.	magnaporthe oryzae is a hemibiotrophic fungal pathogen that causes rice (oryza sativa) blast. although m. oryzae as a whole infects a wide variety of monocotyledonous hosts, no dicotyledonous plant has been reported as a host. we found that two rice pathogenic strains of m. oryzae, kj201 and 70-15, interacted differentially with 16 ecotypes of arabidopsis (arabidopsis thaliana). strain kj201 infected all ecotypes with varying degrees of virulence, whereas strain 70-15 caused no symptoms in certa ...	2009	18987215
evidence for a role of hexokinases as conserved glucose sensors in both monocot and dicot plant species.	the role of the hexokinases (hxks) as glucose (glc) sensors has been mainly demonstrated for arabidopsis (arabidopsis thaliana) hxk1 (athxk1) but has yet to be shown in other plant species. in our recent publication, we reported that two rice (oryza sativa) hxks, oshxk5 and oshxk6, also function as glc sensors. these two enzymes harbor both mitochondrial targeting peptides (mtps) and nuclear localization signals (nlss), and we confirmed their dual-targeting ability to nuclei and mitochondria usi ...	2009	19938377
genetic resources for maize cell wall biology.	grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. toward this goal, we are building a knowledge base of the maize (zea mays) genes involved in cell wall biology, their expression ...	2009	19926802
the atg autophagic conjugation system in maize: atg transcripts and abundance of the atg8-lipid adduct are regulated by development and nutrient availability.	plants employ sophisticated mechanisms to recycle intracellular constituents needed for growth, development, and survival under nutrient-limiting conditions. autophagy is one important route in which cytoplasm and organelles are sequestered in bulk into vesicles and subsequently delivered to the vacuole for breakdown by resident hydrolases. the formation and trafficking of autophagic vesicles are directed in part by associated conjugation cascades that couple the autophagy-related8 (atg8) and at ...	2009	18790996
isolation and characterization of conserved non-coding sequences among rice (oryza sativa l.) paralogous regions.	segmental duplication is particularly frequent within plant genomes and the ability of the original single-copy gene to gain a new function for the change of regulatory elements is one of the prominent consequences of duplication. thus, it is important to study the pattern of conserved non-coding sequence (cns) between paralogous genes. we report the result of a survey of cnss among paralogous regions in rice (oryza sativa l.), as well as the comparison of cns dataset between rice and arabidopsi ...	2009	18825415
analysis of the pumpkin phloem proteome provides insights into angiosperm sieve tube function.	increasing evidence suggests that proteins present in the angiosperm sieve tube system play an important role in the long distance signaling system of plants. to identify the nature of these putatively non-cell-autonomous proteins, we adopted a large scale proteomics approach to analyze pumpkin phloem exudates. phloem proteins were fractionated by fast protein liquid chromatography using both anion and cation exchange columns and then either in-solution or in-gel digested following further separ ...	2009	18936055
biochemical insights on degradation of arabidopsis della proteins gained from a cell-free assay system.	the phytohormone gibberellic acid (ga) regulates diverse aspects of plant growth and development. ga responses are triggered by the degradation of della proteins, which function as repressors in ga signaling pathways. recent studies in arabidopsis thaliana and rice (oryza sativa) have implied that the degradation of della proteins occurred via the ubiquitin-proteasome system. here, we developed an arabidopsis cell-free system to recapitulate della protein degradation in vitro. using this cell-fr ...	2009	19717618
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
the wus homeobox-containing (wox) protein family.	the wox genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved dna-binding homeodomain. the analysis of wox gene expression and function shows that wox family members fulfill specialized functions in key developmental processes in plants, such as embryonic patterning, stem-cell maintenance and organ formation. these functions can be related to either promotion of cell division activity and/or prevent ...	2009	20067590
dynamic landscapes of four histone modifications during deetiolation in arabidopsis.	although landscapes of several histone marks are now available for arabidopsis thaliana and oryza sativa, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. here, we analyzed the effects of light on four histone modifications (acetylation and trimethylation of lysines 9 and 27 on histone h3: h3k9ac, h3k9me3, h3k27ac, and h3k27me3, respectively). our genome-wide profiling of h3k9ac and h3k27ac re ...	2009	20008096
isolation and phylogenetic footprinting analysis of the 5'-regulatory region of the floral homeotic gene orcpi from orchis italica (orchidaceae).	the nucleotide sequences of regulatory elements from homologous genes can be strongly divergent. phylogenetic footprinting, a comparative analysis of noncoding regions, can detect putative transcription factor binding sites (tfbss) shared among the regulatory regions of 2 or more homologous genes. these conserved motifs have the potential to serve the same regulatory function in distantly related taxa. we isolated the 5'-noncoding region of the orcpi gene, a mads-box transcription factor involve ...	2009	19861638
seed storage protein gene promoters contain conserved dna motifs in brassicaceae, fabaceae and poaceae.	accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate dna sequences bound by several interacting factors. enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. this provides a basis for the computational identification of cis-regulato ...	2009	19843335
functional analyses of lonely guy cytokinin-activating enzymes reveal the importance of the direct activation pathway in arabidopsis.	cytokinins play crucial roles in diverse aspects of plant growth and development. spatiotemporal distribution of bioactive cytokinins is finely regulated by metabolic enzymes. lonely guy (log) was previously identified as a cytokinin-activating enzyme that works in the direct activation pathway in rice (oryza sativa) shoot meristems. in this work, nine arabidopsis thaliana log genes (at log1 to log9) were predicted as homologs of rice log. seven at logs, which are localized in the cytosol and nu ...	2009	19837870
expression of brd1, a plant defensin from brassica rapa, confers resistance against brown planthopper (nilaparvata lugens) in transgenic rices.	plant defensins are small (5-10 kda) basic peptides thought to be an important component of the defense pathway against fungal and/or bacterial pathogens. to understand the role of plant defensins in protecting plants against the brown planthopper, a type of insect herbivore, we isolated the brassica rapa defensin 1 (brd1) gene and introduced it into rice (oryza sativa l.) to produce stable transgenic plants. the brd1 protein is homologous to other plant defensins and contains both an n-terminal ...	2009	19714315
mitochondrial atpa gene is altered in a new orf220-type cytoplasmic male-sterile line of stem mustard (brassica juncea).	the purpose of this research is to identify the probable mitochondrial factor associated with cytoplasmic male sterility (cms) by comparative analysis of cms and its isogenic maintainer lines in stem mustards. dramatic variations in the morphology of floral organs were observed in cms stem mustard. mitochondrial atpa gene was shown to be altered in cms compared with that in its maintainer line, of which mitochondrial atpa gene from its maintainer line was sequenced to encode 507 amino acids. it ...	2009	18026850
synthesis and herbicidal activity of 12-(aryloxyacyloxyimino)-1,15-pentadecanlactone derivatives.	a series of novel 12-(aryloxyacyloxyimino)-1,15-pentadecanlactone derivatives (3) were synthesized, and their structures including configuration of c=n bond were confirmed by (1)h nmr, elemental analysis and x-ray diffraction analysis. the bioassay showed that some of them exhibited excellent herbicidal activity against amaranthus tricolor l. the activity of compounds 3 except compounds 3a1-2 was much higher than the commercial herbicide 2,4-d and the activity of about half of compounds 3 was co ...	2009	19117417
aromatic-ring-functionalised benzoxazinones in the system oryza sativa-echinochloa crus-galli as biorational herbicide models.	barnyardgrass, echinochloa crus-galli (l.) beauv., is one of the most problematic weeds occurring in rice crops. although efficient chemical control is provided by herbicides available on the market, resistant biotypes provoked by pressure selection have appeared in recent times. this emphasises the need for alternative treatments in which herbicidal compounds from a natural origin could be included.	2009	19551813
characterization of allergenic epitopes of ory s1 protein from oryza sativa and its homologs.	vaccination is the most effective technique suggested now days for allergy treatment. recombinant-based approaches are mostly focused on genetic modification of allergens to produce molecules with reduced allergenic activity and conserved antigenicity. the molecules developed for vaccination in allergy possess significantly reduced allergenicity in terms of ige binding, and therefore will not lead to anaphylactic reactions upon injection. this approach is probably feasible with every peptide all ...	2009	20011147
cross-species amplification tests and diversity analysis using 56 pcr markers in dactylis glomerata and lolium perenne.	we report results of cross-species amplification in dactylis glomerata and lolium perenne of 12 simple sequence repeats (ssrs) isolated from lolium multiflorum×festuca glaucescens, 42 ssrs from festuca arundinacea and two sequence tagged sites from oryza sativa. we compared the transferability and diversity between d. glomerata and l. perenne, which are important forage crops. while nei's gene diversity values were equivalent in both species (from 0.14 to 0.92), the mean number of allele per loc ...	2009	21564590
potential for phytoextraction of copper, lead, and zinc by rice (oryza sativa l.), soybean (glycine max [l.] merr.), and maize (zea mays l.).	phytoextraction by hyperaccumulators has been proposed for decreasing toxic-metal concentrations of contaminated soils. however, hyperaccumulators have several shortcomings to introduce these species into asian monsoon's agricultural fields contaminated with low to moderate toxic-metals. to evaluate the phytoextraction potential, maize (gold dent), soybean (enrei and suzuyutaka), and rice (nipponbare and milyang 23) were pot-grown under aerobic soil conditions for 60d on the andosol or fluvisol ...	2009	18632207
the functional role of pack-mules in rice inferred from purifying selection and expression profile.	gene duplication is an important mechanism for evolution of new genes. in plants, a special group of transposable elements, called pack-mules or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. despite the abundance of pack-mules, the functionality of these duplicates is not clear. here, we present a comprehensive analysis of expression and purifying selection on 2809 pack-mules in rice (oryza sativa), which are derived from 1501 parental genes. at leas ...	2009	19136648
evaluation of elastic modulus and hardness of crop stalks cell walls by nano-indentation.	agricultural biomaterials such as crop stalks are natural sources of cellulosic fiber and have great potential as reinforced materials in bio-composites. in order to evaluate their potential as materials for reinforcement, the nano-mechanical properties of crop-stalk cell walls, i.e. those of cotton (gossypium herbaceu) stalk, soybean (glycine max) stalk, cassava (manihot esculent) stalk, rice (oryza sativa l.) straw, and wheat (triticum aestivum l.) straw, were investigated by means of nano-ind ...	2010	19954968
gynumella flava gen. nov., sp. nov., isolated from the rhizosphere of rice (oryza sativa l.) managed under no-tillage practice.		2010	20068238
nucleotide diversity and molecular evolution of the psy1 gene in zea mays compared to some other grass species.	phytoene synthase (psy), which is encoded by the phytoene synthase 1 (psy1) gene, is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway. in order to examine the genetic diversity and evolution pattern of psy1 within the andropogoneae, sequences of 76 accessions from 5 species (maize, teosinte, tripsacum, coix, and sorghum) of the andropogoneae were tested, along with 4 accessions of rice (oryza sativa l.) included as outliers. both the number and the order of exons and i ...	2010	19885651
nutritional, sensory and physical analysis of pumpkin flour incorporated into weaning mix.	the objective of this study was to develop a cereal-pulse complementary food fortified with different concentrations of pumpkin powder (cucurbita moschata), and to analyse its sensory and physic-chemical parameters. fresh pumpkins(cucurbita moschata) were procured from the market and dehydrated and powdered in the laboratory. sorghum (sorghum vulgare) and whole green gram (vigna radiate) were germinated, dried, pulverised and combined with powdered rice (oryza sativa) in the ratio of 2:1:1. pump ...	2010	22691991
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
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
resistance of cultivated rice varieties to cnaphalocrocis medinalis (lepidoptera: pyralidae).	cnaphalocrocis medinalis guenée (lepidoptera: pyralidae) is a major pest in rice, oryza sativa l. (graminales: poaceae), in asia. the current study investigated the resistance of 17 rice varieties or lines to c. medinalis and behavioral responses of the insect to varieties of different corrected damage ratings (cdrs) and damaged leaves scales (dlss). the results showed that most varieties (or lines) commonly cultured in rice production were susceptible (dls 3 and 5) to damage caused by c. medina ...	2010	20857724
multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature.	agricultural crop databases maintained in gene banks of the consultative group on international agricultural research (cgiar) are valuable sources of information for breeders. these databases provide comparative phenotypic and genotypic information that can help elucidate functional aspects of plant and agricultural biology. to facilitate data sharing within and between these databases and the retrieval of information, the crop ontology (co) database was designed to provide controlled vocabulary ...	2010	22476066
silicon-mediated rice plant resistance to the asiatic rice borer (lepidoptera: crambidae): effects of silicon amendment and rice varietal resistance.	the asiatic rice borer, chilo suppressalis (walker) (lepidoptera: crambidae), is one of the most destructive pests in rice, oryza sativa l., throughout asian countries. the aim of this study was to investigate the potential of applied silicon in mediating rice plant resistance to c. suppressalis in a susceptible (shanyou63) and a moderately resistant (yanfeng47) rice cultivar. silicon-treated plants showed significant increases in silicon content compared with the control. silicon addition signi ...	2010	20857756
selenium accumulation by forage and grain crops and volatilization from seleniferous soils amended with different organic materials.	greenhouse and field experiments were conducted to study the direct and residual effect of applying different organic materials on se accumulation by crops and volatilization from seleniferous soils of northwestern india. among organic manures, press mud and poultry manures proved 4-5 times more effective in reducing se accumulation by different crops than farmyard manure. efficiency of organic manures increased with increase in application rates. application of both press mud and poultry manure ...	2010	20015536
soluble sugar availability of aerobically germinated barley, oat and rice coleoptiles in anoxia.	physiological and metabolic responses to anoxia were compared for aerobically germinated seedlings of barley (hordeum vulgare), oat (avena sativa) and rice (oryza sativa). coleoptile growth of barley, oat and rice seedlings was suppressed by a 24 h-anoxic stress, but the growth of the rice coleoptiles was much greater than that of the barley and oat coleoptiles. atp concentration in the anoxic rice coleoptiles was greater than that in the anoxic barley and oat coleoptiles. concentrations of etha ...	2010	20727618
multifunctionalised benzoxazinones in the systems oryza sativa-echinochloa crus-galli and triticum aestivum-avena fatua as natural-product-based herbicide leads.	fifteen novel derivatives of d-diboa, including aromatic ring modifications and the addition of side chains in positions c-2 and n-4, had previously been synthesised and their phytotoxicity on standard target species (sts) evaluated. this strategy combined steric, electronic, solubility and lipophilicity requirements to achieve the maximum phytotoxic activity. an evaluation of the bioactivity of these compounds on the systems oryza sativa-echinochloa crus-galli and triticum aestivum-avena fatua ...	2010	20628996
indel-associated mutation rate varies with mating system in flowering plants.	a recently proposed mutational mechanism, indel-associated mutation (idam), posits that heterozygous insertions/deletions (indels) increase the point mutation rate at nearby nucleotides due to errors during meiosis. this mechanism could have especially dynamic consequences for the evolution of plant genomes, because the high degree of variation in the rate of self-fertilization among plant species causes differences in the heterozygosity of alleles, including indel alleles, segregating in plant ...	2010	19825943
origin and diversification of basic-helix-loop-helix proteins in plants.	basic helix-loop-helix (bhlh) proteins are a class of transcription factors found throughout eukaryotic organisms. classification of the complete sets of bhlh proteins in the sequenced genomes of arabidopsis thaliana and oryza sativa (rice) has defined the diversity of these proteins among flowering plants. however, the evolutionary relationships of different plant bhlh groups and the diversity of bhlh proteins in more ancestral groups of plants are currently unknown. in this study, we use whole ...	2010	19942615
mef9, an e-subclass pentatricopeptide repeat protein, is required for an rna editing event in the nad7 transcript in mitochondria of arabidopsis.	rna editing in plants alters specific nucleotides from c to u in mrnas in plastids and in mitochondria. i here characterize the nuclear gene mitochondrial editing factor9 (mef9) that is required for rna editing of the site nad7-200 in the nad7 mitochondrial mrna in arabidopsis (arabidopsis thaliana). the mef9 protein belongs to the e subfamily of pentatricopeptide repeat proteins and unlike the three previously identified mitochondrial editing factors mef1 and mef11 in arabidopsis and ogr1 in ri ...	2010	20018598
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
metabolome and photochemical analysis of rice plants overexpressing arabidopsis nad kinase gene.	the chloroplastic nad kinase (nadk2) is reported to stimulate carbon and nitrogen assimilation in arabidopsis (arabidopsis thaliana), which is vulnerable to high light. since rice (oryza sativa) is a monocotyledonous plant that can adapt to high light, we studied the effects of nadk2 expression in rice by developing transgenic rice plants that constitutively expressed the arabidopsis chloroplastic nadk gene (nk2 lines). nk2 lines showed enhanced activity of nadk and accumulation of the nadp(h) p ...	2010	20154096
microrna-mediated signaling involved in plant root development.	microrna (mirna), recently recognized as a critical post-transcriptional modulator of gene expression, is involved in numerous biological processes in both animals and plants. although eudicots and monocots, such as the model plants arabidopsis (arabidopsis thaliana) and rice (oryza sativa), possess distinct root systems, several homologous mirna families are reported to be involved in root growth control in both plants. consistent with recent notion that numerous signaling pathways are implicat ...	2010	20138828
quantitative analysis of plant polyamines including thermospermine during growth and salinity stress.	arabidopsis thaliana was thought to contain two spermine synthase genes, acaulis 5 (acl5) and spms. recent investigations, however, revealed that the acl5 gene encodes thermospermine synthase. in this study, we have established a simple method to separate two isomers of tetraamine, spermine and thermospermine, in extracts from plant tissues of less than 500 mg. polyamines (pas) extracted from plant tissues were benzoylated, and the derivatives were completely resolved by high-performance liquid ...	2010	20137962
over-expression of osa-mir396c decreases salt and alkali stress tolerance.	salt and alkali stress are two of the main environmental factors limiting rice production. thus, understanding the mechanisms of salinity and alkali stress tolerance is necessary to modify rice to increase its resistance to salinity and alkaline stress. micrornas (mirnas) are approximately 21-nucleotide rnas that are ubiquitous regulators of gene expression in eukaryotic organisms. in plants, mirnas constitute one of five classes of small rnas that function primarily as negative regulators for g ...	2010	20135324
genome-wide analysis of ethylene-responsive element binding factor-associated amphiphilic repression motif-containing transcriptional regulators in arabidopsis.	the ethylene-responsive element binding factor-associated amphiphilic repression (ear) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, c2h2, and auxin/indole-3-acetic acid families of transcriptional regulators. sequence comparison of the core ear motif sites from these proteins revealed two distinct conservation patterns: lxlxl and dlnxxp. proteins containing these motifs play key roles in diverse biological functions by negat ...	2010	20097792
characterization of the rice pho1 gene family reveals a key role for ospho1;2 in phosphate homeostasis and the evolution of a distinct clade in dicotyledons.	phosphate homeostasis was studied in a monocotyledonous model plant through the characterization of the pho1 gene family in rice (oryza sativa). bioinformatics and phylogenetic analysis showed that the rice genome has three pho1 homologs, which cluster with the arabidopsis (arabidopsis thaliana) atpho1 and atpho1;h1, the only two genes known to be involved in root-to-shoot transfer of phosphate. in contrast to the arabidopsis pho1 gene family, all three rice pho1 genes have a cis-natural antisen ...	2010	20081045
functional characterization of plant small rnas based on next-generation sequencing data.	the currently developed next-generation sequencing (ngs) technology has significantly enhanced our capacity of small rna (srna) exploration. several ambitious srna projects have been established based on the technical support of ngs. thanks to the high-throughput feature of ngs, huge amounts of srna sequencing data have been generated. however, much more research efforts are needed to further exploit these valuable data. in this study, we carried out functional analyses of srnas from 26 angiospe ...	2010	21030312
genome-wide analysis of wox gene family in rice, sorghum, maize, arabidopsis and poplar.	wuschel-related homeobox (wox) genes form a large gene family specifically expressed in plants. they are known to play important roles in regulating the development of plant tissues and organs by determining cell fate. recent available whole genome sequences allow us to do more comprehensive phylogenetic analysis of the wox genes in plants. in the present study, we identified 11 and 21 woxs from sorghum (sorghum bicolor) and maize (zea mays), respectively. the 72 wox genes from rice (oryza sativ ...	2010	20977659
annotation and comparative analysis of the glycoside hydrolase genes in brachypodium distachyon.	glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. in plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. glycoside hydrolase genes have been previously cataloged for oryza sativa (rice), the model dicotyledonous pla ...	2010	20973991
implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (sr proteins) in plants.	growing interest in alternative splicing in plants and the extensive sequencing of new plant genomes necessitate more precise definition and classification of genes coding for splicing factors. sr proteins are a family of rna binding proteins, which function as essential factors for constitutive and alternative splicing. we propose a unified nomenclature for plant sr proteins, taking into account the newly revised nomenclature of the mammalian sr proteins and a number of plant-specific propertie ...	2010	20884799
digital gene expression signatures for maize development.	genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. in maize (zea mays) inflorescences, mutations in the ramosa (ra) genes affect the determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. in this work, we developed and tested a framework for analysis of tag-based, digital gene expression profiles using illumina's high-throughput sequencing technol ...	2010	20833728
root hair-specific expansin b genes have been selected for graminaceae root hairs.	cell differentiation ultimately relies on the regulation of cell type-specific genes. for a root hair cell to undergo morphogenesis, diverse cellular processes including cell-wall loosening must occur in a root hair cell-specific manner. previously, we identified and characterized root hairspecific cis-elements (rhe) from the genes encoding the cell wall-loosening protein expansin a (expa) which functions preferentially on dicot cell walls. this study reports two root hair-specific grass expb ge ...	2010	20811811
wavy leaf1, an ortholog of arabidopsis hen1, regulates shoot development by maintaining microrna and trans-acting small interfering rna accumulation in rice.	in rice (oryza sativa), trans-acting small interfering rna (ta-sirna) is essential for shoot development, including shoot apical meristem (sam) formation and leaf morphogenesis. the rice wavy leaf1 (waf1) mutant has been identified as an embryonic mutant resembling shoot organization1 (sho1) and sho2, homologs of a loss-of-function mutant of dicer-like4 and a hypomorphic mutant of argonaute7, respectively, which both act in the ta-sirna production pathway. about half of the waf1 mutants showed s ...	2010	20805329
testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms.	different theories for the origin of the angiosperm hermaphrodite flower make different predictions concerning the overlap between the genes expressed in the male and female cones of gymnosperms and the genes expressed in the hermaphrodite flower of angiosperms. the mostly male (mm) theory predicts that, of genes expressed primarily in male versus female gymnosperm cones, an excess of male orthologs will be expressed in flowers, excluding ovules, while out of male (oom) and out of female (oof) t ...	2010	20682074
biochemical changes associated with in vivo rbcl fragmentation by reactive oxygen species under chilling-light conditions.	during physiological stress, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) degradation is accelerated, which is considered to be one of the key factors responsible for photosynthetic decline. a recent study has shown that the large subunit (rbcl) of rubisco is directly fragmented by hydroxyl radicals in cucumis sativus leaves under chilling-light conditions. in the present study, we investigated biochemical aspects associated with this in vivo rbcl fragmentation by reactive oxygen sp ...	2010	20653886
diversification and specialization of plant rbr ubiquitin ligases.	rbr ubiquitin ligases are components of the ubiquitin-proteasome system present in all eukaryotes. they are characterized by having the rbr (ring - ibr - ring) supradomain. in this study, the patterns of emergence of rbr genes in plants are described.	2010	20644651
analysis of bac clones containing homologous sequences on the end of the xq arm and on chromosome 7 in the dioecious plant silene latifolia.	silene latifolia is a model dioecious plant with morphologically distinguishable xy sex chromosomes. the end of the xq arm is quite different from that of the yp arm, although both are located at opposite ends of their respective chromosomes relative to a pseudo-autosomal region. the xq arm does not seem to originate from the same autosome as the yp arm. bacterial artificial chromosome clone #15b12 has an insert containing a 130-kb stretch in which a 313-bp satellite dna is repeated 420 times. p ...	2010	20616862
early evolution of bhlh proteins in plants.	basic-helix-loop-helix (bhlh) proteins are a large family of eukaryotic transcription factors. in plants, they have been shown to be key regulators of a diverse array of developmental and metabolic pathways. we have recently shown that the diversity of bhlh proteins in angiosperms is ancient. most of the bhlh subfamilies present in seed plants such as arabidopsis thaliana and oryza sativa are also present in early diverging groups of land plants, including mosses and lycophytes. in contrast, the ...	2010	20523129
knockout of a bacterial-type atp-binding cassette transporter gene, atstar1, results in increased aluminum sensitivity in arabidopsis.	atp-binding cassette (abc) transporters represent a large family in plants, but the functions of most of these transporters are unknown. here we report a gene, atstar1, only encoding an atp-binding domain of a bacterial-type abc transporter in arabidopsis (arabidopsis thaliana). atstar1 is an ortholog of rice (oryza sativa) osstar1, which has been implicated in aluminum (al) tolerance. knockout of atstar1 resulted in increased sensitivity to al and earlier flowering. unlike osstar1, atstar1 was ...	2010	20498340
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
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
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
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
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
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
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
expression patterns of aadl, a crabs claw ortholog in asparagus asparagoides (asparagaceae), demonstrate a stepwise evolution of crc/dl subfamily of yabby genes.	understanding the evolutionary path of transcription factors is essential for the elucidation of plant evolution. the crc/dl subfamily of the yabby gene family are functionally diverse, plant-specific, putative transcription factors. in arabidopsis thaliana, crabs claw (crc) is expressed in the abaxial region of carpel primordia and in floral nectaries, where it regulates carpel morphology and nectary development. by contrast, in oryza sativa, drooping leaf (dl) is expressed in the entire carpel ...	2010	21622421
distribution of short interstitial telomere motifs in two plant genomes: putative origin and function.	short interstitial telomere motifs (telo boxes) are short sequences identical to plant telomere repeat units. they are observed within the 5' region of several genes over-expressed in cycling cells. in synergy with various cis-acting elements, these motifs participate in the activation of expression. here, we have analysed the distribution of telo boxes within arabidopsis thaliana and oryza sativa genomes and their association with genes involved in the biogenesis of the translational apparatus.	2010	21171996
common and distinct organ and stress responsive transcriptomic patterns in oryza sativa and arabidopsis thaliana.	arabidopsis thaliana is clearly established as the model plant species. given the ever-growing demand for food, there is a need to translate the knowledge learned in arabidopsis to agronomically important species, such as rice (oryza sativa). to gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of arabidopsis and rice were compared at the level of gene orthology and functional categorisation.	2010	21106056
a rice gid1 suppressor mutant reveals that gibberellin is not always required for interaction between its receptor, gid1, and della proteins.	to investigate gibberellin (ga) signaling using the rice (oryza sativa) ga receptor gibberellin-insensitive dwarf1 (gid1) mutant gid1-8, we isolated a suppressor mutant, suppressor of gid1-1 (sgd-1). sgd-1 is an intragenic mutant containing the original gid1-8 mutation (l45f) and an additional amino acid substitution (p99s) in the loop region. gid1(p99s) interacts with the rice della protein slender rice1 (slr1), even in the absence of ga. substitution of the 99th pro with other amino acids reve ...	2010	21098733
duplication of the class i cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the {alpha}-crystallin domain in the genus rhododendron (ericaceae).	positive selection in the -crystallin domain (acd) of the chloroplast small heat shock protein (cpshsp) gene was found in a previous study and was suggested to be related to the ecological adaptation of rhododendron species in the subgenus hymenanthes. consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other shsp genes, for example class i cytosolic shsp genes (ct1shsps) in rhododendron in taiwan, where many endemic species have evolve ...	2010	19887471
pmrd: plant microrna database.	micrornas (mirna) are approximately 21 nucleotide-long non-coding small rnas, which function as post-transcriptional regulators in eukaryotes. mirnas play essential roles in regulating plant growth and development. in recent years, research into the mechanism and consequences of mirna action has made great progress. with whole genome sequence available in such plants as arabidopsis thaliana, oryza sativa, populus trichocarpa, glycine max, etc., it is desirable to develop a plant mirna database t ...	2010	19808935
morphological study of the relationships between weedy rice accessions (oryza sativa complex) and commercial rice varieties in pulau pinang rice granary area.	weedy rice (wr) is found in many direct-seeded rice fields. wr possesses morphological characteristics that are similar to cultivated rice varieties in the early stage of growth, making them more difficult to control than other weeds. a comparative morphological study was conducted by collecting wr accessions from four sites within the pulau pinang rice growing areas. the objective of the study was to characterise wr accessions of the pulau pinang rice granary by comparing their morphological ch ...	2010	24575197
the molecular basis of white pericarps in african domesticated rice: novel mutations at the rc gene.	repeated phenotypic evolution can occur at both the inter- and intraspecific level and is especially prominent in domesticated plants, where artificial selection has favoured the same traits in many different species and varieties. the question of whether repeated evolution reflects changes at the same or different genes in each lineage can now be addressed using the domestication and improvement genes that have been identified in a variety of crops. here, we document the genetic basis of nonpig ...	2010	21121088
tissue-adapted invasion strategies of the rice blast fungus magnaporthe oryzae.	magnaporthe oryzae causes rice blast, the most serious foliar fungal disease of cultivated rice (oryza sativa). during hemibiotrophic leaf infection, the pathogen simultaneously combines biotrophic and necrotrophic growth. here, we provide cytological and molecular evidence that, in contrast to leaf tissue infection, the fungus adopts a uniquely biotrophic infection strategy in roots for a prolonged period and spreads without causing a loss of host cell viability. consistent with a biotrophic li ...	2010	20858844
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
endophytic fungi from paddy.	endophytic fungi were isolated from different parts of healthy paddy plants (oryza sativa). the most common endophytic fungal genus recovered was fusarium, followed by aspergillus, curvularia, penicillium, gilmaniella and arthrobotrys foliicola. fusarium and curvularia had higher occurrences in the seeds compared with the other fungi. aspergillus was recovered mostly from leaf blades and penicillium from the leaf sheath. gilmaniella and a. foliicola were isolated only from the roots and leaf bla ...	2010	24575194
dynamics of periarbuscular membranes visualized with a fluorescent phosphate transporter in arbuscular mycorrhizal roots of rice.	in arbuscular mycorrhizal (am) symbiosis, host plants supply photosynthates to am fungi and, in return, they receive inorganic nutrients such as phosphate from finely branched fungal arbuscules. plant cortical cells envelope arbuscules with periarbuscular membranes that are continuous with the plant plasma membranes. we prepared transgenic rice (oryza sativa) plants that express a fusion of green fluorescent protein with rice am-inducible phosphate transporter, ospt11-gfp, and grew them with am ...	2010	20097910
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
gene cloning, bacterial expression, and purification of a novel rice (oryza sativa l.) ubiquitin-related protein, rurm1.	a rice ubiquitin-related modifier-1 (rurm1) gene was cloned and transformed in escherichia coli. we successfully expressed the rurm1 protein as a glutathione s-transferase (gst)-fusion protein by cultivating the e. coli cells at 16 degrees c for 16 h. after cleavage of gst, we obtained a single protein of 12 kda. this protein was identified as the rurm1 protein by western blot analysis.	2010	20139593
effect of anthocyanin-rich extract from black rice (oryza sativa l. japonica) on chronically alcohol-induced liver damage in rats.	the study evaluated the protective effect of anthocyanin-rich extract from black rice (aebr) on chronic ethanol-induced biochemical changes in male wistar rats. administration of ethanol (3.7 g/kg/day) to wistar rats for 45 days induced liver damage with a significant increase (p < 0.05) of aspartate transaminase (ast), alanine transaminase (alt), gamma glutamyl transferase (ggt) in the serum and the hepatic malondialdehyde (mda) level. in contrast, administration of aebr (500 mg/kg) along with ...	2010	20143824
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