Publications

root-induced changes to cadmium speciation in the rhizosphere of two rice (oryza sativa l.) genotypes.	our aim was to investigate rhizosphere effects on the chemical behavior of cd. this was done in a glasshouse experiment, where two rice cultivars (zhenong54 and sixizhan) were grown in soil spiked with cadmium (cd) at two levels, 3.9 ± 0.5 and 8.3 ± 0.5 mg kg(-1) soil, placed in a rhizobox until ripening stage. chemical forms of cadmium near the root surface were then assessed using a sequential extraction procedure (sep). there were significant differences in cd species, especially exchangeable ...	2011	21316043
osdog, a gibberellin-induced a20/an1 zinc-finger protein, negatively regulates gibberellin-mediated cell elongation in rice.	the a20/an1 zinc-finger proteins (zfps) play pivotal roles in animal immune responses and plant stress responses. from previous gibberellin (ga) microarray data and a20/an1 zfp family member association, we chose oryza sativa dwarf rice with overexpression of gibberellin-induced gene (osdog) to examine its function in the ga pathway. osdog was induced by gibberellic acid (ga(3)) and repressed by the ga-synthesis inhibitor paclobutrazol. different transgenic lines with constitutive expression of ...	2011	21316795
leaf tip necrosis1 plays a pivotal role in the regulation of multiple phosphate starvation responses in rice.	although phosphate (pi) starvation signaling is well studied in arabidopsis (arabidopsis thaliana), it is still largely unknown in rice (oryza sativa). in this work, a rice leaf tip necrosis1 (ltn1) mutant was identified and characterized. map-based cloning identified ltn1 as loc_os05g48390, the putative ortholog of arabidopsis pho2, which plays important roles in pi starvation signaling. analysis of transgenic plants harboring a ltn1 promoter::β-glucuronidase construct revealed that ltn1 was pr ...	2011	21317339
fine mapping and candidate gene analysis of dense and erect panicle 3, dep3, which confers high grain yield in rice (oryza sativa l.).	architecture of the rice inflorescence, which is determined mainly by the morphology, number and length of primary and secondary inflorescence branches, is an important agronomical trait. in the current study, we characterized a novel dense and erect panicle (ep) mutant, dep3, derived from the oryza sativa ssp. japonica cultivar hwacheong treated with n-methyl-n-nitrosourea. the panicle of the dep3 mutant remained erect from flowering to full maturation, whereas the panicle of the wild type plan ...	2011	21318372
the role of tocopherol cyclase in salt stress tolerance of rice (oryza sativa).	tocopherols synthesized exclusively by photosynthetic organisms are major antioxidants in biomembranes. in plants, tocopherol cyclase (tc/vte1) catalyzes the conversion of 2,3-dimethyl-5-phytyl-1,4-benzoquinone (dmpbq) to γ-tocopherol. in the present study, osvte1, which encodes a rice tocopherol cyclase ortholog, was cloned and characterized. osvte1 was induced significantly by abiotic stresses such as high salt, h(2)o(2), drought, cold and by the plant hormones aba and salicylic acid. the tiss ...	2011	21318489
functional proteomic analysis of rice bran esterases/lipases and characterization of a novel recombinant esterase.	an esterase from rice ( oryza sativa ) bran was identified on two-dimensional gel using 4-methylumbelliferyl butyrate as a substrate. the esterase cdna (870 bp) encoded a 289 amino acid protein (designated osest-b) and was expressed in escherichia coli . the molecular weight of recombinant osest-b (rosest-b) was 27 kda, as measured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. biochemical characterization demonstrated that rosest-b was active over a broad temperature range (optim ...	2011	21322560
evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals.	the evolution of natural product biosynthetic pathways can be envisioned to occur via a number of mechanisms. in the present study we provide evidence that latent plasticity plays a role in such metabolic evolution. in particular, rice (oryza sativa) produces both ent- and syn-cpp (copalyl diphosphate), which are substrates for downstream diterpene synthases. in the present paper we report that several members of this enzymatic family exhibit dual reactivity with some pairing of ent-, syn- or no ...	0	21323642
distinct evolutionary patterns of oryza glaberrima deciphered by genome sequencing and comparative analysis.	here we present the genomic sequence of the african cultivated rice, oryza glaberrima, and compare these data with the genome sequence of asian cultivated rice, oryza sativa. we obtained gene-enriched sequences of o. glaberrima that correspond to about 25% of the gene regions of the o. sativa (japonica) genome by methylation filtration and subtractive hybridization of repetitive sequences. while patterns of amino acid changes did not differ between the two species in terms of the biochemical pro ...	2011	21323774
proteomic identification of oscyp2, a rice cyclophilin that confers salt tolerance in rice (oryza sativa l.) seedlings when overexpressed.	high salinity is a major environmental stress influencing growth and development of rice. comparative proteomic analysis of hybrid rice shoot proteins from shanyou 10 seedlings, a salt-tolerant hybrid variety, and liangyoupeijiu seedlings, a salt-sensitive hybrid variety, was performed to identify new components involved in salt-stress signaling.	2011	21324151
mutation of rice bc12/gdd1, which encodes a kinesin-like protein that binds to a ga biosynthesis gene promoter, leads to dwarfism with impaired cell elongation.	the kinesins are a family of microtubule-based motor proteins that move directionally along microtubules and are involved in many crucial cellular processes, including cell elongation in plants. less is known about kinesins directly regulating gene transcription to affect cellular physiological processes. here, we describe a rice (oryza sativa) mutant, gibberellin-deficient dwarf1 (gdd1), that has a phenotype of greatly reduced length of root, stems, spikes, and seeds. this reduced length is due ...	2011	21325138
high-resolution genetic mapping and candidate gene identification of the slp1 locus that controls glume development in rice.	stunted lemma palea 1 (slp1) is a rice mutant that displays dwarfism, shortened inflorescence lengths, severely degenerated lemmas/paleas, and sterility. the slp1 locus was mapped between markers rm447 and d275 in the distal region of the long arm of chromosome 8, using the f2 progeny derived from the cross between the slp1/slp1 mutant (oryza sativa subsp. japonica) and the variety taichung native 1 (tn1, o. sativa subsp. indica). the slp1 locus was further delimited to a 46.4-kb genomic region ...	2011	21327937
an extract from brown rice inhibits signal transduction of angiotensin ii in vascular smooth muscle cells.	health benefits of brown rice over white rice have been described previously. however, whether the outer bran of rice contains an ingredient useful to prevent cardiovascular diseases remains unknown. the subaleurone layer of rice, which is usually lost by milling brown rice for whitening, is rich in varied nutrients, suggesting that some ingredient contained within this layer may be beneficial for the cardiovascular system.	2011	21331052
rice plants expressing the moss sodium pumping atpase ppena1 maintain greater biomass production under salt stress.	high cytosolic concentrations of na(+) inhibit plant growth and development. to maintain low cytosolic concentrations of na(+) , higher plants use membrane-bound transporters that drive the efflux of na(+) or partition na(+) ions from the cytosol, either to the extracellular compartment or into the vacuole. bryophytes also use an energy-dependent na(+) pumping atpase, not found in higher plants, to efflux na(+) . to investigate whether this transporter can increase the salt tolerance of crop pla ...	2011	21338466
isolation and characterization of microsatellite loci in the asian rice gall midge (orseolia oryzae) (diptera: cecidomyiidae).	microsatellite loci were isolated from the genomic dna of the asian rice gall midge, orseolia oryzae (wood-mason) using a hybridization capture approach. a total of 90 non-redundant primer pairs, representing unique loci, were designed. these simple sequence repeat (ssr) markers represented di (72%), tri (15.3%), and complex repeats (12.7%). three biotypes of gall midge (20 individuals for each biotype) were screened using these ssrs. the results revealed that 15 loci were hyper variable and sho ...	2011	21340012
a recombinant a-dioxygenase from rice to produce fatty aldehydes using e. coli.	fatty aldehydes are an important group of fragrance and flavor compounds that are found in different fruits and flowers. a biotechnological synthesis of fatty aldehydes based on escherichia coli cells expressing an a-dioxygenase (adox) from oryza sativa (rice) is presented. a-dioxygenases are the initial enzymes of a-oxidation in plants and oxidize long and medium-chain c(n) fatty acids to 2-hydroperoxy fatty acids. the latter are converted to c(n-1) fatty aldehydes by spontaneous decarboxylatio ...	2011	21347727
characterization of mercury species in brown and white rice (oryza sativa l.) grown in water-saving paddies.	in china, total hg (hgt) and methylmercury (mehg) were quantified in rice grain grown in three sites using water-saving rice cultivation methods, and in one hg-contaminated site, where rice was grown under flooded conditions. polished white rice concentrations of hgt (water-saving: 3.3±1.6 ng/g; flooded: 110±9.2 ng/g) and mehg (water-saving 1.3±0.56 ng/g; flooded: 12±2.4 ng/g) were positively correlated with root-soil hgt and mehg contents (hgt: r2=0.97, mehg: r2=0.87, p<0.05 for both), which su ...	2011	21349615
ascorbate peroxidase-related (apx-r) is a new heme-containing protein functionally associated with ascorbate peroxidase but evolutionarily divergent.	• peroxidases are involved in several important processes, such as development and responses to environmental cues. in higher plants, most peroxidases are encoded by large, multigenic families that mainly originated from gene and chromosomal duplications. • using phylogenetic, genomic and functional analyses, we have identified and characterized a new class of putative heme peroxidases, called ascorbate peroxidase-related (apx-r), which arose specifically in the lineage of plants. • the apx-r pr ...	2011	21352234
an efficient and reproducible method for regeneration of whole plants from mature seeds of a high yielding indica rice (oryza sativa l.) variety pau 201.	tissue culture is one of the tools necessary for genetic engineering and many other breeding programs. moreover, selection of high regenerating rice varieties is a pre-requisite for success in rice biotechnology. in this report we established a reproducible plant regeneration system through somatic embryogenesis. the explants used for regeneration were embryogenic calli derived from mature seeds cultured on callus induction media. for callus induction mature seeds were cultured on ms medium cont ...	2011	21352959
net sodium fluxes change significantly at anatomically distinct root zones of rice (oryza sativa l.) seedlings.	casparian bands of endodermis and exodermis play crucial roles in blocking apoplastic movement of ions and water into the stele of roots through the cortex. these apoplastic barriers differ considerably in structure and function along the developing root. the present study assessed net na+ fluxes in anatomically distinct root zones of rice seedlings and analyzed parts of individual roots showing different na+ uptake. the results indicated that anatomically distinct root zones contributed differe ...	2011	21353327
sequencing and assembly of low copy and genic regions of isolated triticum aestivum chromosome arm 7ds.	the genome of bread wheat (triticum aestivum) is predicted to be greater than 16 gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. we have reduced genome sequence complexity by isolating chromosome arm 7ds and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. the assembly represents approximately 40% of the chromosome ...	2011	21356002
phytochromes regulate sa and ja signaling pathways in rice and are required for developmentally controlled resistance to magnaporthe grisea.	old leaves of wild-type rice plants (oryza sativa l. cv. nipponbare) are more resistant to blast fungus (magnaporthe grisea) than new leaves. in contrast, both old and new leaves of the rice phytochrome triple mutant (phyaphybphyc) are susceptible to blast fungus. we demonstrate that pathogenesis-related class 1 (pr1) proteins are rapidly and strongly induced during m. grisea infection and following exogenous jasmonate (ja) or salicylic acid (sa) exposure in the old leaves, but not in the new le ...	2011	21357645
a novel rice calmodulin-like gene, osmsr2, enhances drought and salt tolerance and increases aba sensitivity in arabidopsis.	many abiotic stimuli, such as drought and salt stresses, elicit changes in intracellular calcium levels that serve to convey information and activate adaptive responses. ca²⁺ signals are perceived by different ca²⁺ sensors, and calmodulin (cam) is one of the best-characterized ca²⁺ sensors in eukaryotes. calmodulin-like (cml) proteins also exist in plants, but their functions at the physiological and molecular levels are largely unknown. in this report, we present data on osmsr2 (oryza sativa l. ...	2011	21359958
[effects of sedum plumbizincicola--oryza sativa rotation and phosphate amendment on cd and zn uptake by o. sativa].	in a pot experiment, hyperaccumulator sedum plumbizincicola and low-cadmium accumulating oryza sativa cultivar "zhongxiang no. 1" were planted in rotation on a heavy metals-polluted soil, and calcium magnesium phosphate (ca-p) and rock phosphate (p-r) were amended, aimed to study the effects of the rotation and phosphate amendment on the growth of the two plants and the zinc- and cadmium accumulation in their shoots. after the amendment of 50 g p-r x kg(-1), the zn and cd uptake by s. plumbizinc ...	2010	21361023
microarray-based analysis of cadmium-responsive micrornas in rice (oryza sativa).	micrornas (mirnas) are a class of small non-coding rnas that negatively regulate specific target mrnas at the post-transcriptional level. plant mirnas have been implicated in developmental processes and adaptations to environmental stresses. cadmium (cd) is a non-essential heavy metal that is highly toxic to plants. to investigate the responsive functions of mirnas under cd stress, mirna expression in cd-stressed rice (oryza sativa) was profiled using a microarray assay. a total of 19 cd-respons ...	2011	21362738
a study of hassawi rice (oryza sativa l.) in terms of its carbohydrate hydrolysis (in vitro) and glycaemic and insulinaemic indices (in vivo).	a high prevalence of type 2 diabetes exists in saudi arabia. epidemiological evidence suggests that low glycaemic index (gi) diets reduce diabetes risk. yet, little is known about the gi of traditional saudi arabian staples such as hassawi rice (hr). hr was evaluated in terms of its gi and insulinaemic index (ii). comparisons were made in vitro assessing glucose released enzymatically. a long-grain rice variety available in both united kingdom and saudi arabia was studied as a comparison.	2011	21364610
relationship between xanthophyll cycle and non-photochemical quenching in rice (oryza sativa l.) plants in response to light stress.	thirty days old rice plants grown under low and moderate light conditions were transferred to full sunlight to observe the extent of photoinhibitory damage and protective mechanism, and the relationship between xanthophyll cycle and nonphotochemical quenching (qn) under changing light environment. control plants (low, moderate and sun grown) exhibited similar fv/fm ratio, indicating similar photosynthetic efficiency prior to light stress. on exposure to the high light treatment, low light grown ...	2011	21365998
the process of methylmercury accumulation in rice (oryza sativa l.).	recent studies have shown that rice consumption can be an important pathway of methylmercury (mehg) exposure to humans in hg mining areas and also in certain inland areas of southwestern china. the seed of rice has the highest ability to accumulate mehg compared to other tissues. the main objective of this study was to investigate the process of (mehg) accumulation in rice seed (oryza sativa l.) by monitoring mehg levels in specific tissues of rice plants experiencing various levels of hg multis ...	2011	21366217
cloning and functional characterization of a cation-chloride cotransporter gene osccc1.	potassium (k+) and chloride (cl-) are two essential elements for plant growth and development. while it is known that plants possess specific membrane transporters for transporting k+ and cl-, it remains unclear if they actively use k+-coupled cl- cotransporters (kcc), as used in animals, to transport k+ and cl-. we have cloned an oryza sativa cdna encoding for a member of the cation-cl- cotransporter (ccc) family. phylogenetic analysis revealed that plant ccc proteins are highly conserved and t ...	2011	21369877
isolation, characterization and quantification of tricin and flavonolignans in the medicinal rice njavara (oryza sativa l.), as compared to staple varieties.	njavara is an important medicinal rice variety of kerala, india, widely used in ayurveda as a 'health food' and in the treatment of rheumatoid arthritis, paralysis, neurodegenerative diseases and in rejuvenation therapy. phytochemical investigations and spectroscopic studies of the diethyl ether fraction of methanolic extract of njavara black (nb) rice bran gave three important compounds namely, tricin and two rare flavonolignans- tricin 4'-o-(erythro-ß-guaiacylglyceryl) ether and tricin 4'-o-(t ...	2011	21373805
golgi nucleotide sugar transporter modulates cell wall biosynthesis and plant growth in rice.	golgi-localized nucleotide sugar transporters (nsts) are considered essential for the biosynthesis of wall polysaccharides and glycoproteins based on their characteristic transport of a large number of nucleotide sugars to the golgi lumen. the lack of nst mutants in plants has prevented evaluation of this hypothesis in plants. a previously undescribed golgi nst mutant, brittle culm14 (bc14), displays reduced mechanical strength caused by decreased cellulose content and altered wall structure, an ...	2011	21383162
a preliminary study of the protease activities in germinating brown rice (oryza sativa l.).	proteases hydrolyse storage proteins to provide precursors for perpetuating species. the aim of this study was to investigate and characterise different proteases in germinating brown rice.	2011	21384360
diversity and selective sweep in the osamt1;1 genomic region of rice.	ammonium is one of the major forms in which nitrogen is available for plant growth. osamt1;1 is a high-affinity ammonium transporter in rice (oryza sativa l.), responsible for ammonium uptake at low nitrogen concentration. the expression pattern of the gene has been reported. however, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. in this study, nucleotide diversity of the gene osamt1;1 and the diversity pattern of seven ...	2011	21385389
exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis.	extensive dna rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. however, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.	2011	21385395
analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ick/krp family of plant cdk inhibitors.	the cell cycle is controlled by cyclin-dependent kinases (cdks), and cdk inhibitors are major regulators of their activities. the ick/krp family of cdk inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. also, there is a need to understand how these genes and proteins are regulated. furthermore, little information is available on the functional differences among ick/krp family mem ...	2011	21385782
transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves.	plant diurnal oscillation is a 24-hour period based variation. the correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. rice (oryza sativa) is the major food staple for about half of the world's population. the rice flag leaf is essential in providing photosynthates to the grain filling. however, there is still no comprehensive view about the diurnal transcriptome for rice leaves. in this study, we applied rice microarray to m ...	2011	21407816
differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of oryza sativa (rice).	a dwarfing gene (allele) sd1-d has been intensively utilized to develop short-culm indica varieties in southeast asia up to now. before the first sd1-d-carrying variety ir8 was released, rice researchers had recognized the general tendency that culm length is higher in indica varieties than in temperate-japonica ones. inter-subspecific difference of the tall (wild-type) allele sd1 at the sd1 locus was examined on the common genetic background, using five isogenic lines developed by substituting ...	2011	21410466
nitric oxide production is associated with response to brown planthopper infestation in rice.	nilaparvata lugens stål, the brown planthopper (bph), is one of the most destructive phloem-feeding insects of rice (oryza sativa l.) throughout asia. here, we show that bph feeding increases the level of endogenous nitric oxide (no) in the leaf and sheath tissue of both resistant and susceptible rice cultivars. however, in the roots, the no level increased in the resistant cultivar, but decreased in the susceptible one. a burst of no production occurred in the sheath within 1 h of infestation w ...	2011	21411180
cadmium accumulation in and tolerance of rice (oryza sativa l.) varieties with different rates of radial oxygen loss.	cadmium (cd) uptake and tolerance were investigated among 20 rice cultivars based on a field experiment (1.2 mg cd kg⁻¹ in soil) and a soil pot trial (control, 100 mg cd kg⁻¹), and rates of radial oxygen loss (rol) were measured under a deoxygenated solution. significant differences were found among the cultivars in: (1) brown rice cd concentrations (0.11-0.29 mg kg⁻¹) in a field soil, (2) grain cd tolerance (34-113%) and concentrations (2.1-6.5 mg kg⁻¹) in a pot trial, and (3) rates of rol (15- ...	2011	21411196
modulating rice stress tolerance by transcription factors.	plants are non-mobile organisms and have to adapt to environmental stresses mostly by modulating their growth and development in addition to physiological and biochemical changes. transcription factors (tfs) regulate genome expression in response to environmental and physiological signals, and some of them switch on plant adaptive developmental and physiological pathways. one tf is encoded by a single gene but regulates the expression of several other genes leading to the activation of complex a ...	2008	21412363
stagnant deoxygenated growth enhances root suberization and lignifications, but differentially affects water and nacl permeabilities in rice (oryza sativa l.) roots.	it has been shown that rice roots grown in a stagnant medium develop a tight barrier to radial oxygen loss (rol), whereas aerated roots do not. this study investigated whether the induction of a barrier to rol affects water and solute permeabilities. growth in stagnant medium markedly reduced the root growth rate relative to aerated conditions. histochemical studies revealed an early deposition of casparian bands (cbs) and suberin lamellae (sl) in both the endodermis (en) and exodermis, and acce ...	2011	21414017
comprehensive sequence analysis of 24,783 barley full-length cdnas derived from 12 clone libraries.	full-length cdna (flcdna) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (hordeum vulgare 'haruna nijo') under normal and stressed conditions. after sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. by removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley flcdnas, and 1,699 were barley specific. ...	2011	21415278
zinc absorption from low phytic acid genotypes of maize (zea mays l.), barley (hordeum vulgare l.), and rice (oryza sativa l.) assessed in a suckling rat pup model.	dietary phytic acid is a major causative factor for low zn bioavailability in many cereal- and legume-based diets. the bioavailability of zn in seed of low phytic acid (lpa) variants of maize ( zea mays l.), rice ( oryza sativa l.), and barley ( hordeum vulgare l.) was evaluated using a suckling rat pup model. suckling rat pups (14 days old, n = 6-8/treatment) were fasted for 6 h and intubated with (65)zn-radiolabeled suspensions prepared using seed produced by either wild-type (normal phytic ac ...	2011	21417220
rice cyp734as function as multisubstrate and multifunctional enzymes in brassinosteroid catabolism.	catabolism of brassinosteroids regulates the endogenous level of bioactive brassinosteroids. in arabidopsis thaliana, bioactive brassinosteroids such as castasterone (cs) and brassinolide (bl) are inactivated mainly by two cytochrome p450 monooxygenases, cyp734a1/bas1 and cyp72c1/sob7/chi2/shk1; cyp734a1/bas1 inactivates cs and bl by means of c-26 hydroxylation. here, we characterized cyp734a orthologs from oryza sativa (rice). overexpression of rice cyp734as in transgenic rice gave typical bras ...	2011	21418356
genetic analysis of two weak dormancy mutants derived from strong seed dormancy wild type rice n22 (oryza sativa).	two weak dormancy mutants, designated q4359 and q4646, were obtained from the rice cultivar n22 after treatment with 400 gy (60) co gamma-radiation. compared to the n22 cultivar, the dormancy of the mutant seeds was more readily broken when exposed to a period of room temperature storage. the mutants also showed a reduced level of sensitivity to abscisic acid compared to the n22 cultivar, although q4359 was more insensitive than q4646. a genetic analysis indicated that in both mutants, the reduc ...	2011	21418523
ricerbp: a database of experimentally identified rna-binding proteins in oryza sativa l.	rna-binding proteins play critical roles at multiple steps during gene expression, including mrna transport and translation. mrna transport is particularly important in rice (oryza sativa l.) in order to ensure the proper localization of the prolamine and glutelin seed storage proteins. however, relatively little information is available about rna-binding proteins that have been isolated or characterized in plants. the ricerbp database is a novel resource for the analysis of rna-binding proteins ...	2011	21421362
developmental characteristics and aluminum resistance of root border cells in rice seedlings.	the developmental characteristics of root border cells (rbcs) and their role in protection of root apices of rice seedling from al toxicity were evaluated in two rice (oryza sativa l.) cultivars differing in al tolerance. root elongation and rbcs viability were used as indicators for al effects. the formation of rbcs and the emergence of the root tip occurred almost simultaneously. treatment of the root with al inhibited root elongation and increased al accumulation in the root tips. physical re ...	2011	21421421
utilization of weedy rice for development of japonica hybrid rice (oryza sativa l.).	two representative weedy rice lines, three typical japonica varieties and three typical indica varieties were used for 6 pairs of reciprocal crosses. the morphological traits of twelve f(1) hybrid lines, their parents and four elite cultivars were investigated for heterosis over mid-parent (hm), over parent (hp) and competitive heterosis (ch) analysis. traits detected in weedy rice lines seemed larger than those in cultivars and excellent heterosis was produced in weedy rice crossing with japoni ...	2011	21421425
population-specific quantitative trait loci mapping for functional stay-green trait in rice (oryza sativa l.).	the functional stay-green trait gives leaves a longer duration of greenness and photosynthetic capacity during the grain-filling period. we developed two independent recombinant inbred line populations from the intra- and intersubspecific crosses of oryza sativa l. subsp. japonica 'suweon490' (japonica) × o. sativa subsp. japonica 'snu-sg1' (japonica) and o. sativa subsp. indica 'andabyeo' (indica) × o. sativa subsp. japonica 'snu-sg1' (japonica), respectively. the common parental line 'snu-sg1' ...	2011	21423286
patterns of sequence divergence and evolution of the s orthologous regions between asian and african cultivated rice species.	a strong postzygotic reproductive barrier separates the recently diverged asian and african cultivated rice species, oryza sativa and o. glaberrima. recently a model of genetic incompatibilities between three adjacent loci: s(1)a, s(1) and s(1)b (called together the s(1) regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. two candidate factors for the s(1) locus (including a putative f-box gene) were proposed, but candid ...	2011	21423767
high-resolution mapping of rsn1, a locus controlling sensitivity of rice to a necrosis-inducing phytotoxin from rhizoctonia solani ag1-ia.	rhizoctonia solani is a necrotrophic fungal pathogen that causes disease on many crop-plant species. anastomosis group 1-ia is the causal agent of sheath blight of rice (oryza sativa l.), one of the most important rice diseases worldwide. r. solani ag1-ia produces a necrosis-inducing phytotoxin and rice cultivar's sensitivity to the toxin correlates with disease susceptibility. unlike genetic analyses of sheath blight resistance where resistance loci have been reported as quantitative trait loci ...	2011	21424397
rice root-associated bacteria: insights into community structures across 10 cultivars.	in this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. thus, total bacteria, alpha- and betaproteobacteria, pseudomonas and actinobacteria were studied using pcr, followed by denaturing gradient gel electrophoresis (pcr-dgge). rice genotype determined, to a large extent, the composition of the different bacterial communities across cultivars. several cultivars belongin ...	2011	21426364
integrated proteome and metabolite analysis of the de-etiolation process in plastids from rice (oryza sativa l.).	we have analyzed the dynamics of the rice etioplast membrane proteome during the early phase of de-etiolation using itraq-based relative protein quantification. several hundred plastid proteins were identified from enriched membranes, including 36 putative transporters. hierarchical clustering revealed the coordinated light induction of thylakoid membrane proteins with proteins involved in translation and fatty acid metabolism. no other functional category of identified proteins showed a similar ...	2011	21433289
functional diversity of isoamylase oligomers: the isa1 homo-oligomer is essential for amylopectin biosynthesis in rice endosperm.	rice (oryza sativa) endosperm has two isoamylase (isa) oligomers, isa1 homo-oligomer and isa1-isa2 hetero-oligomer. to examine their contribution to starch synthesis, expression of the isa1 or isa2 gene was differently regulated in various transgenic plants. although suppression of isa2 gene expression caused the endosperm to have only the homo-oligomer, no significant effects were detected on the starch phenotypes. in contrast, isa2 overexpression led to endosperm having only the hetero-oligome ...	2011	21436381
prediction of new abiotic stress genes in arabidopsis thaliana and oryza sativa according to enumeration-based statistical analysis.	plants undergo an extensive change in gene regulation during abiotic stress. it is of great agricultural importance to know which genes are affected during stress response. the genome sequence of a number of plant species has been determined, among them arabidopsis and oryza sativa, whose genome has been annotated most completely as of yet, and are well-known organisms widely used as experimental systems. this paper applies a statistical algorithm for predicting new stress-induced motifs and gen ...	2011	21437642
determination of folate content in rice germplasm (oryza sativa l.) using tri-enzyme extraction and microbiological assays.	nutritional deficiencies of folate cause neural tube defects and several other diseases. the tri-enzyme method and microbiological assays were used to investigate folate variation in 78 rice germplasms. the effects of storage and cooking on folate content were also analyzed. folate contents of brown rice varied substantially from 13.3 to 111.4-á++g/100-ág, whereas milled rice varied from 10.3 to 77.7-á++g/100-ág. four cultivars from south china with high folate levels were identified in both sub ...	2011	21438705
antifungal activity of wickerhamomyces anomalus and lactobacillus plantarum during sourdough fermentation: identification of novel compounds and long-term effect during storage of wheat bread.	this study aimed at investigating the antifungal activity of wickerhamomyces anomalus and sourdough lactic acid bacteria to extend the shelf life of wheat flour bread. the antifungal activity was assayed by agar diffusion, growth rate inhibition, and conidial germination assays, using penicillium roqueforti dppmaf1 as the indicator fungus. sourdough fermented by lactobacillus plantarum 1a7 (s1a7) and dough fermented by w. anomalus lcf1695 (d1695) were selected and characterized. the water/salt-s ...	2011	21441340
plantmirnapred: efficient classification of real and pseudo plant pre-mirnas.	micrornas (mirnas) are a set of short (21-24 nt) non-coding rnas that play significant roles as post-transcriptional regulators in animals and plants. while some existing methods use comparative genomic approaches to identify plant precursor mirnas (pre-mirnas), others are based on the complementarity characteristics between mirnas and their target mrnas sequences. however, they can only identify the homologous mirnas or the limited complementary mirnas. furthermore, since the plant pre-mirnas a ...	2011	21441575
evolution of the number of lrrs in plant disease resistance genes.	the largest group of plant resistance (r) genes contain the regions that encode the nucleotide-binding site (nbs) and leucine-rich repeat (lrr) domains (nbs-lrr genes). to gain new resistance, amino acid substitutions and changes in number of the lrrs that recognize the presence of pathogens are considered important. in this study, we focus on the evolution of the number of lrrs and analyze the genome data of five plant species, arabidopsis thaliana, oryza sativa, medicago truncatula, lotus japo ...	2011	21442326
an evolutionary view of functional diversity in family 1 glycosyltransferases.	glycosyltransferases (gts) (ec 2.4.x.y) catalyze the transfer of sugar moieties to a wide range of acceptor molecules, such as sugars, lipids, proteins, nucleic acids, antibiotics and other small molecules, including plant secondary metabolites. these enzymes can be classified into at least 92 families, of which family 1 glycosyltransferases (gt1), often referred to as udp glycosyltransferases (ugts), is the largest in the plant kingdom. to understand how ugts expanded in both number and functio ...	2011	21443631
complex evolution of s5, a major reproductive barrier regulator, in the cultivated rice oryza sativa and its wild relatives.	• the hybrid sterility gene s5 comprises three types of alleles in cultivated rice. such tri-allelic system provided a unique opportunity to study the molecular bases of evolutionary changes underlying reproductive isolation in plants. • we analysed the sequence diversity and evolutionary history of s5 in 138 oryza accessions. we also examined the effect of the two functional variations (c819a and c1412t) in determining hybrid sterility by transformation. • nineteen haplotypes were identified, w ...	2011	21443693
high time for a roll call: gene duplication and phylogenetic relationships of tcp-like genes in monocots.	the tcp family is an ancient group of plant developmental transcription factors that regulate cell division in vegetative and reproductive structures and are essential in the establishment of flower zygomorphy. in-depth research on eudicot tcps has documented their evolutionary and developmental role. this has not happened to the same extent in monocots, although zygomorphy has been critical for the diversification of orchidaceae and poaceae, the largest families of this group. investigating the ...	2011	21444336
genetic interaction of osmads3, drooping leaf, and osmads13 in specifying rice floral organ identities and meristem determinacy.	grass plants develop unique floral patterns that determine grain production. however, the molecular mechanism underlying the specification of floral organ identities and meristem determinacy, including the interaction among floral homeotic genes, remains largely unknown in grasses. here, we report the interactions of rice (oryza sativa) floral homeotic genes, osmads3 (a c-class gene), osmads13 (a d-class gene), and drooping leaf (dl), in specifying floral organ identities and floral meristem det ...	2011	21444646
[dna-identification of rice varieties (oryza sativa l.) of ukrainian selection].	genetic diversity of 11 rice varieties of the institute of rice uaas was assessed using a set of 25 ssr loci. based on analyses of 12 polymorphic microsatillite loci the procedures for composing genetic formulas of varieties and their identification have been elaborated. upgma-cluster-analysis based on genetic distance coefficients clearly separated all the varieties into two groups, and showed that the ukrainian rice varieties are closely related. although the genetic diversity was low, ssrs pr ...	2015	21446157
mutations in the f-box gene larger panicle improve the panicle architecture and enhance the grain yield in rice.	panicle architecture is one of the most important agronomical traits that directly contribute to grain yield in rice (oryza sativa l.). we report herein an in-depth characterization of two allelic larger panicle (lp) mutants that show significantly increased panicle size as well as improved plant architecture. morphological analyses reveal that panicles of two mutants produced more inflorescence branches, especially the primary branches, and contained more grains. moreover, mutant plants also di ...	2011	21447055
exploration of plant genomes in the flagdb++ environment.	in the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas.	2011	21447150
rice gh3 gene family: regulators of growth and development.	auxin is an indispensable hormone throughout the lifetime of nearly all plant species. several aspects of plant growth and development are rigidly governed by auxin, from micro to macro hierarchies; auxin also has a close relationship with plant-pathogen interactions. undoubtedly, precise auxin levels are vitally important to plants, which have many effective mechanisms to maintain auxin homeostasis. one mechanism is conjugating amino acid to excessive indole-3-acetic acid (iaa; main form of aux ...	2011	21447996
transgenic rice expressing amyloid ß-peptide for oral immunization.	various vaccine therapies for alzheimer's disease (ad) have been investigated. here we report transgenic rice expressing amyloid ß-peptide (aß). the aß42 gene fused with a green fluorescent protein gene was introduced into rice using the agrobacterium method. when transgenic brown rice expressing aß was orally administered to mice, serum anti-aß antibody titers were elevated. the same results were observed when mice were fed boiled, transgenic brown rice. the results indicate that an edible vacc ...	2011	21448341
integration of crop rotation and arbuscular mycorrhiza (am) inoculum application for enhancing am activity to improve phosphorus nutrition and yield of upland rice (oryza sativa l.).	upland rice (oryza sativa l.) is a major crop of eastern india grown during the wet season (june/july to september/october). aerobic soils of the upland rice system, which are acidic and inherently phosphorus (p) limiting, support native arbuscular mycorrhizal (am) activity. attempts were made to improve p nutrition of upland rice by exploiting this natural situation through different crop rotations and application of am fungal (amf) inoculum. the effect of a 2-year crop rotation of maize (zea m ...	2011	21448812
rice-map: a new-generation rice genome browser.	the concurrent release of rice genome sequences for two subspecies (oryza sativa l. ssp. japonica and oryza sativa l. ssp. indica) facilitates rice studies at the whole genome level. since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. based on next-generation web technologies and high-throughput experimental data, we have dev ...	2011	21450055
overexpression of the mitogen-activated protein kinase gene osmapk33 enhances sensitivity to salt stress in rice (oryza sativa l.).	mitogen-activated protein kinases (mapk) signalling cascades are activated by extracellular stimuli such as environmental stresses and pathogens in higher eukaryotic plants. to know more about mapk signalling in plants, amapk cdna clone, osmapk33, was isolated from rice. the gene is mainly induced by drought stress. in phylogenetic analysis, osmapk33 (os02g0148100) showed approximately 47-93% identity at the amino acid level with other plant mapks. it was found to exhibit organ-specific expressi ...	2011	21451255
studies of o,o-dimethyl α-(2,4-dichlorophenoxyacetoxy)ethylphosphonate (hw02) as a new herbicide. 1. synthesis and herbicidal activity of hw02 and analogues as novel inhibitors of pyruvate dehydrogenase complex.	on the basis of the previous work for optimization of o,o-diethyl α-(substituted phenoxyacetoxy)alkylphosphonates, further extensive synthetic modifications were made to the substituents in alkylphosphonate and phenoxy moieties of the title compounds. new o,o-dimethyl α-(substituted phenoxyacetoxy)alkylphosphonates were synthesized as potential inhibitors of pyruvate dehydorogenase complex (pdhc). their herbicidal activity and efficacy in vitro against pdhc were examined. some of these compounds ...	2011	21452831
three-dimensional root phenotyping with a novel imaging and software platform.	a novel imaging and software platform was developed for the high-throughput phenotyping of three-dimensional root traits during seedling development. to demonstrate the platform's capacity, plants of two rice (oryza sativa) genotypes, azucena and ir64, were grown in a transparent gellan gum system and imaged daily for 10 d. rotational image sequences consisting of 40 two-dimensional images were captured using an optically corrected digital imaging system. three-dimensional root reconstructions w ...	2011	21454799
genotypic variation in sulphur assimilation and metabolism of onion (allium cepa l.). ii: characterisation of atp sulphurylase activity.	to investigate the regulation of sulphur (s)-assimilation in onion further at the biochemical level, the pungent cultivar w202a and the milder cultivar texas grano 438 pvp (tg) have been grown in s-sufficient (s(+); 4meqs(-1)) or s-deficient (s(-); 0.1meqs(-1)) growth conditions, and tissues excised at the seedling stage (pre-bulbing; ca. 10-weeks-old) and at the mature stage (bulbing; ca. 16-weeks-old). s-supply negatively influenced adenosine-5'-phosphosulphate (aps) reductase (apr) enzyme act ...	2011	21459393
lessons from engineering a single-cell c(4) photosynthetic pathway into rice.	the transfer of c(4) plant traits into c(3) plants has long been a strategy for improving the photosynthetic performance of c(3) plants. the introduction of a pathway mimicking the c(4) photosynthetic pathway into the mesophyll cells of c(3) plants was only a realistic approach when transgenic technology was sufficiently well developed and widely adopted. here an attempt to introduce a single-cell c(4)-like pathway in which co(2) capture and release occur in the mesophyll cell, such as the one f ...	2011	21459764
a possible new mechanism involved in ferro-cyanide metabolism by plants.	ferro-cyanide is one of the commonly found species at cyanide-contaminated soils and groundwater. unlike botanical metabolism of kcn via the β-cyanoalanine pathway, processes involved in the plant-mediated assimilation of ferro-cyanide are still unclear. the objective of this study was to investigate a possible mechanism involved in uptake and assimilation of ferro-cyanide by plants.	2011	21465162
influence of short-term silicon application on endogenous physiohormonal levels of oryza sativa l. under wounding stress.	the current study was conducted in order to investigate the short-term effects (6, 12, and 24 h) of silicon (si) on the endogenous hormonal composition of rice (oryza sativa l. cv. dongjin-beyo), with and without wounding stress. si applied in different concentrations (0.5, 1.0, and 2.0 mm) significantly promoted shoot length, plant biomass, and chlorophyll content of rice plants. plants treated with different concentrations of sole si for 6, 12, and 24 h had higher endogenous jasmonic acid cont ...	2011	21465280
rice apoptosis inhibitor5 coupled with two dead-box adenosine 5'-triphosphate-dependent rna helicases regulates tapetum degeneration.	programmed cell death (pcd) during tapetum degeneration in postmeiotic anthers is critical for the proper development of male gametophytes in flowering plants. although several genes involved in this process have been identified recently, the molecular mechanism is still poorly understood. here, we show that knockout of rice (oryza sativa) apoptosis inhibitor5 (api5), which encodes a putative homolog of antiapoptosis protein api5 in animals, results in delayed degeneration of the tapetum due to ...	2011	21467577
unlocking the barley genome by chromosomal and comparative genomics.	we used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (hordeum vulgare) genes to individual chromosome arms. using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (oryza sativa), sorghum (sorghum bicolor), and brachypodium distachyon in a conserved synteny model, we were able to as ...	2011	21467582
collinearity-based marker mining for the fine mapping of pm6, a powdery mildew resistance gene in wheat.	the genome sequences of rice (oryza sativa l.) and brachypodium distachyon and the comprehensive triticeae est (expressed sequence tag) resources provide invaluable information for comparative genomics analysis. the powdery mildew resistance gene, pm6, which was introgressed into common wheat from triticum timopheevii, was previously mapped to the wheat chromosome bin of 2bl [fraction length (fl) 0.50-1.00] with limited dna markers. in this study, we saturated the pm6 locus in wheat using the co ...	2011	21468676
comparative genetic analysis of a wheat seed dormancy qtl with rice and brachypodium identifies candidate genes for aba perception and calcium signaling.	wheat preharvest sprouting (phs) occurs when seed germinates on the plant before harvest resulting in reduced grain quality. in wheat, phs susceptibility is correlated with low levels of seed dormancy. a previous mapping of quantitative trait loci (qtl) revealed a major phs/seed dormancy qtl, qphs.cnl-2b.1, located on wheat chromosome 2b. a comparative genetic study with the related grass species rice (oryza sativa l.) and brachypodium distachyon at the homologous region to the qphs.cnl-2b.1 int ...	2011	21468744
mitigation effects of silicon rich amendments on heavy metal accumulation in rice (oryza sativa l.) planted on multi-metal contaminated acidic soil.	the mechanisms of stabilization by silicon-rich amendments of cadmium, zinc, copper and lead in a multi-metal contaminated acidic soil and the mitigation of metal accumulation in rice were investigated in this study. the results from a pot experiment indicated that the application of fly ash (20 and 40gkg(-1)) and steel slag (3 and 6gkg(-1)) increased soil ph from 4.0 to 5.0-6.4, decreased the phytoavailability of heavy metals by at least 60%, and further suppressed metal uptake by rice. diffusi ...	2011	21470654
gene space dynamics during the evolution of aegilops tauschii, brachypodium distachyon, oryza sativa, and sorghum bicolor genomes.	nine different regions totaling 9.7 mb of the 4.02 gb aegilops tauschii genome were sequenced using the sanger sequencing technology and compared with orthologous brachypodium distachyon, oryza sativa (rice), and sorghum bicolor (sorghum) genomic sequences. the ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. the total gene number in the extant ae. tauschii geno ...	2011	21470968
the interconversion of udp-arabinopyranose and udp-arabinofuranose is indispensable for plant development in arabidopsis.	l-ara, an important constituent of plant cell walls, is found predominantly in the furanose rather than in the thermodynamically more stable pyranose form. nucleotide sugar mutases have been demonstrated to interconvert udp-l-arabinopyranose (udp-arap) and udp-l-arabinofuranose (udp-araf) in rice (oryza sativa). these enzymes belong to a small gene family encoding the previously named reversibly glycosylated proteins (rgps). rgps are plant-specific cytosolic proteins that tend to associate with ...	2011	21478444
expression of rice sub1a and sub1c transcription factors in arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism.	submergence of plant organs perturbs homeostasis by limiting diffusion of oxygen, carbon dioxide and ethylene. in rice (oryza sativa l.), the haplotype at the multigenic submergence1 (sub1) locus determines whether plants survive prolonged submergence. sub1 encodes two or three transcription factors of the group vii ethylene response factor family: sub1a, sub1b and sub1c. the presence of sub1a-1 and its strong submergence-triggered ethylene-mediated induction confers submergence tolerance throug ...	2011	21481028
expression analysis of the nucleocytoplasmic lectin 'orysata' from rice in pichia pastoris.	the oryza sativa lectin, abbreviated orysata, is a mannose-specific, jacalin-related lectin expressed in rice plants after exposure to certain stress conditions. expression of a fusion construct containing the rice lectin sequence linked to enhanced green fluorescent protein in bright yellow 2 tobacco cells revealed that orysata is located in the nucleus and the cytoplasm of the plant cell, indicating that it belongs to the class of nucleocytoplasmic jacalin-related lectins. since the expression ...	2011	21481190
a conserved cysteine motif is critical for rice ceramide kinase activity and function.	ceramide kinase (cerk) is a key regulator of cell survival in dicotyledonous plants and animals. much less is known about the roles of cerk and ceramides in mediating cellular processes in monocot plants. here, we report the characterization of a ceramide kinase, oscerk, from rice (oryza sativa spp. japonica cv. nipponbare) and investigate the effects of ceramides on rice cell viability.	2011	21483860
rice osnar2.1 interacts with osnrt2.1, osnrt2.2 and osnrt2.3a nitrate transporters to provide uptake over high and low concentration ranges.	plants take up both nitrate and ammonium as main nitrogen (n) sources. although ammonium is the predominant form in anaerobic-flooded paddy soil, it has been proposed that rice and other wetland plants may take up significant amounts of nitrate formed by nitrification of ammonium in the rhizosphere. a two-component system for nitrate transport including nrt2s with a partner protein (nar2 or nrt3.1) has been identified in arabidopsis. we report the physiological function of another member of the ...	2011	21486304
the bphi008a gene interacts with the ethylene pathway and transcriptionally regulates mapk genes in the response of rice to brown planthopper feeding.	we examined ways in which the brown planthopper induced008a (bphi008a; ay256682) gene of rice (oryza sativa) enhances the plant's resistance to a specialist herbivore, the brown planthopper (bph; nilaparvata lugens). measurement of the expression levels of ethylene synthases and of ethylene emissions showed that bph feeding rapidly initiated the ethylene signaling pathway and up-regulated bphi008a transcript levels after 6 to 96 h of feeding. in contrast, blocking ethylene transduction (using 1- ...	2011	21487048
bio-concentration of chromium--an in situ phytoremediation study at south kaliapani chromite mining area of orissa, india.	mine waste water at south kaliapani usually contains toxic levels of hexavalent cr(vi). the present in situ study was conducted at south kaliapani chromite mine area in orissa state, india, to assess the phytoremediation ability of three plants, namely, rice (oryza sativa l.), paragrass (brachiaria mutica), and an aquatic weed (eichhornia crassipes), in attenuating cr(vi) from mine waste water and to correlate the bio-concentration factors (bcf) of cr. water hyacinth (e. crassipes) showed 24% to ...	2012	21487717
distinct mechanisms for aerenchyma formation in leaf sheaths of rice genotypes displaying a quiescence or escape strategy for flooding tolerance.	rice is one of the few crops able to withstand periods of partial or even complete submergence. one of the adaptive traits of rice is the constitutive presence and further development of aerenchyma which enables oxygen to be transported to submerged organs. the development of lysigenous aerenchyma is promoted by ethylene accumulating within the submerged plant tissues, although other signalling mechanisms may also co-exist. in this study, aerenchyma development was analysed in two rice (oryza sa ...	2011	21489969
high-resolution secondary ion mass spectrometry reveals the contrasting subcellular distribution of arsenic and silicon in rice roots.	rice (oryza sativa) takes up arsenite mainly through the silicic acid transport pathway. understanding the uptake and sequestration of arsenic (as) into the rice plant is important for developing strategies to reduce as concentration in rice grain. in this study, the cellular and subcellular distributions of as and silicon (si) in rice roots were investigated using high-pressure freezing, high-resolution secondary ion mass spectrometry, and transmission electron microscopy. rice plants, both the ...	2011	21490163
crystal structure of the branching enzyme i (bei) from oryza sativa l with implications for catalysis and substrate binding.	starch branching enzyme (sbe) catalyzes the cleavage of α-1,4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. sequence analysis of the rice branching enzyme i (bei) indicated a modular structure in which the central α-amylase domain is flanked on each side by the n-terminal carbohydrate binding module (cbm48) and the α-amylase c-domain. we determined the crystal structure of bei at a resolution of 1.9 å by molecular replacement using the escheri ...	2011	21493662
biochemical and structural properties of cyanases from arabidopsis thaliana and oryza sativa.	cyanate is toxic to all organisms. cyanase converts cyanate to co₂ and nh₃ in a bicarbonate-dependent reaction. the biophysical functions and biochemical characteristics of plant cyanases are poorly studied, although it has been investigated in a variety of proteobacteria, cyanobacteria and fungi. in this study, we characterised plant cyanases from arabidopsis thaliana and oryza sativa (atcyn and oscyn). prokaryotic-expressed atcyn and oscyn both showed cyanase activity in vitro. temperature had ...	2011	21494323
freshwater toxic cyanobacteria induced dna damage in apple (malus pumila), rape (brassica napus) and rice (oryza sativa).	cyanobacteria in freshwater ecosystems can present a harmful effect on growth and development of plants through irrigation with contaminated water. in this study, the effects of microcystins (mcs)-containing cyanobacteria extract (ce) on dna damage of apple, rape and rice were investigated to explore the phytotoxic mechanism of mcs through dna fragmentation and rapd analysis. determination of dna fragmentation by fluorescent dye dapi showed that significant dna damage was observed in rice seedli ...	2011	21497440
the physiological mechanism of a drooping leaf2 mutation in rice.	here we characterized a classic rice (oryza sativa) drooping leaf2 mutant (named dl2). the dl2 allele affects both the midrib development and the total leaf venation pattern. leaf anatomy results revealed the central vein lacks both clear cells and the adaxial small vascular bundle in dl2 mutant, which seemed to cause the drooping leaf phenotype. the dl2 leaves contain more small veins, and the size of the vascular cylinder in dl2 leaf is also altered. furthermore, similar anatomy alteration was ...	2011	21497711
improved agrobacterium-mediated co-transformation and selectable marker elimination in transgenic rice by using a high copy number pbin19-derived binary vector.	a high copy number, selectable marker gene (smg)-free agrobacterium binary vector pbin19δnptii was constructed by deleting the nptii gene from pbin19. the binary vectors with the rk2 and pvs replication origins exist in 12 and 3 copies, respectively, in agrobacterium. the tobacco osmotin gene (ap24) was cloned in pbin19δnptii and the resultant plasmid pbin19δnptii-ap24 was mobilized into the agrobacterium tumefaciens strain c58c1 rif(r) harbouring the single-copy cointegrate vector pgv2260::pssj ...	2011	21497712
overexpression of osrdcp1, a rice ring domain-containing e3 ubiquitin ligase, increased tolerance to drought stress in rice (oryza sativa l.).	carma1h1 was previously identified as a hot pepper drought-induced ring e3 ub ligase. we have identified five putative proteins that display a significant sequence identity with carma1h1 in the rice genome database (http://signal.salk.edu/cgi-bin/ricege). these five rice paralogs possess a single ring motif in their n-terminal regions, consistent with the notion that ring proteins are encoded by a multi-gene family. therefore, these proteins were named osrdcps (oryza sativa ring domain-containin ...	2011	21497713
ossdir1 overexpression greatly improves drought tolerance in transgenic rice.	recent genomic and genetic analyses based on arabidopsis suggest that ubiquitination plays crucial roles in the plant response to abiotic stress and the phytohormone abscisic acid (aba). however, few such studies have been reported in rice as a monocotyledonous model plant. taking advantage of strategies in biochemistry, molecular cell biology and genetics, the ring-finger containing e3 ligase ossdir1 (oryza sativa salt-and drought-induced ring finger 1) was found to be a candidate drought toler ...	2011	21499841
phosphate transporter gene, ospht1;8, is involved in phosphate homeostasis in rice.	plant phosphate transporters (pts) are active in the uptake of inorganic phosphate (pi) from the soil and it's translocation within the plant. here, we report on the biological properties and physiological roles of ospht1;8 (ospt8), one of the pts belonging to the pht1 family in rice (oryza sativa l.). expression of gus (£-glucuronidase) & gfp (green fluorescent protein) reporter gene driven by ospt8 promoter showed that ospt8 is expressed in various tissue organs from roots to seeds independent ...	2011	21502185
identification of a cis-acting element of art1, a c2h2-type zinc-finger transcription factor for aluminum tolerance in rice.	rice (oryza sativa) is one of the most aluminum (al)-tolerant species among small-grain cereals. recent identification of a transcription factor al resistance transcription factor1 (art1) revealed that this high al tolerance in rice is achieved by multiple genes involved in detoxification of al at different cellular levels. art1 is a c2h2-type zinc-finger transcription factor and regulates the expression of 31 genes in the downstream. in this study, we attempted to identify a cis-acting element ...	2011	21502187