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independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication.asian rice (oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (phr) phenotype. grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. by contrast, the grains of japonica do not discolor. this distinction may reflect the divergent domestication of these two subspecies. the phr is controlled by a single gene, phr1; here, we rep ...200819033526
arbuscular mycorrhiza-specific signaling in rice transcends the common symbiosis signaling pathway.knowledge about signaling in arbuscular mycorrhizal (am) symbioses is currently restricted to the common symbiosis (sym) signaling pathway discovered in legumes. this pathway includes calcium as a second messenger and regulates both am and rhizobial symbioses. both monocotyledons and dicotyledons form symbiotic associations with am fungi, and although they differ markedly in the organization of their root systems, the morphology of colonization is similar. to identify and dissect am-specific sig ...200819033527
ricd: a rice indica cdna database resource for rice functional genomics.the oryza sativa l. indica subspecies is the most widely cultivated rice. during the last few years, we have collected over 20,000 putative full-length cdnas and over 40,000 ests isolated from various cdna libraries of two indica varieties guangluai 4 and minghui 63. a database of the rice indica cdnas was therefore built to provide a comprehensive web data source for searching and retrieving the indica cdna clones.200819036133
identification of an apoplastic protein involved in the initial phase of salt stress response in rice root by two-dimensional electrophoresis.the apoplast of plant cells, which carries out multiple functions in plant metabolism and signaling, is not only a barrier but also the linker between the environment and the protoplast. to investigate the role of apoplastic proteins in the salt stress response, 10-d-old rice (oryza sativa) plants were treated with 200 mm nacl for 1, 3, or 6 h, and the soluble apoplast proteins were extracted for differential analysis compared with untreated controls using two-dimensional electrophoresis. ten pr ...200919036832
structural basis for gibberellin recognition by its receptor gid1.gibberellins (gas) are phytohormones essential for many developmental processes in plants. a nuclear ga receptor, gibberellin insensitive dwarf1 (gid1), has a primary structure similar to that of the hormone-sensitive lipases (hsls). here we analyse the crystal structure of oryza sativa gid1 (osgid1) bound with ga(4) and ga(3) at 1.9 a resolution. the overall structure of both complexes shows an alpha/beta-hydrolase fold similar to that of hsls except for an amino-terminal lid. the ga-binding po ...200819037316
a novel wall-associated receptor-like protein kinase gene, oswak1, plays important roles in rice blast disease resistance.wall-associated protein kinases (waks) are a new group of receptor-like kinases (rlk) recently identified in arabidopsis. a cdna encoding a novel wak was isolated from rice and was named oswak1 (oryza sativa wak). the deduced amino acid sequence of oswak1 showed 27.6% identity to wak2 from arabidopsis. oswak1 not only has the ability of autophosphorylation but also can phosphorylate osrfp1, a putative transcription regulator recently identified in rice. osrfp1 strongly interacts with the kinase ...200919039666
rice osysl15 is an iron-regulated iron(iii)-deoxymugineic acid transporter expressed in the roots and is essential for iron uptake in early growth of the seedlings.graminaceous plants take up iron through ys1 (yellow stripe 1) and ys1-like (ysl) transporters using iron-chelating compounds known as mugineic acid family phytosiderophores. we examined the expression of 18 rice (oryza sativa l.) ysl genes (osysl1-18) in the epidermis/exodermis, cortex, and stele of rice roots. expression of osysl15 in root epidermis and stele was induced by iron deficiency and showed daily fluctuation. osysl15 restored a yeast mutant defective in iron uptake when supplied with ...200919049971
wheat cryptochromes: subcellular localization and involvement in photomorphogenesis and osmotic stress responses.cryptochromes (crys) are blue light receptors important for plant growth and development. comprehensive information on monocot crys is currently only available for rice (oryza sativa). we report here the molecular and functional characterization of two cry genes, tacry1a and tacry2, from the monocot wheat (triticum aestivum). the expression of tacry1a was most abundant in seedling leaves and barely detected in roots and germinating embryos under normal growth conditions. the expression of tacry2 ...200919052154
physicochemical rheological and thermal properties of njavara rice (oryza sativa) starch.njavara rice starch was studied for its morphological, physicochemical, and thermal properties and was found to be different from the native chamba variety of rice. njavara rice starch has bigger granule and has a high (85 degrees c) gelatinization temperature and shows high thermal stability. the swelling power, solubility, water absorption capacity, and enthalpy of gelatinization were found to be high compared to the native rice starch. the 6% (w/v) njavara rice starch gel had 87.45% clarity a ...200819053396
the c-terminal variable region specifies the dynamic properties of arabidopsis microtubule-associated protein map65 isotypes.the microtubule-associated protein, map65, is a member of a family of divergent microtubule-associated proteins from different organisms generally involved in maintaining the integrity of the central spindle in mitosis. the dicotyledon arabidopsis thaliana and the monocotyledon rice (oryza sativa) genomes contain 9 and 11 map65 genes, respectively. in this work, we show that the majority of these proteins fall into five phylogenetic clades, with the greatest variation between clades being in the ...200819060108
a novel bacterial blight resistance gene from oryza nivara mapped to 38 kb region on chromosome 4l and transferred to oryza sativa l.bacterial blight (bb) of rice caused by xanthomonas oryzae pv oryzae (xoo) is one of the major constraints to productivity in south-east asia. the strategy of using major genes, singly or in combination, continues to be the most effective approach for bb management. currently, more than two dozen genes have been designated but not all the known genes are effective against all the prevalent pathotypes. the challenge, therefore, is to continue to expand the gene pool of effective and potentially d ...200819061530
effects of n and k applications on agronomic characteristics of two iranian and landrace rice (oryza sativa l.) cultivars.nutrition elements like nitrogen and potassium are restricting yield performance of rice cultivars and affecting on their characteristics. in order to consider effects of different amount of nitrogen and potassium on yield and chemical compounds of two rice cultivars (tarrom and neda which are landrace and improved iranian genotypes, respectively), current experiment has been undertaken in 2004 and 2005. four levels of nitrogen fertilizer (0, 50, 100 and 150 kg n ha(-1) from urea source) and fou ...200719069882
response of rice cultivars to rates of nitrogen and potassium application in field and pot conditions.nitrogen and potassium are the yield-limiting nutrients in rice production regions of iran. use of n and k efficient cultivars is an important complementary strategy in improving rice yield, increasing the quality properties of rice grains and reducing cost of production. in order to consider the effects of different amounts of n and k application on rice (oryza sativa l.) yield and yield components in pot and field conditions these experiments were undertaken in 2004 at sari agricultural statio ...200719069953
an assessment of wx microsatellite allele, alkali degradation and differentiation of chloroplast dna in traditional black rice (oryza sativa l.) from thailand and lao pdr.thailand and lao pdr are the country's rich rice diversity. to contribute a significant knowledge for development new rice varieties, a collection of 142 black rice (oryza sativa) accessions were determined for variation of physico-chemical properties, wx microsatellite allele, wx allele and chloroplast dna type. the results showed that amylose content of black rice accessions were ranged from 1.9 to 6.8%. all of the alkali disintegration types (high, intermediate and low) was observed in these ...200719070026
evolutionary and expression study of the aldehyde dehydrogenase (aldh) gene superfamily in rice (oryza sativa).aldehyde dehydrogenase (aldh) superfamily represents a group of nad(p)(+)-dependent enzymes that catalyze the oxidation of endogenous and exogenous aldehydes to the corresponding carboxylic acids. a total of twenty aldh genes were identified in the rice genome. they were grouped into 10 distinct families based on protein sequence identity. the whole genome duplication (wgd) predating the divergence of cereals and tandem duplications represent the major mechanism for this superfamily expansion. i ...019071198
mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of rna instability in the germination process.transcriptome and metabolite profiling of rice (oryza sativa) embryo tissue during a detailed time course formed a foundation for examining transcriptional and posttranscriptional processes during germination. one hour after imbibition (hai), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, tricarboxylic acid cycle intermediates, and gamma-aminobutyric acid. later changes in the metabolome, including those involved in ca ...200919074628
dispersal of viable row-crop seeds of commercial agriculture by farmland birds: implication for genetically modified crops.to address some concerns about the expansion of genetically engineered pharmaceutical and industrial crops to outdoor plantings and potential impacts on the human food supply, we determined whether commercial agriculture seeds of maize or corn zea mays l., barley hordeum vulgare l., safflower carthamus tinctorius l. and rice oryza sativa l. are digested or pass viably through the digestive tract, or are transported externally, by captive mallard ducks anas platyrhynchos l., ring-necked pheasants ...200819081011
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 ...200919084081
constitutive expression of a rice gtpase-activating protein induces defense responses.g-proteins (guanine nucleotide-binding proteins that usually exhibit gtpase activities) and related signal transduction processes play important roles in mediating plant defense responses; here, a rice (oryza sativa) cdna clone, osgap1, encoding a gtpase-activating protein (gap) that also contains a protein kinase c conserved region 2 (c2) domain is reported. an interacting g-protein partner for the osgap1 protein was identified by yeast two-hybrid library screening and confirmed by co-immunopre ...200819086295
study of growth factors, alpha-amylase and peroxidase activity in various cultivars of rice (oryza sativa l.) under vanillic acid stress.the effects of vanillic acid (va) on germination, seedling and adult plant of rice (oryza sativa l.) were investigated. four cultivars, traditional (taroom mahalli and taroom deilamani) and improved (shafagh and onda) were studied. for germination, seeds were sterilized and then placed on petri dish at 30 degrees c at different concentrations (0, 10, 20 and 25 mm) for 7 days and growth factors of seedling were measured after 14 days. seedling (10 days) planted in hydroponic medium including nutr ...200719086516
effects of nitrogen and potassium fertilizers on rice (oryza sativa l.) genotypes processing characteristics.in order to consider effects of various levels of nitrogen and potassium application on kernel processing characteristics of rice cultivars, an experiment was developed in 2004 and 2005 using tarrom (a local iranian landrace) and neda (an iranian improved cultivar). in this experiment four levels of nitrogen fertilizer (0, 50, 100 and 150 kg n ha(-1) from urea source) and four levels of potassium fertilizer (0, 75, 150 and 225 kg k2o ha(-1) from potassium sulfate source) have been applied using ...200719086545
response of rice (oryza sativa l.) cooking quality properties to nitrogen and potassium application.in order to consider effects of various levels of nitrogen and potassium application on cooking quality traits of rice cultivars, an experiment was conducted in 2004 and 2005 using tarrom (a local iranian landrace) and neda (an iranian improved cultivar). in this experiment four levels of nitrogen fertilizer (0, 50, 100 and 150 kg n ha(-2) from urea source) and four levels of potassium fertilizer (0, 75, 150 and 225 kg k2o ha(-2) from potassium sulfate source) have been applied using a split fac ...200719086555
measurements of oxygen permeability coefficients of rice (oryza sativa l.) roots using a new perfusion technique.a new approach is described to analyse the barrier properties of the outer part of rice (oryza sativa l.) roots towards oxygen. by using a root-sleeving o(2) electrode, radial oxygen loss at different distances from the root apex was measured and related to the corresponding root structure. in addition, internal oxygen concentrations were precisely adjusted using a newly developed perfusion technique. thus, the oxygen permeability coefficient of the outer part of the root (opr) could be calculat ...200919088333
microcalorimetric investigation on effects of la(iii) on metabolic activity of mitochondria isolated from hybrid rice.rare earth elements (rees) have beneficial influence on plant growth and are widely used in agriculture practice, but little is known about the behavior of the rees in mitochondria of plant cell. thermogenic metabolic curves were determined by the ampoule method at 303 k using a tam air isothermal microcalorimeter in mitochondria isolated from hybrid rice liangyoupeijiu (oryza sativa l.), and the effect of la(iii) on its mitochondrial metabolism was investigated. from the obtained heat flux curv ...200819089826
effect of planting density on agronomical characteristics of rice (oryza sativa l.) varieties in north of iran.in order to study the effects of plant density on agronomical characteristics of rice varieties a field experiment was carried out in field of ghaemshahr azad university in 2006. this experiment was laid out in split plot in basis of randomized completely block design with three replications. main factor was rice variety in three levels (hashemi tarom, fajr, neda) and minor factor was planting density (including 10 x 8.3, 10 x 10, 12.5 x 10, 16.6 x 10, 16.6 x 15 and 25 x 20 cm or 120, 100, 80, 6 ...200719090127
study the effect of nitrogen fertilizer management on dry matter remobilization of three cultivars of rice (oryza sativa l.).in order to study the effect of nitrogen fertilizer management on dry matter remobilization among three rice cultivars, a field experiment was carried out at the rice research institute of iran-deputy of mazandaran (amol). in 2005, a split-split experiment in the basis of randomized complete block design with 3 replications and 3 factors were used in which fertilizer rate (100, 150 and 200 kg ha(-1) from urea source), fertilizer split application (3 levels in variable ratios in transplanting, ti ...200719090163
analyses of advanced rice anther transcriptomes reveal global tapetum secretory functions and potential proteins for lipid exine formation.the anthers in flowers perform important functions in sexual reproduction. several recent studies used microarrays to study anther transcriptomes to explore genes controlling anther development. to analyze the secretion and other functions of the tapetum, we produced transcriptomes of anthers of rice (oryza sativa subsp. japonica) at six progressive developmental stages and pollen with sequencing-by-synthesis technology. the transcriptomes included at least 18,000 unique transcripts, about 25% o ...200919091874
in vivo interference with attcp20 function induces severe plant growth alterations and deregulates the expression of many genes important for development.attcp20 is a transcription factor belonging to the arabidopsis (arabidopsis thaliana) tcp-p subfamily, characterized by its capacity to bind to site ii motifs (tgggcy). our aim was to understand the role of attcp20 in plant development. the expression pattern of a translational fusion of prom(tcp20):cds20gusgfp suggested a function for attcp20 in several plant organs and stages of development. the role of attcp20 was challenged in planta by inducing expression of attcp20 proteins fused with eith ...200919091878
in vitro plant regeneration through anther culture of some iranian local rice (oryza sativa l.) cultivars.in this study, effect of different genotypes, different callus induction and regeneration media were investigated using seven iranian local rice. anthers were cultured on n6, fj and l8 media containing the same hormonal combination 3 mg l(-1) naa, 0.5 mg l(-1) kn and 0.5 mg l(-1) 2, 4-d and incubated at 25 +/- 1 degree c in dark for callus induction. all varieties in l8 medium, five varieties in fj medium and six varieties in n6 medium produced highest percentage of callus. calli induced in diff ...200719093446
anatomical and chemical alterations but not photosynthetic dynamics and apoplastic transport changes are involved in the brittleness culm mutation of rice.brittleness culm is an important agronomic trait that has a potential usefulness in agricultural activity as animal forage although the developmental mechanism is not clear yet. in the present study, the anatomical and chemical characteristics as well as some ecophysiological features in the brittleness culm mutation of rice (oryza sativa l.) were investigated. compared with the wild type (wt), the brittleness culm mutant (bcm) exhibited higher culm vascular bundle distance and lower culm wall t ...200819093969
interactions of mixed organic contaminants in uptake by rice seedlings.uptakes of o-chlorophenol (cp), 2,4-dichlorophenol (dcp), trichloroethylene (tce), and atrazine (atr), as single and mixed contaminants, by roots and shoots of rice seedlings (oryza sativa l.) from hydroponic solutions were measured following a 48-h exposure of plant roots. as single contaminants, the concentrations of cp, dcp, and atr in rice roots and shoots increased significantly with increasing concentrations in external solutions; however, tce concentrations in rice roots and shoots decrea ...200919095283
genetic analysis and fine-mapping of a dwarfing with withered leaf-tip mutant in rice.a dwarf mutant of rice (oryza sativa l.) by mutagenesis of ethylene methylsulfonate (ems) treatment from nipponbare was identified. the mutant exhibited phenotypes of dwarfism and withered leaf tip (dwl1). based on the internode length of dwl1, this mutant belongs to the dm type of dwarfing. analysis of elongation of the second sheath and alpha-amylase activity in endosperm showed that the phenotype caused by dwl1 was insensitive to gibberellin acid treatment. using a large f2 population derived ...200819103426
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 ...200919106179
a rice kinase-protein interaction map.plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (oryza sativa) genome, little is known of their functions. genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. we previously developed a cost-effective high-throughput yeast two-hybrid system. using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 ...200919109415
characterization of cadmium uptake and translocation in a cadmium-sensitive mutant of rice (oryza sativa l. ssp. japonica).to understand the physiological mechanism that confers cd sensitivity/tolerance, cd uptake and translocation by cd-sensitive mutant and wild-type rice seedlings were characterized using radioactive tracer. time-dependent cd accumulation during 210 min was 1.8-fold higher in roots of the mutant than of wild-type rice. the kinetics of cd uptake showed that two processes were involved: a first, fast, probably passive process and a second, slower, possibly physiological process. after 96 h, more cd ...200919112560
isolation and some characteristics of lipoxygenase from aromatic brown rice (oryza sativa l.) cv. khao dawk mali 105.lipoxygenase from khao dawk mali 105 aromatic brown rice was isolated by extracting brown rice liquid nitrogen powder using 0.2 m phosphate buffer ph 7, fractionating with 30-60% (nh(4))(2)so(4), dialyzing and gel filtration on sephadex g-200. the optimum phs for dialyzed lipoxygenase activity were around 7.5 and 9.5. the enzyme appeared to be completely inactivated after heating 30 min at 70 degrees c, 20 min at 80 degrees c and 10 min at 90 degrees c. the enzyme could be inhibited by mgcl(2), ...200919117206
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 ...200919117417
hormones in the grains and roots in relation to post-anthesis development of inferior and superior spikelets in japonica/indica hybrid rice.grain filling is usually not adequate in later-flowering inferior spikelets in japonica/indica (j/i) hybrid rice (oryza sativa) although it shows stronger hybrid vigor than indica/indica (i/i) hybrid. this study investigated the potential causes by examining changes in zeatin (z)+zeatin riboside (zr), indole-3-acetic acid (iaa), gibberellins (gas, ga(1)+ga(4)), and abscisic acid (aba) in spikelets and roots during the grain filling period. the inferior spikelets of j/i hybrid exhibited low rate ...200919117763
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 ...200919118127
a transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.the functions of the plant body rely on interactions among distinct and nonequivalent cell types. the comparison of transcriptomes from different cell types should expose the transcriptional networks that underlie cellular attributes and contributions. using laser microdissection and microarray profiling, we have produced a cell type transcriptome atlas that includes 40 cell types from rice (oryza sativa) shoot, root and germinating seed at several developmental stages, providing patterns of cel ...200919122662
overexpressed glutamine synthetase gene modifies nitrogen metabolism and abiotic stress responses in rice.glutamine synthetase (gs; ec 6.3.1.2) is a key enzyme in nitrogen metabolism; it catalyzes the critical incorporation of inorganic ammonium into glutamine. two full-length cdnas that encode the rice (oryza sativa) cytosolic glutamine synthetase1 genes (osgs1;1 and osgs1;2) were isolated from a minghui 63 normalized cdna library, and glna encoding gs in escherichia coli was isolated by pcr amplification. transformants for gs gene (gs1;1, gs1;2, and glna) in rice were produced by an agrobacterium ...200919123004
[changes of microbial biomass carbon and enzyme activities in rice-barnyard grass coexisted soils].taking barnyard grass (echinochloa crus-galli), allelopathic rice (oryza sativa) pi312777, and non-allelopathic rice liaojing-9 as test materials, this paper studied the changes of microbial biomass c and of dehydrogenase, urease and invertase activities in soils under 1 : 1 rice-barnyard grass coexistence. the results showed that with the coexistence of barnyard grass, the microbial biomass c in rhizosphere soil of pi312777 was decreased by 50.52% (p < 0.01), while that in inter-row soil was in ...200819123361
methylobacterium phyllosphaerae sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice.a pink-pigmented, aerobic, facultatively methylotrophic bacterial strain, cbmb27t, isolated from leaf tissues of rice (oryza sativa l. 'dong-jin'), was analysed using a polyphasic taxonomic approach. comparative 16s rrna gene sequence-based phylogenetic analysis placed the strain in a clade with the species methylobacterium oryzae, methylobacterium fujisawaense and methylobacterium mesophilicum; strain cbmb27t showed sequence similarities of 98.3, 98.5 and 97.3 %, respectively, to the type strai ...200919126717
a green fluorescent protein fused to rice prolamin forms protein body-like structures in transgenic rice.prolamins, a group of rice (oryza sativa) seed storage proteins, are synthesized on the rough endoplasmic reticulum (er) and deposited in er-derived type i protein bodies (pb-is) in rice endosperm cells. the accumulation mechanism of prolamins, which do not possess the well-known er retention signal, remains unclear. in order to elucidate whether the accumulation of prolamin in the er requires seed-specific factors, the subcellular localization of the constitutively expressed green fluorescent p ...200919129168
insight into the salt tolerance factors of a wild halophytic rice, porteresia coarctata: a physiological and proteomic approach.salinity poses a serious threat to yield performance of cultivated rice in south asian countries. to understand the mechanism of salt-tolerance of the wild halophytic rice, porteresia coarctata in contrast to the salt-sensitive domesticated rice oryza sativa, we have compared p. coarctata with the domesticated o. sativa rice varieties under salinity stress with respect to several physiological parameters and changes in leaf protein expression. p. coarctata showed a better growth performance and ...200919130079
bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among oryza sativa l. germplasms.association mapping can be a powerful tool for detecting quantitative trait loci (qtls) without requiring line-crossing experiments. we previously proposed a bayesian approach for simultaneously mapping multiple qtls by a regression method that directly incorporates estimates of the population structure. in the present study, we extended our method to analyze ordinal and censored traits, since both types of traits are common in the evaluation of germplasm collections. ordinal-probit and tobit mo ...200919132337
spaceflight induces both transient and heritable alterations in dna methylation and gene expression in rice (oryza sativa l.).spaceflight represents a complex environmental condition in which several interacting factors such as cosmic radiation, microgravity and space magnetic fields are involved, which may provoke stress responses and jeopardize genome integrity. given the inherent property of epigenetic modifications to respond to intrinsic as well as external perturbations, it is conceivable that epigenetic markers like dna methylation may undergo alterations in response to spaceflight. we report here that extensive ...200919135069
the plastidial 2-c-methyl-d-erythritol 4-phosphate pathway provides the isoprenyl moiety for protein geranylgeranylation in tobacco by-2 cells.protein farnesylation and geranylgeranylation are important posttranslational modifications in eukaryotic cells. we visualized in transformed nicotiana tabacum bright yellow-2 (by-2) cells the geranylgeranylation and plasma membrane localization of gfp-bd-cvil, which consists of green fluorescent protein (gfp) fused to the c-terminal polybasic domain (bd) and cvil isoprenylation motif from the oryza sativa calmodulin, cam61. treatment with fosmidomycin (fos) or oxoclomazone (oc), inhibitors of t ...200919136647
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 ...200919136648
drought stress effects on root anatomical characteristics of rice cultivars (oryza sativa l.).the objective of this study was to compare some aspects of root anatomy of rice cultivars under irrigation and submerged conditions. seedling of three new rice cultivars (zayande-rood, 829 and 216) were transferred to 9 lysiometers (200 x 120 x 100 cm) according to a randomized block design with two treatments (submerged and aerated condition) in three replicates. the amount of water consumption was recorded during growing season. cross-sections of plant roots were obtained at two different time ...200819137825
rice shoot branching requires an atp-binding cassette subfamily g protein.* shoot branching is important for the establishment of plant architecture and productivity. * here, characterization of rice (oryza sativa) reduced culm number 1 (rcn1) mutants revealed that rcn1 positively controls shoot branching by promoting the outgrowth of lateral shoots. molecular studies revealed that rcn1 encodes a novel member of atp-binding cassette protein subfamily g (abcg subfamily), also known as the white-brown complex (wbc) subfamily, and is designated osabcg5. * rcn1 is express ...200919140940
agriculture and the new challenges for photosynthesis research.a rising human population and changing patterns of land use mean that world food production rates will need to be increased by at least 50% by 2050, a massive rise in harvestable yield per hectare of the major crops such as rice (oryza sativa) and wheat (triticum aestivum). combinations of breeding for improved morphology-related traits such as harvest index and increased inputs of water and fertilizer, which have sustained yield increases since the 1960s, will be neither sufficient nor sustaina ...200919140947
epidermal cell death in rice is confined to cells with a distinct molecular identity and is mediated by ethylene and h2o2 through an autoamplified signal pathway.rice (oryza sativa) forms adventitious root primordia at stem nodes during normal development. root emergence is preceded by ethylene-induced, h(2)o(2)-mediated local death of epidermal cells. exogenous h(2)o(2) or enhancement of endogenous h(2)o(2) promoted epidermal cell death in a dose-dependent manner. inhibition of nadph oxidase lowered ethylene-induced cell death rates. inhibition of ethylene perception by 1-methylcyclopropene did not abolish h(2)o(2)-induced cell death, indicating that h( ...200919141708
deacidification of high free fatty acid-containing rice bran oil by non-conventional reesterification process.rice bran (oryza sativa) oil is known for containing higher amount of free fatty acid (ffa) generated by hydrolytic enzyme. this ffa causes heavy neutral oil losses due to saponification and emulsification since it produces large amount of soap in the conventional alkali refining process. in the present study the ffa of degummed rice bran oil (rbo) was significantly reduced by reesterifying it with glycerol. the reesterification process was carried out by varying the temperature and amount of ex ...200919145058
consensus features of microsatellite distribution: microsatellite contents are universally correlated with recombination rates and are preferentially depressed by centromeres in multicellular eukaryotic genomes.microsatellite dna is highly polymorphic and informative, which makes its distribution pattern and its associations very valuable for marker applications and genomic research in evolution. using computational and statistical approaches, based on database technology, we have demonstrated that microsatellite content is consistently and significantly 2 to 5 fold lower than the average chromosomal level in the centromeric and pericentromeric regions of the chromosomes of two plant species, arabidops ...200919146945
identification and mapping of pi41, a major gene conferring resistance to rice blast in the oryza sativa subsp. indica reference cultivar, 93-11.the oryza sativa subsp. indica reference cultivar (cv.), 93-11 is completely resistant to many chinese isolates of the rice blast fungus. resistance segregated in a 3:1 (resistance/susceptible) ratio in an f(2) population from the cross between 93-11 and the japonica reference cv. nipponbare, when challenged with two independent blast isolates. the chromosomal location of this monogenic resistance was mapped to a region of the long arm of chromosome 12 by bulk segregant analysis, using 180 evenl ...200919153709
the vacuolar processing enzyme osvpe1 is required for efficient glutelin processing in rice.rice (oryza sativa l.) accumulates prolamines and glutelins as its major storage proteins. glutelins are synthesized on rough endoplasmic reticulum as 57-kda precursors; they are then sorted into protein storage vacuoles where they are processed into acidic and basic subunits. we report a novel rice glutelin mutant, w379, which accumulates higher levels of the 57-kda glutelin precursor. genetic analysis revealed that the w379 phenotype is controlled by a single recessive nuclear gene. using a ma ...200919154227
evidence for separate translocation pathways in determining cadmium accumulation in grain and aerial plant parts in rice.cadmium (cd) translocation and accumulation in the grain and aerial plant parts of rice (oryza sativa l.) is an important aspect of food safety and phytoextraction in areas with contaminated soil. because control of cd translocation and accumulation is likely to be determined by the plants genetics, the cd contents of grain and the aerial parts of rice may be manipulated to improve food safety and for phytoextraction ability. this study studied cd translocation and accumulation and their genetic ...200919154618
crossability barriers in the interspecific hybridization between oryza sativa and o. meyeriana.oryza meyeriana baill (gg genome) is a precious germplasm in the tertiary gene pool of cultivated rice (aa genome), and possesses important traits such as resistance and tolerance to biotic and abiotic stress. however, interspecific crossability barrier, a critical bottleneck restricting genes transfer from o. meyeriana to cultivars has led to no hybrids through conventional reproduction. therefore, the reasons underlying incrossability were investigated in the present report. the results showed ...200919166490
expression analysis of phytohormone-regulated micrornas in rice, implying their regulation roles in plant hormone signaling.twenty-two conserved mirnas were chosen to investigate the expression pattern in response to phytohormone treatments, in which the effects of five classic plant hormone stresses were surveyed in oryza sativa. the results showed that 11 mirnas were found to be dysregulated by one or more phytohormone treatments. the target genes of these mirnas were validated in vivo and their expression profiling were revealed. we also analyzed the promoter regions of the 22 conserved mirnas for phytohormone-res ...200919167382
salt-inducible isoform of plasma membrane h+atpase gene in rice remains constitutively expressed in natural halophyte, suaeda maritima.to look into a possible involvement of plasma membrane h+atpase (pm-h+atpase, ec 3.6.3.6) in mitigation of physiological disturbances imposed by salt stress, response of the enzyme was studied in two oryza sativa indica cultivars, salt-tolerant lunishri and non-tolerant badami, and a natural halophyte suaeda maritima after challenge of the young plants with nacl. significant increase in activity of the enzyme was observed in response to nacl in all the test plants with s. maritima showing maximu ...200919167778
molecular and functional characterization of pebp genes in barley reveal the diversification of their roles in flowering.five barley (hordeum vulgare) pebp (for phosphatidylethanolamine-binding protein) genes were analyzed to clarify their functional roles in flowering using transgenic, expression, and quantitative trait locus analyses. introduction of hvtfl1 and hvmft1 into rice (oryza sativa) plants did not result in any changes in flowering, suggesting that these two genes have functions distinct from flowering. overexpression of hvft1, hvft2, and hvft3 in rice resulted in early heading, indicating that these f ...200919168644
sucrose transporter1 functions in phloem loading in maize leaves.in most plants, sucrose is exported from source leaves to carbon-importing sink tissues to sustain their growth and metabolism. apoplastic phloem-loading species require sucrose transporters (suts) to transport sucrose into the phloem. in many dicot plants, genetic and biochemical evidence has established that sut1-type proteins function in phloem loading. however, the role of sut1 in phloem loading in monocot plants is not clear since the rice (oryza sativa) and sugarcane (saccharum hybrid) sut ...200919181865
rubisco content and photosynthesis of leaves at different positions in transgenic rice with an overexpression of rbcs.as ribulose 1.5-bisphosphate carboxylase/oxygenase (rubisco) activity limits light-saturated photosynthesis under present atmospheric condition, the effects of an overexpression of rbcson rubisco content and photosynthesis were examined in the leaves at different positions in rice (oryza sativa l.). rubisco content in the transformant was significantly greater in the uppermost, fully expanded leaves but decreased to levels similar to those in wild-type plants in the lower leaves. the mrna levels ...200919183297
the identification of candidate genes associated with pch2 eyespot resistance in wheat using cdna-aflp.eyespot is a fungal disease of the stem base of cereal crops and causes lodging and the premature ripening of grain. wheat cultivar cappelle desprez contains a highly durable eyespot resistance gene, pch2 on the long arm of chromosome 7a. a cdna-amplified fragment length polymorphism (aflp) platform was used to identify genes differentially expressed between the eyespot susceptible variety chinese spring (cs) and the cs chromosome substitution line cappelle desprez 7a (cs/cd7a) which contains pc ...200919183860
characterization of pullulanase (pul)-deficient mutants of rice (oryza sativa l.) and the function of pul on starch biosynthesis in the developing rice endosperm.rice (oryza sativa) allelic sugary1 (sug1) mutants defective in isoamylase 1 (isa1) accumulate varying levels of starch and phytoglycogen in their endosperm, and the activity of a pullulanase-type of a debranching enzyme (pul) was found to correlate closely with the severity of the sug1 phenotype. thus, three pul-deficient mutants were generated to investigate the function of pul in starch biosynthesis. the reduction of pul activity had no pleiotropic effects on the other enzymes involved in sta ...200919190097
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 ...200919192190
oshsf7 gene in rice, oryza sativa l., encodes a transcription factor that functions as a high temperature receptive and responsive factor.three novel class a genes that encode heat shock transcription factor (hsf) were cloned from oryza sativa l using a yeast hybrid method. the oshsf7 gene was found to be rapidly expressed in high levels in response to temperature, which indicates that it may be involved in heat stress reception and response. over-expression of oshsf7 in transgenic arabidopsis could not induced over the expression of most target heat stress-inducible genes of hsfs; however, the transcription of some hsf target gen ...200919192388
antisense phenotypes reveal a functional expression of osarf1, an auxin response factor, in transgenic rice.osarf1 is the first full-length member of auxin response factor (arf) gene family to be cloned from monocot plant. using quantitative rt-pcr this study found that, the transcript abundance of osarf1 was significantly higher in embryonic tissues than in vegetative tissues. to investigate the effect of osarf1 on the phenotype of rice, a cdna fragment of osarf1 was inserted in inverse orientation to the 35s promoter in vector pbin438 to produce an antisense (as) construction. the as-osarf1 construc ...200919193962
different responses of two genes associated with disease resistance loci in maize (zea mays l.) to 3-allyloxy-1,2-benzothiazole 1,1-dioxide.probenazole (3-allyloxy-1,2-benzothiazole 1,1-dioxide, pbz) is a bactericide and fungicide that acts by inducing plant defense systems. it has been shown to induce the expression of nbs-lrr genes like rpr1 (rice probenazole-response gene) in rice (oryza sativa l.) and systemic acquired resistance (sar)-like disease resistance. two maize (zea mays l.) genes zmnbslrr1 (a nbs-lrr gene, cloned from a disease resistance analog pic11 based) and zmgc1, (a putative guanylyl cyclase-like gene) have both ...200919193968
proteomic identification of small, copper-responsive proteins in germinating embryos of oryza sativa.although copper (cu) is an essential micronutrient for plants and algae, excess cu is toxic to most plants and can cause a wide range of deleterious effects. to investigate the response of rice (oryza sativa) to cu stress, a proteomic approach was used to analyse cu stress-induced changes in the expression of low molecular-weight proteins in germinating rice seed embryos.200919201764
arsenic uptake and metabolism in plants.arsenic (as) is an element that is nonessential for and toxic to plants. arsenic contamination in the environment occurs in many regions, and, depending on environmental factors, its accumulation in food crops may pose a health risk to humans.recent progress in understanding the mechanisms of as uptake and metabolism in plants is reviewed here. arsenate is taken up by phosphate transporters. a number of the aquaporin nodulin26-like intrinsic proteins (nips) are able to transport arsenite,the pre ...200919207683
computational prediction of novel non-coding rnas in arabidopsis thaliana.non-coding rna (ncrna) genes do not encode proteins but produce functional rna molecules that play crucial roles in many key biological processes. recent genome-wide transcriptional profiling studies using tiling arrays in organisms such as human and arabidopsis have revealed a great number of transcripts, a large portion of which have little or no capability to encode proteins. this unexpected finding suggests that the currently known repertoire of ncrnas may only represent a small fraction of ...200919208137
circadian clock- and phytochrome-regulated dof-like gene, rdd1, is associated with grain size in rice.we report here on the characterization of a putative dof transcription factor gene in rice (oryza sativa)--rice dof daily fluctuations 1 (rdd1). daily oscillations in rdd1 expression were retained after transferring to continuous dark (dd) or light (ll) conditions, indicating circadian regulation. however, rdd1 showed arrhythmic expression in etiolated coleoptiles. experiments revealed that the rdd1 transcript accumulated up to 1 h after transferring from dd to ll conditions and decreased therea ...200919210638
methyl jasmonate reduces grain yield by mediating stress signals to alter spikelet development in rice.jasmonic acid (ja) is involved in plant development and the defense response. transgenic overexpression of the arabidopsis (arabidopsis thaliana) jasmonic acid carboxyl methyltransferase gene (atjmt) linked to the ubi1 promoter increased levels of methyl jasmonate (meja) by 6-fold in young panicles. grain yield was greatly reduced in ubi1:atjmt plants due to a lower numbers of spikelets and lower filling rates than were observed for nontransgenic (nt) controls. ubi1:atjmt plants had altered numb ...200919211695
mitochondrial proteome during salt stress-induced programmed cell death in rice.it has been shown that mitochondria play a pivotal role in plant programmed cell death (pcd). previous study established a salt stress-induced pcd model in rice (oryza sativa l. cv. wyj 8th) root tip cells, demonstrated by dna laddering, cytochrome c release, and tunel positive reaction. in this study, the role of mitochondria during the early phase of pcd (2h-pcd) was analyzed in rice roots. after 2h-pcd induction, the integrity of mitochondria decreased slightly, consistent with a small releas ...200919217306
studies on rice seed quality through analysis of a large-scale t-dna insertion population.a rice (oryza sativa) t-dna insertion population, which included more than 63 000 independent transgenic lines and 8 840 identified flanking sequence tags (fsts) that were mapped onto the rice genome, was developed to systemically study the rice seed quality control. genome-wide analysis of the fst distribution showed that t-dna insertions were positively correlated with expressed genes, but negatively with transposable elements and small rnas. in addition, the recovered t-dnas were preferential ...200919223856
cytoplasmic male sterility-related protein kinase, osnek3, is regulated downstream of mitochondrial protein phosphatase 2c, dcw11.osnek3 (oryza sativa l. nima-related kinase) and dcw11 encoding a mitochondrial putative protein phosphatase 2c were found in our previous microarray study as down-regulated genes in the rice cw-cms line, which lacked pollen germination ability. further analysis of dcw11 revealed that dcw11 is strongly correlated with cw-cms occurrence. here we show the relationship between osnek3 and dcw11. osnek3 was preferentially expressed in mature pollen. a knockout mutant with tos17 inserted into osnek3 d ...200919224952
osmt1a, a type 1 metallothionein, plays the pivotal role in zinc homeostasis and drought tolerance in rice.metallothioneins (mts) are small, cysteine-rich, metal-binding proteins that may be involved in metal homeostasis and detoxification in both plants and animals. osmt1a, encoding a type 1 metallothionein, was isolated via suppression subtractive hybridization from brazilian upland rice (oryza sativa l. cv. iapar 9). expression analysis revealed that osmt1a predominantly expressed in the roots, and was induced by dehydration. interestingly, the osmt1a expression was also induced specifically by zn ...200919229638
not just a grain of rice: the quest for quality.a better understanding of the factors that contribute to the overall grain quality of rice (oryza sativa) will lay the foundation for developing new breeding and selection strategies for combining high quality, with high yield. this is necessary to meet the growing global demand for high quality rice while offering producing countries additional opportunities for generating higher export revenues. several recent developments in genetics, genomics, metabolomics and phenomics are enhancing our und ...200919230745
role of oshal3 protein, a putative 4'-phosphopantothenoylcysteine decarboxylase in rice.in this study, we cloned the oshal3 gene from rice oryza sativa. alignment analysis revealed that oshal3 has a high sequence identity to dfp protein in escherichia coli and athal3a protein in arabidopsis thaliana, which have 4'-phosphopantothenoylcysteine decarboxylase (ppc-dc) activity. oshal3 can complement mutation in the e. coli dfp gene encoding ppc-dc, so that the mutant strains with oshal3 can grow on rich media at 42 degrees c and on vb minimal media at 30 degrees c. complementation test ...200919232050
fine mapping and candidate gene analysis of a green-revertible albino gene gra(t) in rice.green-revertible albino is a novel type of chlorophyll deficiency in rice (oryza sativa l.), which is helpful for further research in chlorophyll synthesis and chloroplast development to illuminate their molecular mechanism. in the previous study, we had reported a single recessive gene, gra(t), controlling this trait on the long arm of chromosome 2. in this paper, we mapped the gra(t) gene using 1,936 recessive individuals with albino phenotype in the f(2) population derived from the cross betw ...200919232310
nitric oxide alleviates arsenic toxicity by reducing oxidative damage in the roots of oryza sativa (rice).nitric oxide (no) is a bioactive gaseous, multifunctional molecule playing a central role and mediating a variety of physiological processes and responses to biotic and abiotic stresses including heavy metals. the present study investigated whether no applied exogenously as sodium nitroprusside (snp) has any protective role against arsenic (as) toxicity in oryza sativa (rice). treatment with 50 microm snp (a no donor) significantly ameliorated the as-induced (25 or 50 microm) decrease in root an ...200919233306
delimitation of the psh1(t) gene for rice purple leaf sheath to a 23.5 kb dna fragment.leaf sheath color plays an important role as a marker for rice genetic improvement. a recombinant inbred line (ril) population consisting of 220 individuals was developed from a cross between an oryza sativa subsp. indica variety, irbb60, and an oryza sativa subsp. japonica variety, 9407. within the ril population, a line, ri51, was found to have purple leaf sheath (psh). to map the gene governing psh, ri51 was crossed with 9407 green leaf sheath (gsh) to develop an f2 segregating population. th ...200919234555
genome-wide analysis of rice (oryza sativa l. subsp. japonica) tata box and y patch promoter elements.the tata box is one of the best characterized transcription factor binding sites. however, it is not a ubiquitous element of core promoters, and other sequence motifs such as y patches seem to play a major role in plants. here, we present a first genome-wide computational analysis of the tata box and y patch distribution in rice (oryza sativa l. subsp. japonica) promoter sequences. utilizing a probabilistic sequence model, we ascertain that only approximately 19% of rice genes possess the tata b ...200919234558
plantgm: a database for genetic markers in rice (oryza sativa) and chinese cabbage (brassica rapa).the plant genetic map database (plantgm) has been developed as a web-based system which provides information about genetic markers in rice (oryza sativa) and chinese cabbage (brassica rapa). the database has three major parts and functions; (1) map search, (2) marker search, and (3) qtl search. at present, the database provides characterization information for about 3258 genetic markers. it has 2800 rflp and 112 qtl markers related to rice in addition to 321 rflp and 25 pcr-based markers for chi ...200819238232
[effects of elevated ozone on rice (oryza sativa l.) leaf lipid peroxidation and antioxidant system].with rice (oryza sativa l.) cultivar 3694 fan as test material, and by using open top chambers, the effects of different ozone (o3) concentration on the leaf soluble protein content, lipid peroxidation, and antioxidant system were applied. three treatments were applied, i.e., charcoal-filtered air (cf, 20 nl o3 x l(-1)), non-filtered ambient air (nf, 40 nl o3 x l(-1)), and elevated o3 (eo, 75 nl o3 x l(-1)). the results showed that there were no significant differences in the test variables betw ...200819238851
cloning and characterization of drought responsive partial gene sequence(s) from oryza sativa l. subsp. indica.differential display gels were run for the drought tolerant (n-22) and drought susceptible (panidhan) genotypes of rice (oryza sativa) to identify the genes showing differential expression with respect to moisture stress. differential cdna products were cloned in pcr-trap vector and analyzed for differential expression by northern hybridization. two clones namely r4a and r7g were found to be associated with water deficit stress (wds). sequencing revealed an insert of 244 bp in the clone r4a. bla ...200819239124
detection of a quantitative trait locus controlling carbon isotope discrimination and its contribution to stomatal conductance in japonica rice.increasing leaf photosynthesis offers a possible way to improve yield potential in rice (oryza sativa l.). carbon isotope discrimination (delta(13)c) has potential as an indirect selection criterion. in this study, we searched for quantitative trait loci (qtls) controlling delta(13)c, and assessed their association with leaf photosynthesis. substitution mapping by using chromosome segment substitution lines (cssls), that carry segments from the indica cultivar kasalath in the genetic background ...200919242671
laboratory study of vibrio cholerae o1 survival on three types of boiled rice (oryza sativa l.) held at room temperature.this study examined whether the survival of vibrio cholerae o1 on contaminated cooked rice was influenced by the type of rice. vibrios survived unchanged on clumps of glutinous white rice (wet, grains adhered) held at room temperature for 24 h. on nonglutinous white rice (slightly moist, grains separate), 30% viable vibrios remained at 24 h. on nonglutinous brown rice (moist, separate, covered with a mucus-like substance), the number of vibrios increased 2.7-fold at 24 h. survival rates of vibri ...200819244898
isolation and characterization of bioactive and antibacterial compound from helianthus annuus linn.a bioactive compound with antibacterial activity was isolated and purified from the extract of leaves of sunflower, helianthus annuus. the bioactive compound was characterized using 1h and 13c nmr. the compound induced auxin, gibberellins and cytokinin in oryza sativa and phaseolus mungo. it also showed activity against xanthomonas oryzae pv. oryzae.200819245180
occurrence of d-serine in rice and characterization of rice serine racemase.germinated, unpolished rice was found to contain a substantial amount of d-serine, with the ratio of the d-enantiomer to the l-enantiomer being higher for serine than for other amino acids. the relative amount of d-serine (d/(d+l)%) reached approximately 10% six days after germination. a putative serine racemase gene (serr, clone no. 001-110-b03) was found in chromosome 4 of the genomic dna of oryza sativa l. ssp. japonica cv. nipponbare. this was expressed as serr in escherichia coli and its ge ...200919249065
the er chaperone lhs1 is involved in asexual development and rice infection by the blast fungus magnaporthe oryzae.in planta secretion of fungal pathogen proteins, including effectors destined for the plant cell cytoplasm, is critical for disease progression. however, little is known about the endoplasmic reticulum (er) secretion mechanisms used by these pathogens. to determine if normal er function is crucial for fungal pathogenicity, magnaporthe oryzae genes encoding proteins homologous to yeast lhs1p and kar2p, members of the heat shock protein 70 family in saccharomyces cerevisiae, were cloned and charac ...200919252083
comparative evaluation of three different extraction methods for rice (oryza sativa l.) genomic dna.recently, more immediate and precise cultivar-identifying methods targeting the specific and/or introduced gene(s) have been put into practical use for various rice cultivars. however trustworthy and innovative the biotechnological analyses may be, dna purity and quality do have unpredictable influences upon the identification. extraction methods of rice dna have hardly ever been compared in a comprehensive manner. in this study, we investigated extraction characteristics of three methods by usi ...200919253951
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 ...200919255090
influence of cooking on anthocyanins in black rice (oryza sativa l. japonica var. sbr).the composition and thermal stability of anthocyanins in black rice (oryza sativa l. japonica var. sbr) produced in california were investigated. six anthocyanin pigments were identified and quantified by high performance liquid chromatography using photo diode-array detection (hplc-pda) and electrospray ionization mass spectrometry [lc-(esi)ms/ms]. the predominant anthocyanins are cyanidin-3-glucoside (572.47 microg/g; 91.13% of total) and peonidin-3-glucoside (29.78 microg/g; 4.74% of total). ...200919256557
the wuschel-related homeobox gene wox11 is required to activate shoot-borne crown root development in rice.in rice (oryza sativa), the shoot-borne crown roots are the major root type and are initiated at lower stem nodes as part of normal plant development. however, the regulatory mechanism of crown root development is poorly understood. in this work, we show that a wuschel-related homeobox (wox) gene, wox11, is involved in the activation of crown root emergence and growth. wox11 was found to be expressed in emerging crown roots and later in cell division regions of the root meristem. the expression ...200919258439
description of tylenchorhynchus qasimii sp. n. with a new report of t. kegasawaiminagawa, 1995 from pakistan.a new stunt nematode, from soil around the roots of coconut (cocos nucifera l.) and rice (oryza sativa l.) from karachi, pakistan, is described and illustrated as tylenchorhynchus qasimii n. sp. this new species is characterized by having females with 3-4 head annules, anteriorly directed stylet knobs, absence of post anal extension, presence of rounded sperm filled spermatheca and conoid to bluntly rounded hemispherical tail terminus. males are common. also included is the record of t. kegasawa ...200819259514
expression profile of calcium-dependent protein kinase (cdpks) genes during the whole lifespan and under phytohormone treatment conditions in rice (oryza sativa l. ssp. indica).calcium-dependent protein kinases (cdpks) control plant development and response to various stress environments through the important roles in the regulation of ca(2+) signaling. thirty-one cdpk genes have been identified in the rice genome by a complete search of the genome based upon hmm profiles. in this study, the expression of this gene family was analyzed using the affymetrix rice genome array in three rice cultivars: minghui 63, zhenshan 97, and their hybrid shanyou 63 independently. twen ...200919263224
inducible antisense suppression of glycolate oxidase reveals its strong regulation over photosynthesis in rice.photorespiration is one of the most intensively studied topics in plant biology. while a number of mutants deficient in photorespiratory enzymes have been identified and characterized for their physiological functions, efforts on glycolate oxidase (glo; ec 1.1.3.15) have not been so successful. this is a report about the generation of transgenic rice (oryza sativa l.) plants carrying a glo antisense gene driven by an estradiol-inducible promoter, which allowed for controllable suppressions of gl ...200919264754
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