Publications

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
gc-biased gene conversion and selection affect gc content in the oryza genus (rice).	base composition varies among and within eukaryote genomes. while mutational bias and selection have initially been invoked, more recently gc-biased gene conversion (gbgc) has been proposed to play a central role in shaping nucleotide landscapes, especially in yeast, mammals, and birds. gbgc is a kind of meiotic drive in favor of g and c alleles, associated with recombination. previous studies have also suggested that gbgc could be at work in grass genomes. however, these studies were carried on ...	2011	21504892
purple rice berry is neuroprotective and enhances cognition in a rat model of alzheimer's disease.	abstract alzheimer's disease, a neurodegenerative disease characterized by progressive memory loss and cognitive impairment, is the most common type of dementia in aging populations due to severe loss of cholinergic neurons in a specific area. oxidative stress is known to be involved in the pathogenesis of this condition. therefore, the cognition-enhancing and neuroprotective effects of rice berry (oryza sativa), a purple-pigmented rice that is rich in antioxidant substances, was evaluated. youn ...	2011	21510741
characterization of recombinant β-amylases from oryza sativa.	four putative β-amylase genes found in the oryza sativa cdna sequence database (kome) were expressed in escherichia coli. recombinant proteins from two of these genes showed β-amylase activity. similarly to β-amylases from other plants, the optimum ph of the recombinant rice β-amylases was about 5.5-6.0, but they exhibited inferior heat stability to soybean β-amylase.	2011	21512221
arsenic biotransformation and volatilization in transgenic rice.	• biotransformation of arsenic includes oxidation, reduction, methylation, and conversion to more complex organic arsenicals. members of the class of arsenite (as(iii)) s-adenosylmethyltransferase enzymes catalyze as(iii) methylation to a variety of mono-, di-, and trimethylated species, some of which are less toxic than as(iii) itself. however, no methyltransferase gene has been identified in plants. • here, an arsm gene from the soil bacterium rhodopseudomonas palustris was expressed in japoni ...	2011	21517874
chemical residence time and hydrological conditions influence treatment of fipronil in vegetated aquatic mesocosms.	fipronil, a phenyl-pyrazole insecticide, is often used in rice (oryza sativa l.) production agriculture, with elevated runoff concentrations and loads having potential toxicological effects on downstream aquatic environments. this study evaluated two species of aquatic plants-broadleaf cattail (typha latifolia l.) and powdery alligator-flag (thalia dealbata fraser ex roscoe)-placed in series against a nonvegetated mesocosm in reducing concentrations and loads of fipronil, and associated metaboli ...	2011	21520763
the crystal structure of rice (oryza sativa l.) os4bglu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing β-glucosidase with significant thioglucohydrolase activity.	rice os4bglu12, a glycoside hydrolase family 1 (gh1) β-glucosidase, hydrolyzes β-(1,4)-linked oligosaccharides of 3-6 glucosyl residues and the β-(1,3)-linked disaccharide laminaribiose, as well as certain glycosides. the crystal structures of apo os4bglu12, and its complexes with 2,4-dinitrophenyl-2-deoxyl-2-fluoroglucoside (dnp2fg) and 2-deoxy-2-fluoroglucose (g2f) were solved at 2.50, 2.45 and 2.40å resolution, respectively. the overall structure of rice os4bglu12 is typical of gh1 enzymes, b ...	2011	21521631
towards establishment of a rice stress response interactome.	rice (oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. a major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%-60% yield losses globally each year. to elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (y2h) assays around key regulators of the rice biotic and abi ...	2011	21533176
molecular evidence for a single evolutionary origin of domesticated rice.	asian rice, oryza sativa, is one of world's oldest and most important crop species. rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. a single-origin model suggests that two main subspecies of asian rice, indica and japonica, were domesticated from the wild rice o. rufipogon. in contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species ...	2011	21536870
silicon-induced brown spot resistance in rice (oryza sativa l.).		2011	21539216
application of gene targeting to designed mutation breeding of high-tryptophan rice.	site-directed mutagenesis via gene targeting (gt) based on homologous recombination is the ultimate mutation breeding technology because it enables useful information acquired from structural- and computational-based protein engineering to be applied directly to molecular breeding, including metabolic engineering, of crops. here, we employed this rationale to introduce precise mutations in oasa2-a key enzyme of tryptophan (trp) biosynthesis in rice-via gt, with subsequent selection of gt cells u ...	2011	21543727
osccamk genotype determines bacterial communities in rice roots under paddy and upland field conditions.	the effects of osccamk genotype (dominant homozygous, d; heterozygous, h; recessive homozygous, r) on rice root-associated bacteria, including endophytes and epiphytes, were examined by using a tos17 rice mutant line under paddy and upland field conditions. roots were sampled at flowering stage and were subjected to clone library analyses. the relative abundance of alphaproteobacteria was noticeably decreased in r plants under both paddy and upland conditions (0.8% and 3.0%, respectively) relati ...	2011	21551283
analyses of two rice (oryza sativa) cyclin-dependent kinase inhibitors and effects of transgenic expression of osiick6 on plant growth and development.	background and aims plants have a family of proteins referred to as icks (inhibitors of cyclin-dependent kinase, cdk) or krps (kip-related proteins) that function to regulate the activities of cdk. knowledge of these plant cdk inhibitors has been gained mostly from studies of selected members in dicotyledonous plants, particularly arabidopsis. much remains to be learned regarding the differences among various members of the ick/krp family, and regarding the function and regulation of these prote ...	2011	21558459
functional incorporation of sorghum small subunit increases the catalytic turnover rate of rubisco in transgenic rice.	ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) limits photosynthetic co2 fixation because of its low catalytic turnover rate (kcat) and competing oxygenase reaction. previous attempts to improve the catalytic efficiency of rubisco by genetic engineering have gained little progress. here we demonstrate that the introduction of the small subunit (rbcs) of high kcat rubisco from the c4 plant sorghum (sorghum bicolor) significantly enhances kcat of rubisco in transgenic rice (oryza sativa ...	2011	21562335
bioethanol production from dedicated energy crops and residues in arkansas, usa.	globally, one of the major technologic goals is to achieve cost-effective lignocellulosic ethanol production from biomass feedstocks. lignocellulosic biomass of four dedicated energy crops [giant reed (arundo donax l.), elephantgrass (pennisetum purpureum (schumach), miscanthus × giganteus (illinois clone), and (clone q42641) {hybrid of miscanthus sinensis anderss. and miscanthus sacchariflorus (maxim)}, hack. called giant miscanthus, and sugarcane clone us 84-1028 (saccharum l. spp. hybrid)] an ...	2011	21086455
pollen-specific expression of oryza sativa indica pollen allergen gene (osipa) promoter in rice and arabidopsis transgenic systems.	earlier, a pollen-specific oryza sativa indica pollen allergen gene (osipa), coding for expansins/pollen allergens, was isolated from rice, and its promoter--upon expression in tobacco and arabidopsis--was found active during the late stages of pollen development. in this investigation, to analyze the effects of different putative regulatory motifs of osipa promoter, a series of 5' deletions were fused to β-glucuronidase gene (gus) which were stably introduced into rice and arabidopsis. histoche ...	2011	21061188
oshma3, a p1b-type of atpase affects root-to-shoot cadmium translocation in rice by mediating efflux into vacuoles.	• the cadmium (cd) over-accumulating rice (oryza sativa) cv cho-ko-koku was previously shown to have an enhanced rate of root-to-shoot cd translocation. this trait is controlled by a single recessive allele located at qcdt7. • in this study, using positional cloning and transgenic strategies, heavy metal atpase 3 (oshma3) was identified as the gene that controls root-to-shoot cd translocation rates. the subcellular localization and cd-transporting activity of the gene products were also investig ...	2011	20840506
gene transfer into solanum tuberosum via rhizobium spp.	agrobacterium tumefaciens-mediated transformation (atmt) is the preferred technique for gene transfer into crops. a major disadvantage of the technology remains the complexity of the patent landscape that surrounds atmt which restricts its use for commercial applications. an alternative system has been described (broothaerts et al. in nature 433:629-633, 2005) detailing the propensity of three rhizobia to transform the model crop arabidopsis thaliana, the non-food crop nicotiana tabacum and, at ...	2011	20582626
actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a thai jasmine rice plant.	the novel strain gmku 370(t) was isolated from roots of a thai jasmine rice plant (oryza sativa l. 'kdml 105') collected from pathum thani rice research center, pathum thani province, thailand. a phylogenetic analysis based on 16s rrna gene sequences indicated that strain gmku 370(t) formed a distinct clade within the genus actinoallomurus. strain gmku 370(t) contained meso-diaminopimelic acid and lysine in the cell-wall peptidoglycan and galactose and madurose as whole-cell sugars. no mycolic a ...	2011	20418407
roles of xanthophylls and exogenous aba in protection against nacl-induced photodamage in rice (oryza sativa l) and cabbage (brassica campestris).	changes in actual efficiency of ps ii photochemistry, non-photochemical quenching (npq), content of xanthophylls and kinetics of de-epoxidation were studied in aba-fed and non-aba-fed leaves of rice and cabbage under nacl stress. salt stress induced more progressive decrease in actual efficiency of ps ii photochemistry (фps ii), higher reduction state of ps ii, and a small significant increase in npq in nacl-sensitive rice plants as compared with nacl-tolerant cabbage plants, whereas exogenously ...	2011	21642236
conservation and purifying selection of transcribed genes located in a rice centromere.	recombination is strongly suppressed in centromeric regions. in chromosomal regions with suppressed recombination, deleterious mutations can easily accumulate and cause degeneration of genes and genomes. surprisingly, the centromere of chromosome8 (cen8) of rice (oryza sativa) contains several transcribed genes. however, it remains unclear as to what selective forces drive the evolution and existence of transcribed genes in cen8. sequencing of orthologous cen8 regions from two additional oryza s ...	2011	21856794
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
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
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
crop genome sequencing: lessons and rationales.	2010 marks the 10th anniversary of the completion of the first plant genome sequence (arabidopsis thaliana). triggered by advancements in sequencing technologies, many crop genome sequences have been produced, with eight published since 2008. to date, however, only the rice (oryza sativa) genome sequence has been finished to a quality level similar to that of the arabidopsis sequence. this trend to produce draft genomes could affect the ability of researchers to address biological questions of s ...	2011	21081278
evolutionary analysis of three gibberellin oxidase genes in rice, arabidopsis, and soybean.	gas are plant hormones that play fundamental roles in plant growth and development. ga2ox, ga3ox, and ga20ox are three key enzymes in ga biosynthesis. these enzymes belong to the 2og-fe (ii) oxygenase superfamily and are independently encoded by different gene families. to date, genome-wide comparative analyses of ga oxidases in plant species have not been thoroughly carried out. in the present work, 61 ga oxidase family genes from rice (oryza sativa), arabidopsis, and soybean (glycine max) were ...	2011	21056641
barbarea vulgaris linkage map and quantitative trait loci for saponins, glucosinolates, hairiness and resistance to the herbivore phyllotreta nemorum.	combined genomics and metabolomics approaches were used to unravel molecular mechanisms behind interactions between winter cress (barbarea vulgaris) and flea beetle (phyllotreta nemorum). b. vulgaris comprises two morphologically, biochemically and cytologically deviating types, which differ in flea beetle resistance, saponin and glucosinolate profiles, as well as leaf pubescence. an f2 population generated from a cross between the two b. vulgaris types was used to construct a b. vulgaris geneti ...	2011	21130479
balancing forces in the photoperiodic control of flowering.	in many plant species, the duration of the daily exposure to light (photoperiod) provides a seasonal cue that helps to adjust flowering time to the most favourable time of the year. in arabidopsis thaliana, the core mechanism of acceleration of flowering by long days involves the stabilisation of the constans (co) protein by light reaching the leaves, the direct induction of the expression of flowering locus t (ft) by co and the migration of ft to the apex to promote flowering. in rice (oryza sa ...	2011	21125113
allelic variation in the perennial ryegrass flowering locus t gene is associated with changes in flowering time across a range of populations.	the arabidopsis (arabidopsis thaliana) flowering locus t (ft) gene and its orthologs in other plant species (e.g. rice [oryza sativa] osftl2/hd3a) have an established role in the photoperiodic induction of flowering response. the genomic and phenotypic variations associated with the perennial ryegrass (lolium perenne) ortholog of ft, designated lpft3, was assessed in a diverse collection of nine european germplasm populations, which together constituted an association panel of 864 plants. sequen ...	2011	21115808
the genome sequence of the north-european cucumber (cucumis sativus l.) unravels evolutionary adaptation mechanisms in plants.	cucumber (cucumis sativus l.), a widely cultivated crop, has originated from eastern himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. we wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. here we present the draft genome sequence of the cucumis sativus genome ...	2011	21829493
gibberellin control of stamen development: a fertile field.	stamen development is governed by a conserved genetic pathway, within which the role of hormones has been the subject of considerable recent research. our understanding of the involvement of gibberellin (ga) signalling in this developmental process is further advanced than for the other phytohormones, and here we review recent experimental results in rice (oryza sativa) and arabidopsis (arabidopsis thaliana) that have provided insight into the timing and mechanisms of ga regulation of stamen dev ...	2011	21824801
characterization of the sulfurtransferase family from oryza sativa l.	sulfurtransferases (str) comprise a group of enzymes widely distributed in archaea, eubacteria, and eukaryota which catalyze the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. neither the in vivo sulfur donors nor the acceptors of str could be clearly identified in any of the organisms investigated so far. in oryza sativa l. 24 str (osstr) encoding genes have been identified and subdivided into six groups according to their sequence homology. to half of t ...	2011	21821426
survey and characterization of nbs-lrr (r) genes in curcuma longa transcriptome.	resistance genes are among the most important gene classes for plant breeding purposes being responsible for activation of plant defense mechanisms. among them, the nucleotide binding site-leucine rich repeat (nbs-lrr) class r-genes are the most abundant and actively found in all types of plants. insilico characterization of est database resulted in the detection of 28 nbs types r-gene sequences in curcuma longa. all the 28 sequences represented the nb-arc domain, 21 of which were found to have ...	2011	21814396
14-3-3 proteins act as intracellular receptors for rice hd3a florigen.	'florigen' was proposed 75 years ago to be synthesized in the leaf and transported to the shoot apex, where it induces flowering. only recently have genetic and biochemical studies established that florigen is encoded by flowering locus t (ft), a gene that is universally conserved in higher plants. nonetheless, the exact function of florigen during floral induction remains poorly understood and receptors for florigen have not been identified. here we show that the rice ft homologue hd3a interact ...	2011	21804566
exploiting leaf starch synthesis as a transient sink to elevate photosynthesis, plant productivity and yields.	improvements in plant productivity (biomass) and yield have centered on increasing the efficiency of leaf co(2) fixation and utilization of products by non-photosynthetic sink organs. we had previously demonstrated a correlation between photosynthetic capacity, plant growth, and the extent of leaf starch synthesis utilizing starch-deficient mutants. this finding suggested that leaf starch is used as a transient photosynthetic sink to recycle inorganic phosphate and, in turn, maximize photosynthe ...	2011	21763538
osphf1 regulates the plasma membrane localization of low- and high-affinity inorganic phosphate transporters and determines inorganic phosphate uptake and translocation in rice.	phosphate transporter traffic facilitator1 (phf1) is known to regulate the plasma membrane localization of pht1;1, a high-affinity inorganic phosphate (pi) transporter in arabidopsis (arabidopsis thaliana). osphf1, a rice (oryza sativa) gene homologous to atphf1, was isolated and found to regulate the localization of both low- and high-affinity pi transporters to the plasma membrane. three osphf1 allelic mutants carrying one-point mutations at the fifth wd-repeat motif and two at the transmembra ...	2011	21753117
functional analysis of two isoforms of leaf-type ferredoxin-nadp(+)-oxidoreductase in rice using the heterologous expression system of arabidopsis.	ferredoxin-nadp(+)-oxidoreductase (fnr) mediates electron transfer between ferredoxin (fd) and nadp(+); therefore, it is a key enzyme that provides the reducing power used in the calvin cycle. other than fnr, nitrite reductase, sulfite reductase, glutamate synthase, and fd-thioredoxin reductase also accept electrons from fd, an electron carrier protein in the stroma. therefore, the regulation of electron partitioning in the chloroplast is important for photosynthesis and other metabolic pathways ...	2011	21734114
a white spruce gene catalog for conifer genome analyses.	several angiosperm plant genomes, including arabidopsis (arabidopsis thaliana), rice (oryza sativa), poplar (populus trichocarpa), and grapevine (vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. a gene catalog was developed for the conifer tree picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cdna sequen ...	2011	21730200
defective pollen wall is required for anther and microspore development in rice and encodes a fatty acyl carrier protein reductase.	aliphatic alcohols naturally exist in many organisms as important cellular components; however, their roles in extracellular polymer biosynthesis are poorly defined. we report here the isolation and characterization of a rice (oryza sativa) male-sterile mutant, defective pollen wall (dpw), which displays defective anther development and degenerated pollen grains with an irregular exine. chemical analysis revealed that dpw anthers had a dramatic reduction in cutin monomers and an altered composit ...	2011	21705642
the cop1 ortholog pps regulates the juvenile-adult and vegetative-reproductive phase changes in rice.	because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. we identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (oryza sativa) and showed that rice pps is an ortholog of arabidopsis thaliana constitutive photomorphogenic1. the pps-1 mutant exhibits delayed expression of mir156 and mir172 and the suppression of ga biosynthetic genes, reducing ...	2011	21705640
dcl2 is highly expressed in the egg cell in both rice and arabidopsis.	small rnas are riboregulators that play critical roles in eukaryotic cells. they repress gene expression by acting either on dna to guide sequence elimination and chromatin remodeling, or on rna to guide cleavage and translation repression. arabidopsis thaliana and oryza sativa contain four and six dicer-like (dcl) genes with specialized functions in small rna biogenesis for rna interference-related processes. we recently profiled genome-wide gene expression in egg and synergid cells in rice. in ...	2011	21673515
origin and evolution of genes related to aba metabolism and its signaling pathways.	since plants cannot move to avoid stress, they have sophisticated acclimation mechanisms against a variety of abiotic stresses. the phytohormone abscisic acid (aba) plays essential roles in abiotic stress tolerances in land plants. therefore, it is interesting to address the evolutionary origins of aba metabolism and its signaling pathways in land plants. here, we focused on 48 aba-related arabidopsis thaliana genes with 11 protein functions, and generated 11 orthologous clusters of aba-related ...	2011	21626211
the biotron breeding system: a rapid and reliable procedure for genetic studies and breeding in rice.	oryza sativa is widely used as a model organism for many aspects of research in monocots and cereals. however, it has certain disadvantages as a model species compared with arabidopsis thaliana, the eudicot species most widely used in plant sciences: first, it has a long cultivation time; and second, it requires considerably more space for growth. here, we introduce a biotron breeding system, which allows rapid and reliable rice cultivation using a well-equipped artificial environmental chamber. ...	2011	21622665
a physical map for the amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.	recent phylogenetic analyses have identified amborella trichopoda, an understory tree species endemic to the forests of new caledonia, as sister to a clade including all other known flowering plant species. the amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. a physical map, bac end sequences and sample shotgun sequences provide a first view of the 870 mbp amborella genome.	2011	21619600
leaf rolling controlled by the homeodomain leucine zipper class iv gene roc5 in rice.	leaf rolling is considered an important agronomic trait in rice (oryza sativa) breeding. to understand the molecular mechanism controlling leaf rolling, we screened a rice t-dna insertion population and isolated the outcurved leaf1 (oul1) mutant showing abaxial leaf rolling. the phenotypes were caused by knockout of rice outermost cell-specific gene5 (roc5), an ortholog of the arabidopsis (arabidopsis thaliana) homeodomain leucine zipper class iv gene glabra2. interestingly, overexpression of ro ...	2011	21596949
os-gigantea confers robust diurnal rhythms on the global transcriptome of rice in the field.	the circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. under natural field conditions, however, little is known about the significance of the circadian clock in plants. by time-course transcriptome analyses of rice (oryza sativa) leaves, using a newly isolated rice circadian clock-related mutant carrying a null mutation in os-gigantea (os-gi), we show here that os-gi controlled 75% (false discovery rate = 0.05) ...	2011	21571948
comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in arabidopsis and rice.	microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species arabidopsis (arabidopsis thaliana) and rice (oryza sativa). expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. we developed a robust framework to measure expression context conservation (ecc) and found, by analyzing 4,630 pairs ...	2011	21571672
expression and genome-wide analysis of the xylogen-type gene family.	in higher plants, many extracellular proteins are involved in developmental processes, including cell-cell signaling and cell wall construction. xylogen is an extracellular arabinogalactan protein (agp) isolated from zinnia elegans xylogenic culture medium, which promotes xylem cell differentiation. xylogen has a unique structure, containing a non-specific lipid transfer protein (nsltp) domain and agp domains. we searched for xylogen-type genes in the genomes of land plants, including arabidopsi ...	2011	21558309
ip6k gene identification in plant genomes by tag searching.	plants have played a special role in inositol polyphosphate (ip) research since in plant seeds was discovered the first ip, the fully phosphorylated inositol ring of phytic acid (ip6). it is now known that phytic acid is further metabolized by the ip6 kinases (ip6ks) to generate ip containing pyro-phosphate moiety. the ip6k are evolutionary conserved enzymes identified in several mammalian, fungi and amoebae species. although ip6k has not yet been identified in plant chromosomes, there are many ...	2011	21554757
genome-scale computational analysis of dna curvature and repeats in arabidopsis and rice uncovers plant-specific genomic properties.	due to its overarching role in genome function, sequence-dependent dna curvature continues to attract great attention. the dna double helix is not a rigid cylinder, but presents both curvature and flexibility in different regions, depending on the sequence. more in depth knowledge of the various orders of complexity of genomic dna structure has allowed the design of sophisticated bioinformatics tools for its analysis and manipulation, which, in turn, have yielded a better understanding of the ge ...	2011	21548945
rice abi5-like1 regulates abscisic acid and auxin responses by affecting the expression of abre-containing genes.	abscisic acid (aba) regulates plant development and is crucial for plant responses to biotic and abiotic stresses. studies have identified the key components of aba signaling in arabidopsis (arabidopsis thaliana), some of which regulate aba responses by the transcriptional regulation of downstream genes. here, we report the functional identification of rice (oryza sativa) abi5-like1 (abl1), which is a basic region/leucine zipper motif transcription factor. abl1 is expressed in various tissues an ...	2011	21546455
tandem termination signal in plant mrnas.	it was proposed that if some mrna characteristics resulted in a low efficiency of termination signal, an additional closely located stop codon (tandem stop codons) could be used to prevent the harmful readthrough. however, the role of tandem terminators in higher eukaryotes was not verified and remains hypothetical. in this work the sequence features of arabidopsis thaliana and oryza sativa mrnas were analyzed. it was found that plant mrnas with uga terminator were characterized by a higher freq ...	2011	21539902
dna free energy-based promoter prediction and comparative analysis of arabidopsis and rice genomes.	the cis-regulatory regions on dna serve as binding sites for proteins such as transcription factors and rna polymerase. the combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. we present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of arabidopsis (arabidopsis thaliana) and rice (oryza sativa) on the basis o ...	2011	21531900
persistent tapetal cell1 encodes a phd-finger protein that is required for tapetal cell death and pollen development in rice.	in higher plants, timely degradation of tapetal cells, the innermost sporophytic cells of the anther wall layer, is a prerequisite for the development of viable pollen grains. however, relatively little is known about the mechanism underlying programmed tapetal cell development and degradation. here, we report a key regulator in monocot rice (oryza sativa), persistant tapetal cell1 (ptc1), which controls programmed tapetal development and functional pollen formation. the evolutionary significanc ...	2011	21515697
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
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
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
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
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
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
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
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
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
rnai mediated silencing of a wall associated kinase, osiwak1 in oryza sativa results in impaired root development and sterility due to anther indehiscence: wall associated kinases from oryza sativa.	the wall-associated kinase, one of the receptor-like kinase (rlk) gene families in plant, plays important roles in cell expansion, pathogen resistance and heavy metal stress tolerance in arabidopsis thaliana. here, we isolated a cdna encoding a novel wak from indica rice and designated as osiwak1 (oryza sativa indica wak-1). in this study, the rnai construct with osiwak1 gene cloned in sense and antisense orientation separated by a functional intron under constitutive promoter, was introduced th ...	2011	23572996
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
new allele of hvbri1 gene encoding brassinosteroid receptor in barley.	the aim of these studies was to characterize nucleotide substitutions leading to the phenotype of brassinosteroid-insensitive, semi-dwarf barley mutant 093ar. two substitutions in the sequence of barley hvbri1 gene, encoding leucine-rich repeats receptor kinase (lrr-rk), which participates in brassinosteroid (br) signalling, were identified in this chemically-induced barley mutant of the cv. aramir. the lrr-rk is a transmembrane protein phosphorylating downstream components. the identified subst ...	2011	21302020
a stress-associated protein containing a20/an1 zing-finger domains expressed in medicago truncatula seeds.	mtsap1 (medicago truncatula stress-associated protein 1) was revealed as a down-regulated gene by suppressive subtractive hybridization between two mrna populations of embryo axes harvested before and after radicle emergence. mtsap1 is the first gene encoding a sap with a20 and an1 zinc-finger domains characterized in m. truncatula. mtsap1 protein shares 54% and 62% homology with atsap7 (arabidopsis thaliana) and osisap8 (oryza sativa) respectively, with in particular a strong homology in the a2 ...	2011	21296585
uncoupling phosphate deficiency from its major effects on growth and transcriptome via pho1 expression in arabidopsis.	inorganic phosphate (pi) is one of the most limiting nutrients for plant growth in both natural and agricultural contexts. pi-deficiency leads to a strong decrease in shoot growth, and triggers extensive changes at the developmental, biochemical and gene expression levels that are presumably aimed at improving the acquisition of this nutrient and sustaining growth. the arabidopsis thaliana pho1 gene has previously been shown to participate in the transport of pi from roots to shoots, and the nul ...	2011	21288266
genome-wide analysis of clustering patterns and flanking characteristics for plant microrna genes.	micrornas (mirnas) have been proven to play important roles at the post-transcriptional level in animals and plants. to investigate clustering patterns and specific sequence characteristics in the flanking regions of plant mirna genes, we performed genome-wide analyses of arabidopsis thaliana, populus trichocarpa, oryza sativa and sorghum bicolor. our results showed that mirna pair distances were significantly higher than would have been expected to occur at random and that the number of mirna g ...	2011	21223508
coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice.	cellulose from plant biomass is the largest renewable energy resource of carbon fixed from the atmosphere, which can be converted into fermentable sugars for production into ethanol. however, the cellulose present as lignocellulosic biomass is embedded in a hemicellulose and lignin matrix from which it needs to be extracted for efficient processing. here, we show that expression of an arabidopsis (arabidopsis thaliana) transcription factor, shine (shn), in rice (oryza sativa), a model for the gr ...	2011	21205614
in the light of evolution: a reevaluation of conservation in the co-ft regulon and its role in photoperiodic regulation of flowering time.	in order to maximize reproductive success, plants have evolved different strategies to control the critical developmental shift marked by the transition to flowering. as plants have adapted to diverse environments across the globe, these strategies have evolved to recognize and respond to local seasonal cues through the induction of specific downstream genetic pathways, thereby ensuring that the floral transition occurs in favorable conditions. determining the genetic factors involved in control ...	2011	22639612
from models to crop species: caveats and solutions for translational metabolomics.	although plant metabolomics is largely carried out on arabidopsis it is essentially genome-independent, and thus potentially applicable to a wide range of species. however, transfer between species, or even between different tissues of the same species, is not facile. this is because the reliability of protocols for harvesting, handling and analysis depends on the biological features and chemical composition of the plant tissue. in parallel with the diversification of model species it is importa ...	2011	22639601
pmirkb: a plant microrna knowledge base.	micrornas (mirnas), one type of small rnas (srnas) in plants, play an essential role in gene regulation. several mirna databases were established; however, successively generated new datasets need to be collected, organized and analyzed. to this end, we have constructed a plant mirna knowledge base (pmirkb) that provides four major functional modules. in the 'snp' module, single nucleotide polymorphism (snp) data of seven arabidopsis (arabidopsis thaliana) accessions and 21 rice (oryza sativa) s ...	2011	20719744
testing the imeter on rice introns and other aspects of intron-mediated enhancement of gene expression.	in many eukaryotes, spliceosomal introns are able to influence the level and site of gene expression. the mechanism of this intron mediated enhancement (ime) has not yet been elucidated, but regulation of gene expression is likely to occur at several steps during and after transcription. different introns have different intrinsic enhancing properties, but the determinants of these differences remain unknown. recently, an algorithm called imeter, which is able to predict the ime potential of intr ...	2011	20855457
association of commercial rice varieties with weedy rice accessions (oryza sativa complex) in pulau pinang's rice granary area.	weedy rice (wr) is the most significant weed in direct-seeded fields. it has morphological characteristics similar to those of cultivated rice varieties. wr is more difficult to control than other weeds. we collected wr accessions from four sites within the pulau pinang rice growing areas. thirty six different accessions were collected from each site: b, the northern site; p, the central site; a, the southern site; and n, the southwestern site. wild rice (oryza rufipogon), which grows in the sam ...	2011	24575213
effects of rapeseed residue on lead and cadmium availability and uptake by rice plants in heavy metal contaminated paddy soil.	rapeseed (brassica napus l.) has been cultivated for biodiesel production worldwide. winter rapeseed is commonly grown in the southern part of korea under a rice-rapeseed double cropping system. in this study, a greenhouse pot experiment was conducted to assess the effects of rapeseed residue applied as a green manure alone or in combinations with mineral n fertilizer on cd and pb speciation in the contaminated paddy soil and their availability to rice plant (oryza sativa l.). the changes in soi ...	2011	21764102
seasonal expression of bt proteins in transgenic rice lines and the resistance against asiatic rice borer chilo suppressalis (walker).	laboratory bioassays and field surveys were carried out to compare the resistance of three transgenic rice (oryza sativa l.) lines including bt-dl expressing a single gene cry1ab, bt-kf6 expressing stacked genes cry1ac and cpti genes and bt-sy63 expressing a fusion gene cry1ab/cry1ac, respectively, to an important rice pest chilo suppressalis (walker). in addition, enzyme-linked immunosorbent assays (elisa) were conducted to monitor the bt protein expressions in rice leaves and stems at differen ...	2011	22251743
an ear-motif-containing erf transcription factor affects herbivore-induced signaling, defense and resistance in rice.	ethylene responsive factors (erfs) are a large family of plant-specific transcription factors that are involved in the regulation of plant development and stress responses. however, little to nothing is known about their role in herbivore-induced defense. we discovered a nucleus-localized erf gene in rice (oryza sativa), oserf3, that was rapidly up-regulated in response to feeding by the rice striped stem borer (ssb) chilo suppressalis. antisense and over-expression of oserf3 revealed that it po ...	2011	21831212
the study of the e-class sepallata3-like mads-box genes in wild-type and mutant flowers of cultivated saffron crocus (crocus sativus l.) and its putative progenitors.	to further understand flowering and flower organ formation in the monocot crop saffron crocus (crocus sativus l.), we cloned four mikc(c) type ii mads-box cdna sequences of the e-class sepallata3 (sep3) subfamily designated csatsep3a/b/c/c_as as well as the three respective genomic sequences. sequence analysis showed that cdna sequences of csatsep3 c and c_as are the products of alternative splicing of the csatsep3c gene. bioinformatics analysis with putative orthologous sequences from various p ...	2011	21621873
breeding of commercially acceptable allelopathic rice cultivars in china.	one promising area of paddy weed control is the potential for exploiting the weed-suppressing ability of rice. this study was conducted to develop commercially acceptable allelopathic rice cultivars using crosses between allelopathic rice variety pi312777 and commercial chinese cultivars (n2s, n9s, huahui354, peiai64s and tehuazhan35), and to assess their weed suppression and grain yield in paddy fields in relation to their parents.	2011	21520392
the rice miniature inverted repeat transposable element mping is an effective insertional mutagen in soybean.	insertional mutagenesis of legume genomes such as soybean (glycine max) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality. the relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations. however, existing transposon-tagging tools being used in legumes are of limited utility because of restricted transpositi ...	2011	21844309
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
a snp in gmbadh2 gene associates with fragrance in vegetable soybean variety "kaori" and snap marker development for the fragrance.	fragrance in soybean is due to the presence of 2-acetyl-1-pyrroline (2ap). badh2 gene coding for betaine aldehyde dehydrogenase has been identified as the candidate gene responsible for fragrance in rice (oryza sativa l.). in this study, using the ril population derived from fragrant soybean cultivar "kaori" and non-fragrant soybean cultivar "chiang mai 60" (cm60), sts markers designed from badh2 homolog were found associating with 2ap production. genetic mapping demonstrated that qtl position o ...	2011	21046066
deficiency in the amino aldehyde dehydrogenase encoded by gmamadh2, the homologue of rice os2ap, enhances 2-acetyl-1-pyrroline biosynthesis in soybeans (glycine max l.).	2-acetyl-1-pyrroline (2ap), the volatile compound that provides the 'popcorn-like' aroma in a large variety of cereal and food products, is widely found in nature. deficiency in amino aldehyde dehydrogenase (amadh) was previously shown to be the likely cause of 2ap biosynthesis in rice (oryza sativa l.). in this study, the validity of this mechanism was investigated in soybeans (glycine max l.). an assay of amadh activity in soybeans revealed that the aromatic soybean, which contains 2ap, also l ...	2011	20497370
mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines.	mapping chromosome regions responsible for quantitative phenotypic variation in recombinant populations provides an effective means to characterize the genetic basis of complex traits. we conducted a quantitative trait loci (qtl) analysis of 150 rice recombinant inbred lines (rils) derived from a cross between two cultivars, oryza sativa ssp. indica cv. 93-11 and oryza sativa ssp. japonica cv. nipponbare. the rils were genotyped through next-generation sequencing, which accurately determined the ...	2011	20878143
phytochrome-regulated ebl1 contributes to aco1 upregulation in rice.	the 1-aminocyclopropane-1-carboxylate oxidase gene (aco1) was upregulated in rice (oryza sativa l.) phyaphybphyc mutants lacking any phytochrome and containing the gcc box element, a binding site for rice ethylene-responsive element binding protein 1 (oserebp1), in its promoter region. since the oserebp1-like gene ebl1 (oserebp1-like 1) was significantly downregulated in phyaphybphyc mutants, ebl1 was suspected to repress aco1 expression in wild-type plants. however, aco1 was downregulated in eb ...	2011	20872166
root-specific transcript profiling of contrasting rice genotypes in response to salinity stress.	elevated salinity imposes osmotic and ion toxicity stresses on living cells and requires a multitude of responses in order to enable plant survival. building on earlier work profiling transcript levels in rice (oryza sativa) shoots of fl478, a salt-tolerant indica recombinant inbred line, and ir29, a salt-sensitive cultivar, transcript levels were compared in roots of these two accessions as well as in the roots of two additional salt-tolerant indica genotypes, the landrace pokkali and the recom ...	2011	20924028
development of an efficient inverse pcr method for isolating gene tags from t-dna insertional mutants in rice.	the central goal of current genomics research in plants, as in other organisms, is to elucidate the functions of every gene. insertional mutagenesis using known dna sequences such as t-dna is a powerful tool in functional genomics. development of efficient methods for isolating the genomic sequences flanking insertion elements accelerates the systematic cataloging of insertional mutants, and thus allows functions to be assigned to uncharacterized genes via reverse genetic approaches. in our curr ...	2011	20931378
fine mapping and candidate gene analysis of ptgms2-1, the photoperiod-thermo-sensitive genic male sterile gene in rice (oryza sativa l.).	photoperiod-thermo-sensitive genic male sterile (ptgms) rice exhibits a number of desirable traits for hybrid rice production. the cloning genes responsible for ptgms and those elucidating male sterility mechanisms and reversibility to fertility would be of great significance to provide a foundation to develop new male sterile lines. guangzhan63s, a ptgms line, is one of the most widely used indica two-line hybrid rice breeding systems in china. in this study, genetic analysis based on f(2) and ...	2011	20938764
differential histone modification and protein expression associated with cell wall removal and regeneration in rice (oryza sativa).	the cell wall is a critical extracellular structure that provides protection and structural support in plant cells. to study the biological function of the cell wall and the regulation of cell wall resynthesis, we examined cellular responses to enzymatic removal of the cell wall in rice (oryza sativa) suspension cells using proteomic approaches. we find that removal of cell wall stimulates cell wall synthesis from multiple sites in protoplasts instead of from a single site as in cytokinesis. nuc ...	2011	20958091
ovp1, a vacuolar h+-translocating inorganic pyrophosphatase (v-ppase), overexpression improved rice cold tolerance.	vacuolar h(+)-translocating inorganic pyrophosphatase (v-ppase, ec 3.6.1.1) is an electrogenic proton pump and has been studied in many plants. here we report characterization of the ovp1 gene from rice (oryza sativa l.). quantitative reverse transcriptase-polymerase chain reaction analysis (rt-qpcr) showed that ovp1 was induced by cold stress. ovp1 overexpression resulted in enhanced cold tolerance in transgenic rice, which was related to an increased integrity of cell membrane, decreased mda c ...	2011	20974539
origins of functional nucleotide polymorphisms in a major quantitative trait locus, qltg3-1, controlling low-temperature germinability in rice.	qltg3-1 is a major quantitative trait locus (qtl) controlling tolerance to low-temperature at the seed germination stage (termed low-temperature germinability) in rice using a population derived from the cross between italica livorno from italy and hayamasari from japan. map-based cloning identified that qltg3-1 encodes a protein of unknown function. the molecular identification of this major qtl could make it possible to identify allelic variation and favorable alleles for rice breeding program ...	2011	20960223
identification of a novel mitochondrial protein, short postembryonic roots 1 (spr1), involved in root development and iron homeostasis in oryza sativa.	• a rice mutant, oryza sativa short postembryonic roots 1 (osspr1), has been characterized. it has short postembryonic roots, including adventitious and lateral roots, and a lower iron content in its leaves. • osspr1 was identified by map-based cloning. it encodes a novel mitochondrial protein with the armadillo-like repeat domain. • osspr1 mutants exhibited decreased root cell elongation. the iron content of the mutant shoots was significantly altered compared with that of wild-type shoots. a s ...	2011	21039568
aerenchyma formation in the rice stem and its promotion by h2o2.	• gas spaces (aerenchyma) form as an adaptation to submergence to facilitate gas exchange. in rice (oryza sativa), aerenchyma develop by cell death and lysis, which are poorly understood at the cellular level. • aerenchyma formation was studied in rice stems by light microscopy. it was analyzed in response to submergence, ethylene and hydrogen peroxide (h(2)o(2)) treatment, and in the mt2b::tos17 mutant. o(2)·(-) was detected with nitroblue tetrazolium and an epinephrine assay. h(2)o(2) was dete ...	2011	21039565
a rice β-1,3-glucanase gene osg1 is required for callose degradation in pollen development.	plant β-1,3-glucanases are involved in plant defense and development. in rice (oryza sativa), 14 genes encoding putative β-1,3-glucanases have been isolated and sequenced. however, only limited information is available on the function of these β-1,3-glucanase genes. in this study, we report a detailed functional characterization of one of these genes, osg1. osg1 encodes a glucanase carrying no c-terminal extension. osg1 was found to be expressed throughout the plant and highly expressed in flore ...	2011	21046148
negative feedback regulation of microbe-associated molecular pattern-induced cytosolic ca2+ transients by protein phosphorylation.	microbe/pathogen-associated molecular patterns (mamps/pamps) often induce rises in cytosolic free ca(2+) concentration ([ca(2+)](cyt)) and protein phosphorylation. though they are postulated to play pivotal roles in plant innate immunity, their molecular links and the regulatory mechanisms remain largely unknown. to investigate the regulatory mechanisms for mamp-induced ca(2+) mobilization, we have established a transgenic rice (oryza sativa) cell line stably expressing apoaequorin, and characte ...	2011	21063744
genetic variation in biomass traits among 20 diverse rice varieties.	biofuels provide a promising route of producing energy while reducing reliance on petroleum. developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (oryza sativa). in this study, we analyzed a ...	2011	21062890
effect of ce(iii) on heat production of mitochondria isolated from hybrid rice.	the effect of cerium on mitochondria isolated from hybrid rice shanyou 63 (oryza sativa l) was investigated. through in vivo culture, low dose ce3+ promoted, but higher dose ce3+, restrained mitochondrial heat production. however, through vitro incubation, ce3+ showed only inhibitory action on mitochondrial energy turnover, the concentration required for 50% inhibition being 46.7 μm. in addition, ce3+, like ca2+, induced rice mitochondrial swelling and decreased membrane potential (△ψ), which wa ...	2011	21104337
contrasting dynamics of radial o2-loss barrier induction and aerenchyma formation in rice roots of two lengths.	many wetland species form aerenchyma and a barrier to radial o(2) loss (rol) in roots. these features enhance internal o(2) diffusion to the root apex. barrier formation in rice is induced by growth in stagnant solution, but knowledge of the dynamics of barrier induction and early anatomical changes was lacking.	2011	21097947
rice siz1, a sumo e3 ligase, controls spikelet fertility through regulation of anther dehiscence.	• sumoylation, a post-translational modification, has important functions in both animals and plants. however, the biological function of the sumo e3 ligase, siz1, in rice (oryza sativa) is still under investigation. • in this study, we employed two different genetic approaches, the use of siz1 t-dna mutant and siz1-rnai transgenic plants, to characterize the function of rice siz1. • genetic results revealed the co-segregation of single t-dna insertional recessive mutation with the observed phen ...	2011	21083564