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prediction of methyl mercury uptake by rice plants ( oryza sativa l.) using the diffusive gradient in thin films technique.rice consumption is the primary pathway for methyl mercury (mehg) exposure at inland mercury (hg) mining areas of sw china. mechanistic information on mehg accumulation in rice is, however, limited. the process of mehg exchange between paddy soil and rice plants predominantly occurs in pore water. the detection of bioavailable mehg in pore water is therefore important to predict mehg uptake by rice plants ( oryza sativa l.). this study investigated mehg dynamics and spatial mehg trends in pore w ...201222957473
sequence variations in osagpase significantly associated with amylose content and viscosity properties in rice (oryza sativa l.).sequence-based variations in starch synthesis-related genes (ssrgs) exert a basic influence on the determination of eating quality in rice (oryza sativa l.). this study aimed to investigate the relationship between the sequence variations from parts of 10 ssrgs and the amylose content (ac) plus rapid viscosity analysis (rva) profiles in a heuristic rice core set by association mapping (am). in total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide poly ...201222950899
serpins in rice: protein sequence analysis, phylogeny and gene expression during development.most members of the serpin family of proteins are potent, irreversible inhibitors of specific serine or cysteine proteinases. inhibitory serpins are distinguished from members of other families of proteinase inhibitors by their metastable structure and unique suicide-substrate mechanism. animal serpins exert control over a remarkable diversity of physiological processes including blood coagulation, fibrinolysis, innate immunity and aspects of development. relatively little is known about the com ...201222947050
lesser grain borers, rhyzopertha dominica, select rough rice kernels with cracked hulls for reproduction.tests were conducted to determine whether the lesser grain borer, rhyzopertha dominica (f.) (coleoptera: bostrychidae), selects rough rice (oryza sativa l. (poales: poaceae)) kernels with cracked hulls for reproduction when these kernels are mixed with intact kernels. differing amounts of kernels with cracked hulls (0, 5, 10, and 20%) of the varieties francis and wells were mixed with intact kernels, and the number of adult progeny emerging from intact kernels and from kernels with cracked hulls ...201222943499
a putative gene sbe3-rs for resistant starch mutated from sbe3 for starch branching enzyme in rice (oryza sativa l.).foods high in resistant starch (rs) are beneficial to prevent various diseases including diabetes, colon cancers, diarrhea and chronic renal or hepatic diseases. elevated rs in rice is important for public health since rice is a staple food for half of the world population. a japonica mutant 'jiangtangdao 1' (rs = 11.67%) was crossed with an indica cultivar 'miyang 23' (rs = 0.41%). the mutant sbe3-rs that explained 60.4% of rs variation was mapped between rm6611 and rm13366 on chromosome 2 (lod ...201222937009
characterization of osmads6-5, a null allele, reveals that osmads6 is a critical regulator for early flower development in rice (oryza sativa l.).agl6-clade genes are a subfamily of mads-box genes and preferentially expressed in floral organs. osmads6 and osmads17 are two agl6-like genes in rice. osmads17 has been shown to play a minor role in floral development and appears to result from a duplication of osmads6. osmads6 was initially named as mfo1 for mosaic floral organs based on its moderate mutant phenotypes. so far, four moderate or weak mutant alleles of osmads6 have been described, providing valuable insights into its role in flow ...201222933119
regulation of atg6/beclin-1 homologs by abiotic stresses and hormones in rice (oryza sativa l.).autophagy, a complex and conserved mechanism, serving as a defense response in all eukaryotic organisms, is regulated by several proteins, among which atg proteins are the most important due to their involvement in autophagosome formation. atg6/beclin-1 proteins, reported to be essential for autophagosome formation and assigned as a conserved domain, were subjected to database searches. we found three homologs in the rice (oryza sativa) genome. a phylogeny tree was constructed to establish their ...201222930426
suppression of ku70/80 or lig4 leads to decreased stable transformation and enhanced homologous recombination in rice.evidence for the involvement of the nonhomologous end joining (nhej) pathway in agrobacterium-mediated transferred dna (t-dna) integration into the genome of the model plant arabidopsis remains inconclusive. having established a rapid and highly efficient agrobacterium-mediated transformation system in rice (oryza sativa) using scutellum-derived calli, we examined here the involvement of the nhej pathway in agrobacterium-mediated stable transformation in rice. rice calli from osku70, osku80 and ...201223050791
micrornas targeting dead-box helicases are involved in salinity stress response in rice (oryza sativa l.).rice (oryza sativa l.), one of the most important food crop in the world, is considered to be a salt-sensitive crop. excess levels of salt adversely affect all the major metabolic activities, including cell wall damage, cytoplasmic lysis and genomic stability. in order to cope with salt stress, plants have evolved high degrees of developmental plasticity, including adaptation via cascades of molecular networks and changes in gene expression profiles. posttranscriptional regulation, through the a ...201223043463
physico-chemical properties of cationic niosomes loaded with fraction of rice (oryza sativa) bran extract.the aim of this study was to investigate the physico-chemical properties of cationic niosomes (tween61/cholesterol/ctab) loaded with fraction no. 3 of oryza sativa bran extract (osf3) at 0.1, 0.5, 1.0 and 2.0% (w/v), respectively, before and after ultra-centrifugation. more white milky translucent appearance of the niosomes was observed at the higher loaded amount of osf3. the entrapment efficiency of 0.5% osf3 in niosomes was 86.22 +/- 1.43%. the sizes of the niosomes were slightly increased (1 ...201223035474
rumen digestion of rice straw structural polysaccharides: effect of ammonia treatment and lucerne extract supplementation in vitro.the combined effects of lucerne (medicago sativa l.) extract supplementation and ammonia treatment of rice straw (oryza sativa, variety thaibonnet) on the ruminal digestion of cell wall components were investigated in six continuous culture systems using a randomised complete block design. data were fitted to second-order polynomial models. untreated rice straw had higher contents of ash-free cell wall residues (cwr; 763 v. 687 g/kg dry matter (dm)) and non-cellulosic sugars (191 v. 166 g/kg dm) ...201223031563
molecular control of male reproductive development and pollen fertility in rice.anther development and male fertility are essential biological processes for flowering plants and are important for crop seed production. genetic manipulation of male fertility/sterility is critical for crop hybrid breeding. rice (oryza sativa l.) male sterility phenotypes, including genic male sterility, hybrid male sterility, and cytoplasmic male sterility, are generally caused by mutations of fertility-related genes, by incompatible interactions between divergent allelic or non-allelic genes, ...201223025662
gibberellin indirectly promotes chloroplast biogenesis as a means to maintain the chloroplast population of expanded cells.chloroplast biogenesis needs to be well coordinated with cell division and cell expansion during plant growth and development to achieve optimal photosynthesis rates. previous studies showed that gibberellins (gas) regulate many important plant developmental processes, including cell division and cell expansion. however, the relationship between chloroplast biogenesis with cell division and cell expansion, and how ga coordinately regulates these processes, remains poorly understood. in this stud ...201223020316
osmiox, a myo-inositol oxygenase gene, improves drought tolerance through scavenging of reactive oxygen species in rice (oryza sativa l.).myo-inositol oxygenase (miox), a unique monooxygenase, catalyzes the oxidation of myo-inositol to d-glucuronic acid. however, the protective role of miox in plants against oxidative stress or drought stress remains unknown. in this study, the functional characterization of miox obtained from the cdna library of upland rice (oryza sativa l. cv. irat109), was performed. osmiox was expressed predominantly in the roots and induced by drought, h₂o₂, salt, cold and abscisic acid. the transgenic rice l ...201223017909
hydrogen peroxide-mediated growth of the root system occurs via auxin signaling modification and variations in the expression of cell-cycle genes in rice seedlings exposed to cadmium stress.the link between root growth, h₂o₂, auxin signaling, and the cell cycle in cadmium (cd)-stressed rice (oryza sativa l. cv. zhonghua no. 11) was analyzed in this study. exposure to cd induced a significant accumulation of cd, but caused a decrease in zinc (zn) content which resulted from the decreased expression of oshma9 and oszip. analysis using a cd-specific probe showed that cd was mainly localized in the meristematic zone and vascular tissues. formation and elongation of the root system were ...201223013333
biochemical and structural characterization of recombinant human serum transferrin from rice (oryza sativa l.).the fe(3+) binding protein human serum transferrin (htf) is well known for its role in cellular iron delivery via the transferrin receptor (tfr). a new application is the use of htf as a therapy and targeted drug delivery system for a number of diseases. recently, production of htf in plants has been reported; such systems provide a relatively inexpensive, animal-free (eliminating potential contamination by animal pathogens) method to produce large amounts of recombinant proteins for such biopha ...201223010327
down-regulation of the tagw2 gene by rna interference results in decreased grain size and weight in wheat.for important food crops such as wheat and rice, grain yield depends on grain number and size. in rice (oryza sativa), gw2 was isolated from a major quantitative trait locus for yield and encodes an e3 ring ligase that negatively regulates grain size. wheat (triticum aestivum) has tagw2 homologues in the a, b, and d genomes, and polymorphisms in tagw2-a were associated with grain width. here, to investigate tagw2 function, rna interference (rnai) was used to down-regulate tagw2 transcript levels ...201222996678
silicon nutrition increases grain yield, which, in turn, exerts a feed-forward stimulation of photosynthetic rates via enhanced mesophyll conductance and alters primary metabolism in rice.silicon (si) is not considered to be an essential element for higher plants and is believed to have no effect on primary metabolism in unstressed plants. in rice (oryza sativa), si nutrition improves grain production; however, no attempt has been made to elucidate the physiological mechanisms underlying such responses. here, we assessed crop yield and combined advanced gas exchange analysis with carbon isotope labelling and metabolic profiling to measure the effects of si nutrition on rice photo ...201222994889
effort and contribution of t-dna insertion mutant library for rice functional genomics research in china: review and perspective.with the completion of the rice (oryza sativa l.) genome-sequencing project, the rice research community proposed to characterize the function of every predicted gene in rice by 2020. one of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as t-dna or transposons. since 1999, with support from the ministry of science and technology of china for rice functional genomics programs, large-scale t-dna insert ...201223020748
bio-concentration of chromium--an in situ phytoremediation study at south kaliapani chromite mining area of orissa, india.mine waste water at south kaliapani usually contains toxic levels of hexavalent cr(vi). the present in situ study was conducted at south kaliapani chromite mine area in orissa state, india, to assess the phytoremediation ability of three plants, namely, rice (oryza sativa l.), paragrass (brachiaria mutica), and an aquatic weed (eichhornia crassipes), in attenuating cr(vi) from mine waste water and to correlate the bio-concentration factors (bcf) of cr. water hyacinth (e. crassipes) showed 24% to ...201221487717
post-anthesis alternate wetting and moderate soil drying enhances activities of key enzymes in sucrose-to-starch conversion in inferior spikelets of rice.this study tested the hypothesis that a post-anthesis moderate soil drying can improve grain filling through regulating the key enzymes in the sucrose-to-starch pathway in the grains of rice (oryza sativa l.). two rice cultivars were field grown and two irrigation regimes, alternate wetting and moderate soil drying (wmd) and conventional irrigation (ci, continuously flooded), were imposed during the grain-filling period. the grain-filling rate and activities of four key enzymes in sucrose-to-sta ...201221926094
over-expression of ospin2 leads to increased tiller numbers, angle and shorter plant height through suppression of oslazy1.crop architecture parameters such as tiller number, angle and plant height are important agronomic traits that have been considered for breeding programmes. auxin distribution within the plant has long been recognized to alter architecture. the rice (oryza sativa l.) genome contains 12 putative pin genes encoding auxin efflux transporters, including four pin1 and one pin2 genes. here, we report that over-expression of ospin2 through a transgenic approach in rice (japonica cv. nipponbare) led to ...201221777365
natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice.levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. these relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. in rice, genes are found at highest density in regions with frequent crossing-over. this association betw ...201221917724
evaluating the response of two high yielding indian rice cultivars against ambient and elevated levels of ozone by using open top chambers.a continuous increase in the background level of tropospheric ozone (o(3)) has become a major challenge for present and future agricultural productivity at worldwide. present study was designed to assess the impact of ambient (present) and elevated (future) concentrations of o(3) on two cultivars of indian rice (oryza sativa l. cvs malviya dhan 36 and shivani). shoot and root lengths, number of leaves and total leaf area were severely affected by both ambient and elevated concentrations of o(3). ...201221788100
genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions.the root system is a crucial determinant of plant growth potential because of its important functions, e.g. uptake of water and nutrients, structural support and interaction with symbiotic organisms. elucidating the molecular mechanism of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants, including rice (oryza sativa). as an initial step towards developing a comprehensive understanding of the root system, we performed a large-sca ...201221895812
identification of qsor1, a major rice qtl involved in soil-surface rooting in paddy fields.specific indonesian lowland rice (oryza sativa l.) cultivars elongate thick primary roots on the soil surface of paddy fields. to clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (qtl) analyses using 124 recombinant inbred lines (rils) derived from a cross between gemdjah beton, an indonesian lowland rice cultivar with soil-surface roots, and sasanishiki, a japanese lowland rice cultivar without soil-surface roots. these cultivars and the rils w ...201221894467
a rice calcium-dependent protein kinase oscpk12 oppositely modulates salt-stress tolerance and blast disease resistance.calcium-dependent protein kinases (cdpks) regulate the downstream components in calcium signaling pathways. we investigated the effects of overexpression and disruption of an oryza sativa (rice) cdpk (oscpk12) on the plant's response to abiotic and biotic stresses. oscpk12-overexpressing (oscpk12-ox) plants exhibited increased tolerance to salt stress. the accumulation of hydrogen peroxide (h(2) o(2) ) in the leaves was less in oscpk12-ox plants than in wild-type (wt) plants. genes encoding reac ...201221883553
analysis of transcriptional and upstream regulatory sequence activity of two environmental stress-inducible genes, nbs-str1 and blec-str8, of rice.two abiotic stress-inducible upstream regulatory sequences (urss) from rice have been identified and functionally characterized in rice. nbs-str1 and blec-str8 genes have been identified, by analysing the transcriptome data of cold, salt and desiccation stress-treated 7-day-old rice (oryza sativa l. var. ir64) seedling, to be preferentially responsive to desiccation and salt stress, respectively. nbs-str1 and blec-str8 genes code for putative nbs (nucleotide binding site)-lrr (leucine rich repea ...201221725856
global analysis of expression profiles of rice receptor-like kinase genes.the receptor-like kinases (rlks) play critical roles in plant development and response to stress stimuli. by perceiving or sensing the extracellular signals, rlk activates the downstream signaling pathway through phosphorylating the specific targets. up to now, only a few rlks have been functionally identified, which are even fewer in rice (oryza sativa l.). we here report the systemic analysis of the expression profiles of rice rlk coding genes in different tissues, with the emphasis on seed de ...201221765177
manipulation of plant architecture to enhance lignocellulosic biomass.biofuels hold the promise to replace an appreciable proportion of fossil fuels. not only do they emit significantly lower amounts of greenhouse gases, they are much closer to being 'carbon neutral', since the source plants utilize carbon dioxide for their growth. in particular, second-generation lignocellulosic biofuels from agricultural wastes and non-food crops such as switchgrass promise sustainability and avoid diverting food crops to fuel. currently, available lignocellulosic biomass could ...201223071897
functional complementation of dwf4 mutants of arabidopsis by overexpression of cyp724a1.an essential step in the biosynthesis of bioactive brassinosteroids (brs) in plants is the hydroxylation at c-22, a reaction catalyzed by p450 enzymes of the cyp90b and cyp724b subfamilies. genes for both types of enzymes are present in many species, and in rice (oryza sativa) and tomato (solanum lycopersicum) both cyp90b and cyp724b enzymes contribute to c-22 hydroxylation. in arabidopsis (arabidopsis thaliana), c-22 hydroxylation of brs is catalyzed by cyp90b1 (encoded by dwf4) and null dwf4 m ...201222196800
smartgrain: high-throughput phenotyping software for measuring seed shape through image analysis.seed shape and size are among the most important agronomic traits because they affect yield and market price. to obtain accurate seed size data, a large number of measurements are needed because there is little difference in size among seeds from one plant. to promote genetic analysis and selection for seed shape in plant breeding, efficient, reliable, high-throughput seed phenotyping methods are required. we developed smartgrain software for high-throughput measurement of seed shape. this softw ...201223054566
genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in chinese cabbage (brassica rapa l.).fasciclin-like arabinogalactan proteins (flas), a subclass of arabinogalactan proteins (agps), have both predicted agp-like glycosylated regions and putative fasciclin (fas) domains, which may function in cell adhesion and communication. previous studies have identified 21, 27, and 34 flas in arabidopsis (arabidopsis thaliana), rice (oryza sativa), and wheat (triticum aestivum), respectively. in this study, we identified 33 flas in the annotated genome of chinese cabbage (brassica rapa ssp. peki ...201223053954
heteroexpression of the wheat phytochelatin synthase gene (tapcs1) in rice enhances cadmium sensitivity.phytochelatin synthase (pcs) (ec 2.3.2.15) catalyzes the final step of phytochelatins (pcs) biosynthesis. pcs are a family of cysteine-rich thiol-reactive and heavy metal-binding peptides that play an important role in sequestration and detoxification of heavy metals in plants. previous studies have indicated that plants that overexpressed pcs displayed contrasting phenotypes, ranging from enhanced cadmium (cd) tolerance to cd hypersensitivity in arabidopsis thaliana. in this study, the wheat ph ...201223017837
identification of cis-acting promoter elements in cold- and dehydration-induced transcriptional pathways in arabidopsis, rice, and soybean.the genomes of three plants, arabidopsis (arabidopsis thaliana), rice (oryza sativa), and soybean (glycine max), have been sequenced, and their many genes and promoters have been predicted. in arabidopsis, cis-acting promoter elements involved in cold- and dehydration-responsive gene expression have been extensively analysed; however, the characteristics of such cis-acting promoter sequences in cold- and dehydration-inducible genes of rice and soybean remain to be clarified. in this study, we pe ...201222184637
divergent evolution of oxidosqualene cyclases in plants.triterpenes are one of the largest classes of plant metabolites and have important functions. a diverse array of triterpenoid skeletons are synthesized via the isoprenoid pathway by enzymatic cyclization of 2,3-oxidosqualene. the genomes of the lower plants chlamydomonas reinhardtii and moss (physcomitrella patens) contain just one oxidosqualene cyclase (osc) gene (for sterol biosynthesis), whereas the genomes of higher plants contain nine to 16 osc genes. here we carry out functional analysis o ...201222150097
a rice orthologue of the aba receptor, ospyl/rcar5, is a positive regulator of the aba signal transduction pathway in seed germination and early seedling growth.abscisic acid (aba) is a phytohormone that positively regulates seed dormancy and stress tolerance. pyl/rcars were identified an intracellular aba receptors regulating aba-dependent gene expression in arabidopsis thaliana. however, their function in monocot species has not been characterized yet. herein, it is demonstrated that pyl/rcar orthologues in oryza sativa function as a positive regulator of the aba signal transduction pathway. transgenic rice plants expressing ospyl/rcar5, a pyl/rcar or ...201222071266
cis-regulatory signatures of orthologous stress-associated bzip transcription factors from rice, sorghum and arabidopsis based on phylogenetic footprints.the potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. a core subset of stress-associated bzip transcription factors from rice (oryza sativa) formed ten clusters of orthologous groups (cog) with genes from the monocot sorghum (sorghum bicolor) and dicot arabidopsis (arabidopsis thaliana). the total cis-regulatory information content of each stress-associated cog was examined by phylogenetic footprinting to reveal o ...201222992304
computational analysis and characterization of uce-like elements (ules) in plant genomes.ultraconserved elements (uces), stretches of dna that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. first identified and characterized in mammals, uces have been proposed to play important roles in gene regulation, rna processing, and maintaining genome integrity. however, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. we investigated whet ...201222987666
a comparative study of ethylene growth response kinetics in eudicots and monocots reveals a role for gibberellin in growth inhibition and recovery.time-lapse imaging of dark-grown arabidopsis (arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. this study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. in contrast, with continued application of ethylene, white millet (panicum miliaceum) seedlings had a rap ...201222977279
overexpression of ostlp27 in rice improves chloroplast function and photochemical efficiency.the thylakoid lumen proteins are highly associated with photosynthesis functionally. in this study, we characterized the ostlp27 gene from rice (oryza sativa), which encodes a 27-kda of 257-amino acid with 53% homology to the attlp gene from arabidopsis thaliana. ostlp27 was predicted to encode a thylakoid lumen protein of unknown function in chloroplast, and chloroplast targeting of ostlp27 was confirmed by transient expression of a fusion protein with green fluorescent protein (gfp). ostlp27 t ...201222921006
ddm1 (decrease in dna methylation) genes in rice (oryza sativa).regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. the decrease in dna methylation 1 (ddm1) of arabidopsis thaliana is one of the best characterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic dna. altho ...201222915302
the minor spliceosomal protein u11/u12-31k is an rna chaperone crucial for u12 intron splicing and the development of dicot and monocot plants.u12 intron-specific spliceosomes contain u11 and u12 small nuclear ribonucleoproteins and mediate the removal of u12 introns from precursor-mrnas. among the several proteins unique to the u12-type spliceosomes, an arabidopsis thaliana atu11/u12-31k protein has been shown to be indispensible for proper u12 intron splicing and for normal growth and development of arabidopsis plants. here, we assessed the functional roles of the rice (oryza sativa) osu11/u12-31k protein in u12 intron splicing and d ...201222912901
oself3-1, an ortholog of arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering.arabidopsis thaliana early flowering 3 (elf3) as a zeitnehmer (time taker) is responsible for generation of circadian rhythm and regulation of photoperiodic flowering. there are two orthologs (oself3-1 and oself3-2) of elf3 in rice (oryza sativa), but their roles have not yet been fully identified. here, we performed a functional characterization of oself3-1 and revealed it plays a more predominant role than oself3-2 in rice heading. our results suggest oself3-1 can affect rice circadian systems ...201222912900
pip kinases and their role in plant tip growing cells.phosphatidylinositol (4,5) bisphosphate, [ptdins(4,5)p 2], is a signaling lipid involved in many important processes in animal cells such as cytoskeleton organization, intracellular vesicular trafficking, secretion, cell motility, regulation of ion channels, and nuclear signaling pathways. in the last years ptdins(4,5)p 2 and its synthesizing enzyme, phosphatidylinositol phosphate kinase (pipk), has been intensively studied in plant cells, revealing a key role in the control of polar tip growth. ...201222902694
transcriptional regulation of phosphate acquisition by higher plants.phosphorus (p), an essential macronutrient required for plant growth and development, is often limiting in natural and agro-climatic environments. to cope with heterogeneous or low phosphate (pi) availability, plants have evolved an array of adaptive responses facilitating optimal acquisition and distribution of pi. the root system plays a pivotal role in pi-deficiency-mediated adaptive responses that are regulated by a complex interplay of systemic and local pi sensing. cross-talk with sugar, p ...201222899310
histone acetyltransferases in rice (oryza sativa l.): phylogenetic analysis, subcellular localization and expression.histone acetyltransferases (hats) play an important role in eukaryotic transcription. eight hats identified in rice (oshats) can be organized into four families, namely the cbp (oshac701, oshac703, and oshac704), tafii250 (oshaf701), gnat (oshag702, oshag703, and oshag704), and myst (osham701) families. the biological functions of hats in rice remain unknown, so a comprehensive protein sequence analysis of the hat families was conducted to investigate their potential functions. in addition, the ...201222894565
the histone methyltransferase sdg724 mediates h3k36me2/3 deposition at mads50 and rft1 and promotes flowering in rice.chromatin modifications affect flowering time in the long-day plant arabidopsis thaliana, but the role of histone methylation in flowering time regulation of rice (oryza sativa), a short-day plant, remains to be elucidated. we identified a late-flowering long vegetative phase1 (lvp1) mutant in rice and used map-based cloning to reveal that lvp1 affects the set domain group protein 724 (sdg724). sdg724 functions as a histone methyltransferase in vitro and contributes to a major fraction of global ...201222892321
smrnaome profiling to identify conserved and novel micrornas in stevia rebaudiana bertoni.micrornas (mirnas) constitute a family of small rna (srna) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. extensive studies on mirnas have been performed in different plants such as arabidopsis thaliana, oryza sativa etc. and volume of the mirna database, mirbase, has been increasing on day to day basis. stevia rebaudiana bertoni is an important perennial herb which accumulates high concentratio ...201223116282
genome-wide identification of reverse complementary microrna genes in plants.micrornas (mirnas) are ∼21-nucleotide small rnas (srnas) with essential regulatory roles in plants. they are generated from stem-loop-structured precursors through two sequential dicer-like 1 (dcl1)-mediated cleavages. to date, hundreds of plant mirnas have been uncovered. however, the question, whether the sequences reverse complementary (rc) to the mirna precursors could form hairpin-like structures and produce srna duplexes similar to the mirna/mirna* pairs has not been solved yet. here, we i ...201223110057
molecular cloning and functional analysis of three flowering locus t (ft) homologous genes from chinese cymbidium.the flowering locus t (ft) gene plays crucial roles in regulating the transition from the vegetative to reproductive phase. to understand the molecular mechanism of reproduction, three homologous ft genes were isolated and characterized from cymbidium sinense "qi jian bai mo", cymbidium goeringii and cymbidium ensifolium "jin si ma wei". the three genes contained 618-bp nucleotides with a 531-bp open reading frame (orf) of encoding 176 amino acids (aas). alignment of the aa sequences revealed th ...201223109860
genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.insertion of transposable elements (tes) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization which can enrich the complexity of transcriptomes and proteomes. previously, we performed the first experimental assessment of te exonization by inserting a ds element into each intron of the rice epsps gene. exonization of ds in plants was biased toward providing splice donor sites from the beginning of the inserted ds sequence. additionally, ds ...201223091369
colinearity and similar expression pattern of rice dreb1s reveal their functional conservation in the cold-responsive pathway.the clustered genes c-repeat (crt) binding factor (cbf)1/dehydration-responsive element binding protein (dreb)1b, cbf2/dreb1c, and cbf3/dreb1a play a central role in cold acclimation and facilitate plant resistance to freezing in arabidopsis thaliana. rice (oryza sativa l.) is very sensitive to low temperatures; enhancing the cold stress tolerance of rice is a key challenge to increasing its yield. in this study, we demonstrate chilling acclimation, a phenomenon similar to arabidopsis cold accli ...201223077584
the rice wall-associated receptor-like kinase gene osdees1 plays a role in female gametophyte development.the wall-associated kinase (wak) gene family is a unique subfamily of receptor-like kinases (rlks) in plants. wak-rlks play roles in cell expansion, pathogen resistance, and metal tolerance in arabidopsis (arabidopsis thaliana). rice (oryza sativa) has far more wak-rlk genes than arabidopsis, but the functions of rice wak-rlks are poorly understood. in this study, we found that one rice wak-rlk gene, defect in early embryo sac1 (osdees1), is involved in the regulation of early embryo sac develop ...201222885936
phylogenetic analysis of k(+) transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants.as heritage from early evolution, potassium (k(+)) is absolutely necessary for all living cells. it plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. land plants even enlarged this spectrum of k(+) utilization after having gone ashore, despite the fact that k(+) is far less available in their new oligotrophic habitats than in se ...201222876252
bioinformatic cis-element analyses performed in arabidopsis and rice disclose bzip- and myb-related binding sites as potential auxre-coupling elements in auxin-mediated transcription.in higher plants, a diverse array of developmental and growth-related processes is regulated by the plant hormone auxin. recent publications have proposed that besides the well-characterized auxin response factors (arfs) that bind auxin response elements (auxres), also members of the bzip- and myb-transcription factor (tf) families participate in transcriptional control of auxin-regulated genes via bzip response elements (zres) or myb response elements (mres), respectively.201222852874
identification of genes specifically or preferentially expressed in maize silk reveals similarity and diversity in transcript abundance of different dry stigmas.in plants, pollination is a critical step in reproduction. during pollination, constant communication between male pollen and the female stigma is required for pollen adhesion, germination, and tube growth. the detailed mechanisms of stigma-mediated reproductive processes, however, remain largely unknown. maize (zea mays l.), one of the world's most important crops, has been extensively used as a model species to study molecular mechanisms of pollen and stigma interaction. a comprehensive analys ...201222748054
genome-wide analyses of changes in translation state caused by elevated temperature in oryza sativa.it has been reported that the translational status of mrnas responds dramatically to abiotic stresses. while many useful results have demonstrated translational control in dicotyledonous model plants, little is known about changes in the translation state in response to abiotic stresses in monocotyledonous plants. to understand global changes in translation of mrnas, we performed genome-wide analyses using oryza sativa treated with heat stress (hs). these analyses showed that most mrnas were tra ...201222722767
discovery of novel rules for g-quadruplex-forming sequences in plants by using bioinformatics methods.the g-quadruplex is one of the most frequently studied secondary dna structures and consists of 4 guanine residues that interact through watson-crick and hoogsteen pairing. the g-quadruplex formation is thought to be a molecular switch for gene expression. genome-wide analyses of g-quadruplexes have been published for many species; however, only one genome-wide analysis of g-quadruplexes in plants has been reported. here, we propose a new approach involving a two-step procedure for identifying g ...201222721688
fstval: a new web tool to validate bulk flanking sequence tags.information about a transgene locus is one of the major concerns in transgenic research because expression of the transgene or a gene interrupted by the integration event could be affected. thus, the flanking sequences obtained from transgenic plants need to be analyzed in terms of genomic context, such as genic and intergenic regions. this process may consist of several steps: 1) elimination of a vector sequence from the flanking sequence, 2) finding the locations in the target genome, and 3) s ...201222709793
dwarf and low-tillering acts as a direct downstream target of a gsk3/shaggy-like kinase to mediate brassinosteroid responses in rice.in arabidopsis thaliana, the gsk3/shaggy-like kinase brassinosteroid-insensitive2 (bin2) plays a critical role in the brassinosteroid (br) signaling pathway by negatively regulating the activities of bri1-ems-suppressor1/brassinazole-resistant1 family transcription factors that regulate the expression of downstream br-responsive genes. in this study, we analyzed the function of a rice (oryza sativa) gsk3/shaggy-like kinase (gsk2), which is one of the orthologs of bin2. overexpression of gsk2 (go ...201222685166
physiological significance of the plant circadian clock in natural field conditions.for many decades, researchers have focused on the self-sustainable oscillations of plant circadian clocks, which can only be observed under artificial constant environmental conditions. however, plants have evolved under natural diurnal conditions where several major environmental cues such as light, temperature and humidity are dramatically changing and interacting with each other. therefore, little is known about the roles of the plant circadian clock in natural field conditions. molecular gen ...201222681566
brittle culm15 encodes a membrane-associated chitinase-like protein required for cellulose biosynthesis in rice.plant chitinases, a class of glycosyl hydrolases, participate in various aspects of normal plant growth and development, including cell wall metabolism and disease resistance. the rice (oryza sativa) genome encodes 37 putative chitinases and chitinase-like proteins. however, none of them has been characterized at the genetic level. in this study, we report the isolation of a brittle culm mutant, bc15, and the map-based cloning of the bc15/osctl1 (for chitinase-like1) gene affected in the mutant. ...201222665444
[expression analysis of the medicago truncatula floral specific expression genes].the expression of genes specific to floral organ is important for the floral organ formation and development in medicago truncatula. screening of the genes specifically expressed in m. truncatula flowers and comparing the expression patterns of their orthologous homologous genes among different model plants can provide novel insights into the functions of these genes in controlling the floral organ development in m. truncatula. according to the expression profile data of pistillata (pi), we scre ...201222659435
molecular cloning, sequence characterization of a novel pepper gene nadp-icdh and its effect on cytoplasmic male sterility.nadp-dependent isocitrate dehydrogenase (nadp-icdh) is an important enzyme involved in energy metabolism. the complete coding sequence of the pepper (capsicum annuum) nadp-icdh gene was amplified using a reverse transcriptase pcr based on the conserved sequence information of the tomato and other solanaceae plants and known highly homologous pepper ests. nucleotide sequence analysis revealed that the pepper nadp-icdh gene encodes a protein of 415 amino acids that has high homology with the prote ...201222653649
the arabidopsis ortholog of rice dwarf27 acts upstream of max1 in the control of plant development by strigolactones.strigolactones (sls) are carotenoid-derived plant hormones that regulate shoot branching, secondary growth, root development, and responses to soil phosphate. in arabidopsis (arabidopsis thaliana), sl biosynthesis requires the sequential action of two carotenoid cleavage dioxygenases, more axillary growth3 (max3) and max4, followed by a cytochrome p450, max1. in rice (oryza sativa), the plastid-localized protein dwarf27 (osd27) is also necessary for sl biosynthesis, but the equivalent gene in ar ...201222623516
dynamics of brassinosteroid response modulated by negative regulator lic in rice.brassinosteroids (brs) regulate rice plant architecture, including leaf bending, which affects grain yield. although br signaling has been investigated in arabidopsis thaliana, the components negatively regulating this pathway are less well understood. here, we demonstrate that oryza sativa leaf and tiller angle increased controller (lic) acts as an antagonistic transcription factor of brassinazole-resistant 1 (bzr1) to attenuate the br signaling pathway. the gain-of-function mutant lic-1 and li ...201222570626
mutation in terminal flower1 reverses the photoperiodic requirement for flowering in the wild strawberry fragaria vesca.photoperiodic flowering has been extensively studied in the annual short-day and long-day plants rice (oryza sativa) and arabidopsis (arabidopsis thaliana), whereas less is known about the control of flowering in perennials. in the perennial wild strawberry, fragaria vesca (rosaceae), short-day and perpetual flowering long-day accessions occur. genetic analyses showed that differences in their flowering responses are caused by a single gene, seasonal flowering locus, which may encode the f. vesc ...201222566495
characterization and evolution of microrna genes derived from repetitive elements and duplication events in plants.micrornas (mirnas) are a major class of small non-coding rnas that act as negative regulators at the post-transcriptional level in animals and plants. in this study, all known mirnas in four plant species (arabidopsis thaliana, populus trichocarpa, oryza sativa and sorghum bicolor) have been analyzed, using a combination of computational and comparative genomic approaches, to systematically identify and characterize the mirnas that were derived from repetitive elements and duplication events. th ...201222523544
gene-sharing networks reveal organizing principles of transcriptomes in arabidopsis and other multicellular organisms.understanding tissue-related gene expression patterns can provide important insights into gene, tissue, and organ function. transcriptome analyses often have focused on housekeeping or tissue-specific genes or on gene coexpression. however, by analyzing thousands of single-gene expression distributions in multiple tissues of arabidopsis thaliana, rice (oryza sativa), human (homo sapiens), and mouse (mus musculus), we found that these organisms primarily operate by gene sharing, a phenomenon wher ...201222517316
patterns and evolution of nucleotide landscapes in seed plants.nucleotide landscapes, which are the way base composition is distributed along a genome, strongly vary among species. the underlying causes of these variations have been much debated. though mutational bias and selection were initially invoked, gc-biased gene conversion (gbgc), a recombination-associated process favoring the g and c over a and t bases, is increasingly recognized as a major factor. as opposed to vertebrates, evolution of gc content is less well known in plants. most studies have ...201222492812
transcriptome-wide identification and characterization of mirnas from pinus densata.micrornas (mirnas) play key roles in diverse developmental processes, nutrient homeostasis and responses to biotic and abiotic stresses. the biogenesis and regulatory functions of mirnas have been intensively studied in model angiosperms, such as arabidopsis thaliana, oryza sativa and populus trichocarpa. however, global identification of pinus densata mirnas has not been reported in previous research.201222480283
high-throughput cryopreservation of plant cell cultures for functional genomics.suspension-cultured cell lines from plant species are useful for genetic engineering. however, maintenance of these lines is laborious, involves routine subculturing and hampers wider use of transgenic lines, especially when many lines are required for a high-throughput functional genomics application. cryopreservation of these lines may reduce the need for subculturing. here, we established a simple protocol for cryopreservation of cell lines from five commonly used plant species, arabidopsis t ...201222437846
rapid determination of endogenous cytokinins in plant samples by combination of magnetic solid phase extraction with hydrophilic interaction chromatography-tandem mass spectrometry.a 2-acrylamido-2-methyl-1-propanesulfonic acid-co-ethylene glycol dimethacrylate (fe₃o₄/sio₂/p(amps-co-egdma)) copolymer was prepared and used as a magnetic solid phase extraction (mspe) medium for recovery of endogenous cytokinins (cks) from plant extracts. this magnetic porous polymer was characterized by electron microscopy, nitrogen sorption experiments, elemental analysis and fourier-transformed infrared spectroscopy. it was demonstrated to have high extraction capacity toward cks in plants ...201222401906
osmyb2p-1, an r2r3 myb transcription factor, is involved in the regulation of phosphate-starvation responses and root architecture in rice.an r2r3 myb transcription factor, osmyb2p-1, was identified from microarray data by monitoring the expression profile of rice (oryza sativa ssp. japonica) seedlings exposed to phosphate (pi)-deficient medium. expression of osmyb2p-1 was induced by pi starvation. osmyb2p-1 was localized in the nuclei and exhibited transcriptional activation activity. overexpression of osmyb2p-1 in arabidopsis (arabidopsis thaliana) and rice enhanced tolerance to pi starvation, while suppression of osmyb2p-1 by rn ...201222395576
characterization of genes involved in cytokinin signaling and metabolism from rice.two-component signaling elements play important roles in plants, including a central role in cytokinin signaling. we characterized two-component elements from the monocot rice (oryza sativa) using several complementary approaches. phylogenetic analysis reveals relatively simple orthologous relationships among the histidine kinases in rice and arabidopsis (arabidopsis thaliana). in contrast, the histidine-containing phosphotransfer proteins (oshps) and response regulators (osrrs) display a higher ...201222383541
[progress in cre/lox site-specific recombination system in higher eukaryotes].cre/lox system derived from p1 bacteriaphage can quickly and effectively achieve gene insertion, deletion, replacement, and inversion by means of site-specific recombination. as one of the most important tools for gene targeting at present, cre/lox system has been widely used in arabidopsis thaliana, oryza sativa l., mus musculus, drosophila melanogaster, danio rerio, and other higher eukaryotic organisms. this review roundly described the basic profile of cre/lox system, and its application in ...201222382059
targeted disruption of an orthologue of domains rearranged methylase 2, osdrm2, impairs the growth of rice plants by abnormal dna methylation.recent methylome analyses of the entire arabidopsis thaliana genome using various mutants have provided detailed information about the dna methylation pattern and its function. however, information about dna methylation in other plants is limited, partly because of the lack of mutants. to study dna methylation in rice (oryza sativa) we applied homologous recombination-mediated gene targeting to generate targeted disruptants of osdrm2, a rice orthologue of domains rearranged methylase 1 and 2 (dr ...201222380881
in search of function for hypothetical proteins encoded by genes of sa-ja pathways in oryza sativa by in silico comparison and structural modeling.knowledge of rice genome brings new dimensions to the management of abiotic stresses; however, gene sequences in the rice genome are yet to be assigned structure and function. hydrogen peroxide, salicylates and jasmonates act as signal molecules in plants employing common machinery to manage abiotic stress. the present work is primarily focused to assign a structurefunction relationship by modeling of the hypothetical proteins of sa-ja signaling pathway known in arabidopsis thaliana and compare ...201222359427
large-scale identification of mirtrons in arabidopsis and rice.a new catalog of microrna (mirna) species called mirtrons has been discovered in animals recently, which originate from spliced introns of the gene transcripts. however, only one putative mirtron, osa-mir1429, has been identified in rice (oryza sativa). we employed a high-throughput sequencing (hts) data- and structure-based approach to do a genome-wide search for the mirtron candidate in both arabidopsis (arabidopsis thaliana) and rice. five and eighteen candidates were discovered in the two pl ...201222348048
identification of programmed cell death related genes in bamboo.the event of bamboo flowering and subsequent death of bamboo cells, a rare phenomenon is an interesting model to study gene expression/function in the context of the programmed cell death (pcd) in plant. to identify genes involved in autolytic cell death in bamboo (bambusa arundinacea/bambusa bambos voss), a suppressive subtractive cdna hybridization (ssh) was performed between cdna isolated from control (healthy), as driver and test internodal tissue (45days after setting of seeds), as tester. ...201222326529
comparative phosphoproteomic analysis of microsomal fractions of arabidopsis thaliana and oryza sativa subjected to high salinity.plants respond to salt stress by initiating phosphorylation cascades in their cells. many key phosphorylation events take place at membranes. microsomal fractions from 400 mm salt-treated arabidopsis suspension plants were isolated, followed by trypsin shaving, enrichment using zirconium ion-charged or tio(2) magnetic beads, and tandem mass spectrometry analyses for site mapping. a total of 27 phosphorylation sites from 20 arabidopsis proteins including photosystem ii reaction center protein h p ...201222325874
overexpression of rice cbs domain containing protein improves salinity, oxidative, and heavy metal tolerance in transgenic tobacco.we have recently identified and classified a cystathionine β-synthase domain containing protein family in arabidopsis (arabidopsis thaliana) and rice (oryza sativa l.). based on the microarray and mpss data, we have suggested their involvement in stress tolerance. in this study, we have characterized a rice protein of unknown function, oscbsx4. this gene was found to be upregulated under high salinity, heavy metal, and oxidative stresses at seedling stage. transgenic tobacco plants overexpressin ...201222302312
constitutive activation of transcription factor osbzip46 improves drought tolerance in rice.osbzip46 is one member of the third subfamily of bzip transcription factors in rice (oryza sativa). it has high sequence similarity to aba-responsive element binding factor (abf/areb) transcription factors abi5 and osbzip23, two transcriptional activators positively regulating stress tolerance in arabidopsis (arabidopsis thaliana) and rice, respectively. expression of osbzip46 was strongly induced by drought, heat, hydrogen peroxide, and abscisic acid (aba) treatment; however, it was not induced ...201222301130
the yabby gene tongari-boushi1 is involved in lateral organ development and maintenance of meristem organization in the rice spikelet.the meristem initiates lateral organs in a regular manner, and proper communication between the meristem and the lateral organs ensures the normal development of plants. here, we show that mutation of the rice (oryza sativa) gene tongari-boushi1 (tob1) results in pleiotropic phenotypes in spikelets, such as the formation of a cone-shaped organ instead of the lemma or palea, the development of two florets in a spikelet, or premature termination of the floret meristem, in addition to reduced growt ...201222286138
making sense of low oxygen sensing.plant-specific group vii ethylene response factor (erf) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. in rice (oryza sativa), these proteins regulate contrasting strategies of flooding survival. recent studies on arabidopsis thaliana group vii erfs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the n-end rule pathway of targeted proteolysis. oxygen-dependent sequestration at the plasma membrane maintain ...201222280796
gradual increase of mir156 regulates temporal expression changes of numerous genes during leaf development in rice.the highly conserved plant microrna, mir156, is an essential regulator for plant development. in arabidopsis (arabidopsis thaliana), mir156 modulates phase changing through its temporal expression in the shoot. in contrast to the gradual decrease over time in the shoot (or whole plant), we found that the mir156 level in rice (oryza sativa) gradually increased from young leaf to old leaf after the juvenile stage. however, the mir156-targeted rice squamosa-promoter binding-like (spl) transcription ...201222271747
regulatory functions of snrk1 in stress-responsive gene expression and in plant growth and development.sucrose-nonfermentation1-related protein kinase1 (snrk1) is an evolutionarily conserved energy sensor protein that regulates gene expression in response to energy depletion in plants. efforts to elucidate the functions and mechanisms of this protein kinase are hampered, however, by inherent growth defects of snrk1-null mutant plants. to overcome these limitations and study snrk1 functions in vivo, we applied a method combining transient expression in leaf mesophyll protoplasts and stable express ...201222232383
comparative genomics of the lipid-body-membrane proteins oleosin, caleosin and steroleosin in magnoliophyte, lycophyte and bryophyte.lipid bodies store oils in the form of triacylglycerols. oleosin, caleosin and steroleosin are unique proteins localized on the surface of lipid bodies in seed plants. this study has identified genes encoding lipid body proteins oleosin, caleosin and steroleosin in the genomes of five plants: arabidopsis thaliana, oryza sativa, populus trichocarpa, selaginella moellendorffii and physcomitrella patens. the protein sequence alignment indicated that each oleosin protein contains a highly-conserved ...201223317702
phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants.iron is involved in many metabolic processes, such as respiration and photosynthesis, and therefore an essential element for plant development. comparative analysis of gene copies between crops and lower plant groups can shed light on the evolution of genes important to iron homeostasis. a phylogenetic analysis of five metal homeostasis gene families (nas, nramp, ysl, fro, and irt) selected in monocots, dicots, gymnosperms, and bryophytes was performed. the homologous genes were found using know ...201223231606
uniprotkb amid the turmoil of plant proteomics research.the uniprot knowledgebase (uniprotkb) provides a single, centralized, authoritative resource for protein sequences and functional information. the majority of its records is based on automatic translation of coding sequences (cds) provided by submitters at the time of initial deposition to the nucleotide sequence databases (insdc). this article will give a general overview of the current situation, with some specific illustrations extracted from our annotation of arabidopsis and rice proteomes. ...201223230445
heavy metals health risk assessment for population via consumption of food crops and fruits in owerri, south eastern, nigeria.this study assessed lead, cadmium, and nickel level in food crops, fruits and soil samples from ohaji and umuagwo and owerri in south eastern nigeria and estimated the potential health risks of metals. samples were washed, oven-dried at 70-80°c for 24 h and powdered. samples were digested with perchloric acid and nitric acid. metals were analysed with unicam atomic absorption spectrophotometer.201222853175
mutation in oslms, a gene encoding a protein with two double-stranded rna binding motifs, causes lesion mimic phenotype and early senescence in rice (oryza sativa l.).the rice (oryza sativa l.) lesion mimic and senescence (lms) ems-mutant, identified in a japonica cultivar hitomebore, is characterized by a spontaneous lesion mimic phenotype during its vegetative growth, an accelerated senescence after flowering, and enhanced resistance to rice blast (magnaporthe oryzae). to isolate the oslms gene, we crossed the lms mutant to kasalath (indica), and used mutant f(2) plants to initially map the candidate region to about 322-kb on the long arm of chromosome 2. i ...201222976392
secretome analysis of magnaporthe oryzae using in vitro systems.magnaporthe oryzae is a devastating blast fungal pathogen of rice (oryza sativa l.) that causes dramatic decreases in seed yield and quality. during the early stages of infection by this pathogen, the fungal spore senses the rice leaf surface, germinates, and penetrates the cell via an infectious structure known as an appressorium. during this process, m. oryzae secretes several proteins; however, these proteins are largely unknown mainly due to the lack of a suitable method for isolating secret ...201222539438
in-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches.we report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar nipponbare of rice (oryza sativa l.), called oryza tag line (otl). sixteen thousand eight hundred and fourteen t-dna and 12,410 tos17 discrete insertion sites have been characterized in these lines. we estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence- ...201222369597
two phenylalanine ammonia lyase isoforms are involved in the elicitor-induced response of rice to the fungal pathogen magnaporthe oryzae.suspension cultured cells of a blast-resistant rice genotype (oryza sativa l. cv. gigante vercelli) were treated with cell wall hydrolysates prepared from the fungal pathogen magnaporthe oryzae. as a consequence, a complex pattern of phenylalanine ammonia lyase time course specific activity levels was evident. ion-exchange chromatographic fractionation of crude extracts suggested that the early (6 h) and the late (48-72 h after elicitation) increase of activity relied upon the sequential inducti ...201222137607
identification of quantitative trait loci for blast resistance in bc₂f₃ and bc₂f5 advanced backcross families of rice.advanced backcross families derived from oryza sativa cv mr219/o. rufipogon irgc105491 were utilized for identification of quantitative trait loci (qtl) for blast resistance using simple sequence repeat markers. two hundred and sixty-one bc(2)f(3) families were used to construct a linkage map, using 87 markers, which covered 2375.2 cm of 12 rice chromosomes, with a mean density of 27.3 cm. the families were evaluated in a greenhouse for resistance to blast disease caused by pathotypes p7.2 and p ...201223079822
transcription activator-like (tal) effectors targeting ossweet genes enhance virulence on diverse rice (oryza sativa) varieties when expressed individually in a tal effector-deficient strain of xanthomonas oryzae.genomes of the rice (oryza sativa) xylem and mesophyll pathogens xanthomonas oryzae pv. oryzae (xoo) and pv. oryzicola (xoc) encode numerous secreted transcription factors called transcription activator-like (tal) effectors. in a few studied rice varieties, some of these contribute to virulence by activating corresponding host susceptibility genes. some activate disease resistance genes. the roles of x. oryzae tal effectors in diverse rice backgrounds, however, are poorly understood. xoo tal eff ...201223078195
a tfiiia-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (oryza sativa l.).the tfiiia-type zinc finger transcription factors are involved in plant development and abiotic stress responses. most tfiiia-type zinc finger proteins are transcription repressors due to existence of an ear-motif in their amino acid sequences. in this work, we found that zfp182, a tfiiia-type zinc finger protein, forms a homodimer in the nucleus and exhibits trans-activation activity in yeast cells. the deletion analysis indicated that a leu-rich region at c-terminus is required for the trans-a ...201222930448
hint: high-quality protein interactomes and their applications in understanding human disease.a global map of protein-protein interactions in cellular systems provides key insights into the workings of an organism. a repository of well-validated high-quality protein-protein interactions can be used in both large- and small-scale studies to generate and validate a wide range of functional hypotheses.201222846459
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