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oryspssp: a comparative platform for small secreted proteins from rice and other plants.plants have large diverse families of small secreted proteins (ssps) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. however, there had not been any effort to systematically analyze rice ssps. here, we constructed a comparative platform, oryspssp (http://www.genoportal.org/pssp/index.do), involving >100 000 ssps from ...201323203890
the magnaporthe oryzae effector avrpiz-t targets the ring e3 ubiquitin ligase apip6 to suppress pathogen-associated molecular pattern-triggered immunity in rice.although the functions of a few effector proteins produced by bacterial and oomycete plant pathogens have been elucidated in recent years, information for the vast majority of pathogen effectors is still lacking, particularly for those of plant-pathogenic fungi. here, we show that the avirulence effector avrpiz-t from the rice blast fungus magnaporthe oryzae preferentially accumulates in the specialized structure called the biotrophic interfacial complex and is then translocated into rice (oryza ...201223204406
transposon-mediated alteration of tamate1b expression in wheat confers constitutive citrate efflux from root apices.the tamate1b gene (for multidrug and toxic compound extrusion) from wheat (triticum aestivum) was isolated and shown to encode a citrate transporter that is located on the plasma membrane. tamate1b expression in roots was induced by iron deficiency but not by phosphorus deficiency or aluminum treatment. the coding region of tamate1b was identical in a genotype showing citrate efflux from root apices (cv carazinho) to one that lacked citrate efflux (cv egret). however, sequence upstream of the co ...201323204428
confirming stereochemical structures of strigolactones produced by rice and tobacco.major strigolactones (sls) produced by rice (oryza sativa l. cv. nipponbare) and tobacco (nicotiana tabacum l. cv. michinoku no. 1) were purified and their stereochemical structures were determined by comparing with optically pure synthetic standards for their nmr and cd data and retention times and mass fragmentations in esi-lc/ms and gc-ms. sls purified from root exudates of rice plants were orobanchol, orobanchyl acetate, and ent-2'-epi-5-deoxystrigol. in addition to these sls, 7-oxoorobanchy ...201323204500
the xa21 binding protein xb25 is required for maintaining xa21-mediated disease resistance.plant genomes encode a large number of proteins that potentially function as immune receptors in the defense against pathogen invasion. as a well-characterized receptor kinase consisting of 23 tandem leucine-rich repeats, a transmembrane domain and a serine/threonine kinase, the rice (oryza sativa) protein xa21 confers resistance to a broad spectrum of xanthomonas oryzae pv. oryzae (xoo) races that cause bacterial blight disease. we report here that xa21 binding protein 25 (xb25) belongs to the ...201323206229
[major domestication traits in asian rice].rice (oryza sativa l.) is an excellent model plant in elucidation of cereal domestication. loss of seed shattering, weakened dormancy, and changes in plant architecture were thought to be three key events in the rice domestication and creating the high-yield, uniform-germinating, and densely-planting modern rice. loss of shattering is considered to be the direct morphological evidence for identifying domesticated rice. two major shattering qtls, sh4 and qsh1, have displayed different domesticati ...201223208135
a 286 bp upstream regulatory region of a rice anther-specific gene, osipp3, confers pollen-specific expression in arabidopsis.osipp3 gene (coding for pectin methylesterase inhibitor protein) was isolated from a pre-pollinated inflorescence-specific cdna library by differential screening of stage-specific libraries from oryza sativa. osipp3 is present in the genome of rice as a single copy gene. osipp3 gene was expressed exclusively in the pre-pollinated spikelets of rice. upstream regulatory region (urr) of osipp3 was isolated and a series of 5'-deletions were cloned upstream of gus reporter gene and were used to trans ...201323208453
the putative phytocyanin genes in chinese cabbage (brassica rapa l.): genome-wide identification, classification and expression analysis.phytocyanins (pcs) are a plant-specific family of small copper-containing electron transfer proteins. pcs may bind with a single copper atom to function as electron transporters in various biological systems, such as copper trafficking and plant photosynthesis. evidence indicates that pcs may also be involved in plant developmental processes and stress responses. many pcs possess arabinogalactan protein-like regions and are therefore termed chimeric arabinogalactan proteins (cagps). previously, ...201323212439
internal aeration of paddy field rice (oryza sativa) during complete submergence---importance of light and floodwater o2.flash floods can submerge paddy field rice (oryza sativa), with adverse effects on internal aeration, sugar status and survival. here, we investigated the in situ aeration of roots of rice during complete submergence, and elucidated how underwater photosynthesis and floodwater po(2) influence root aeration in anoxic soil. in the field, root po(2) was measured using microelectrodes during 2 d of complete submergence. leaf gas films that formed on the superhydrophobic leaves were left intact, or e ...201323215967
genetic bases of rice grain shape: so many genes, so little known.rice (oryza sativa) grain shape is a key determinant of grain yield and market values. facilitated by advancements in genomics and various molecular markers, more than 400 quantitative trait loci (qtls) associated with rice grain traits have been identified. in this review, we examine the genetic bases of rice grain shape, focusing on the protein products of 13 genes that have been cloned and the chromosome locations of 15 qtls that have been fine mapped. although more genes affecting grain trai ...201323218902
comparison of pyrolytic products produced from inorganic-rich and demineralized rice straw (oryza sativa l.) by fluidized bed pyrolyzer for future biorefinery approach.the objectives of this study were to investigate the effects of inorganic constituents on the fast pyrolysis of the biomass and to determine the yields as well as physicochemical properties of pyrolytic products. the pyrolytic products were obtained from raw and demineralized rice straw using a fluidized bed type pyrolyzer at different temperatures. as pyrolysis temperature increased, total biooil yield gradually decreased from 46.6 to 29.6 wt.% for the raw-straw, and from 55.4 to 35.3 wt.% for ...201323220113
genetic and physiological analysis of a novel type of interspecific hybrid weakness in rice.hybrid weakness is an important reproductive barrier that hinders genetic exchange between different species at the post-zygotic stage. however, our understanding of the molecular mechanisms underlying hybrid weakness is limited. in this study, we report discovery of a novel interspecific hybrid weakness in a rice chromosome segment substitution line (cssl) library derived from a cross between the indica variety teqing (oryza sativa) and common wild rice (o. rufipogon). the dominant hybrid weakn ...201323220941
comparison of phenotypic versus marker-assisted background selection for the sub1 qtl during backcrossing in rice.marker assisted backcrossing has been used effectively to transfer the submergence tolerance gene sub1 into popular rice varieties, but the approach can be costly. the selection strategy comprising foreground marker and phenotypic selection was investigated as an alternative. the non-significant correlation coefficients between ranking of phenotypic selection and ranking of background marker selection in bc(2)f(1), bc(3)f(1) and bc(3)f(2) generations indicated inefficiency of phenotypic selectio ...201223226081
variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice.to identify quantitative trait loci (qtls) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (bils) derived from crosses between temperate japonica rice cultivars nipponbare and koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout japan. thirty-three of the 50 traits were significantly correlated with heading date. using a linkage map including 647 single-nucleotide polymorphisms (snps), ...201223226082
estimation of the outcrossing rate for annual asian wild rice under field conditions.the asian wild rice, oryza rufipogon, has partial outcrossing behavior and shows high levels of genetic variation. to estimate an accurate outcrossing rate of annual form of o. rufipogon, two backcross lines (lines r1 and r2) between oryza sativa nipponbare and o. rufipogon w630 were examined under field conditions. a chromosome survey confirmed that these lines had wild chromosomal segments at more than 92% of marker loci. as for the traits of glume, stamen and pistil, line r1 showed similar fl ...201223226086
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
oslec1/oshap3e participates in the determination of meristem identity in both vegetative and reproductive developments of rice.in the vegetative phase of plant development, the shoot apical meristem (sam) produces leaf primordia in regular phyllotaxy, and transforms to the inflorescence meristem when the plant enters reproductive growth, which will undergo a series of identity differentiations and will finally form a complete and fertile panicle. our previous studies indicated a tissue-specific expression pattern of the oslec1 (leafy cotyledon) gene, which is homologous to the arabidopsis atlec1 gene and belongs to the ...201323230849
altered expression of the ptr/nrt1 homologue osptr9 affects nitrogen utilization efficiency, growth and grain yield in rice.the plant ptr/nrt1 (peptide transporter/nitrate transporter 1) gene family comprises di/tripeptide and low-affinity nitrate transporters; some members also recognize other substrates such as carboxylates, phytohormones (auxin and abscisic acid), or defence compounds (glucosinolates). little is known about the members of this gene family in rice (oryza sativa l.). here, we report the influence of altered osptr9 expression on nitrogen utilization efficiency, growth, and grain yield. osptr9 express ...201323231455
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
endo-(1,4)-β-glucanase gene families in the grasses: temporal and spatial co-transcription of orthologous genes.endo-(1,4)-β-glucanase (cellulase) glycosyl hydrolase gh9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4)-β-glucosyl residues, and wall loosening during cell elongation.201223231659
qtl analysis of na+ and k+ concentrations in roots and shoots under different levels of nacl stress in rice (oryza sativa l.).the key to plant survival under nacl salt stress is maintaining a low na(+) level or na(+)/k(+) ratio in the cells. a population of recombinant inbred lines (rils, f(2:9)) derived from a cross between the salt-tolerant japonica rice variety jiucaiqing and the salt-sensitive indica variety ir26, was used to determine na(+) and k(+) concentrations in the roots and shoots under three different nacl stress conditions (0, 100 and 120 mm nacl). a total of nine additive qtls were identified by qtl cart ...201223236455
persistence and metabolism of fipronil in rice (oryza sativa linnaeus) field.rice is one of the most important food crops worldwide. however, it is also a valuable tool in assessing toxicity of organic and inorganic compounds. fipronil insecticide has been widely used to control rice pests. the research was conducted to evaluate the fate of fipronil in rice-field. persistence and metabolism of fipronil in rice is studied by applications of regent 0.3g @ 45 and 180 g a.i. ha(-1) was made 7 days after transplanting of paddy. samples of paddy plants were collected at 7, 15, ...201323238826
brk1, a bub1-related kinase, is essential for generating proper tension between homologous kinetochores at metaphase i of rice meiosis.bub1 (for budding uninhibited by benzimidazole 1), one of the main spindle checkpoint kinases, acts as a kinetochore scaffold for assembling other checkpoint proteins. here, we identify a plant bub1-related kinase 1 (brk1) in rice (oryza sativa). the brk1 mutants are sterile due to the precocious separation of sister chromatids at the onset of anaphase i. the centromeric recruitment of shugoshin1 and phosphorylation of histone h2a at thr-134 (h2a-pt134) depend on brk1. although the homologs can ...201223243128
whole genomic sequencing of rt98 mitochondria derived from oryza rufipogon and northern blot analysis to uncover a cytoplasmic male sterility-associated gene.cytoplasmic male sterility (cms) is a maternally inherited trait resulting in the failure to produce functional pollen and is often observed when an alien cytoplasm is transferred into a cultivated species. an rt98a cms line and an rt98c fertility restorer line were obtained by successive backcrossing between oryza rufipogon w1109 and oryza sativa cultivar taichung 65. to uncover the cms-associated mitochondrial genes, we determined the complete sequence of the rt98-cms mitochondrial genome usin ...201323248202
structural, expression and interaction analysis of rice skp1-like genes.the degradation of proteins by the 26s proteasome is initiated by protein polyubiquitination mediated by a three-step cascade. the specific ubiquitination of different target proteins is mediated by different classes of e3 ubiquitin ligases, among which the best known are skp1-cullin-f-box complexes. whereas protists, fungi and some vertebrates have a single skp1 gene, many animal and plant species possess multiple skp1 homologues. in this paper, we report on the structure, phylogeny and express ...201323248203
crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals.in the classical nucleocytoplasmic import pathway, nuclear localization signals (nlss) in cargo proteins are recognized by the import receptor importin-α. importin-α has two separate nls binding sites (the major and the minor site), both of which recognize positively charged amino acid clusters in nlss. little is known about the molecular basis of the unique features of the classical nuclear import pathway in plants. we determined the crystal structure of rice (oryza sativa) importin-α1a at 2-å ...201223250448
extracellular membrane vesicles and phytopathogenicity of acholeplasma laidlawii pg8.for the first time, the phytopathogenicity of extracellular vesicles of acholeplasma laidlawii pg8 (a ubiquitous mycoplasma that is one of the five common species of cell culture contaminants and is a causative agent for phytomycoplasmoses) in oryza sativa l. plants was studied. data on the ability of extracellular vesicles of acholeplasma laidlawii pg8 to penetrate from the nutrient medium into overground parts of oryza sativa l. through the root system and to cause alterations in ultrastructur ...201223251100
live and let die - the b(sister) mads-box gene osmads29 controls the degeneration of cells in maternal tissues during seed development of rice (oryza sativa).b(sister) genes have been identified as the closest relatives of class b floral homeotic genes. previous studies have shown that b(sister) genes from eudicots are involved in cell differentiation during ovule and seed development. however, the complete function of b(sister) genes in eudicots is masked by redundancy with other genes and little is known about the function of b(sister) genes in monocots, and about the evolution of b(sister) gene functions. here we characterize osmads29, one of thre ...201223251532
comparative transcriptome profiling of the early response to magnaporthe oryzae in durable resistant vs susceptible rice (oryza sativa l.) genotypes.durable resistance to blast, the most significant fungal disease of rice, represents an agronomically relevant character. gigante vercelli (gv) and vialone nano (vn) are two old temperate japonica italian rice cultivars with contrasting response to blast infection: gv displays durable and broad resistance while vn is highly susceptible. rna-seq was used to dissect the early molecular processes deployed during the resistance response of gv at 24 h after blast inoculation. differential gene expres ...201223251593
source-sink dynamics and proteomic reprogramming under elevated night temperature and their impact on rice yield and grain quality.high night temperatures (hnts) can reduce significantly the global rice (oryza sativa) yield and quality. a systematic analysis of hnt response at the physiological and molecular levels was performed under field conditions. contrasting rice accessions, n22 (highly tolerant) and gharib (susceptible), were evaluated at 22°c (control) and 28°c (hnt). nitrogen (n) and nonstructural carbohydrate (nsc) translocation from different plant tissues into grains at key developmental stages, and their contri ...201323252708
suppressive subtraction hybridization reveals that rice gall midge attack elicits plant-pathogen-like responses in rice.the asian rice gall midge, orseolia oryzae (diptera: cecidomyiidae), is the third most destructive insect pest of rice (oryza sativa l.). till date, 11 gall midge resistance gene loci have been characterized in different rice varieties. to elucidate molecular basis of incompatible (hypersensitive response plus [hr+] type) and compatible rice-gall midge interactions, two suppressive subtraction hybridization cdna libraries were constructed. these were enriched for differentially expressed transcr ...201323257077
acquisition, conservation, and loss of dual-targeted proteins in land plants.the dual-targeting ability of a variety of proteins from physcomitrella patens, rice (oryza sativa), and arabidopsis (arabidopsis thaliana) was tested to determine when dual targeting arose and to what extent it was conserved in land plants. overall, the targeting ability of over 80 different proteins from rice and p. patens, representing 42 dual-targeted proteins in arabidopsis, was tested. we found that dual targeting arose early in land plant evolution, as it was evident in many cases with p. ...201323257241
a dominant major locus in chromosome 9 of rice (oryza sativa l.) confers tolerance to 48°c high temperature at seedling stage.in an earlier greenhouse screening, we identified a local indica cultivar ht54 tolerant to high temperature at both seedling and grain-filling stages. in this study, we develop an optimized procedure for fine assessment of this heat tolerance. the results indicated that ht54 seedlings could tolerate high temperature up to 48 °c for 79h. the genetic analysis of f(1) and f(2) offspring derived from the cross between ht54 and ht13, a heat-sensitive breeding line, reveals that the heat tolerance of ...201323258571
strand-specific rna-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.cis-natural antisense transcripts (cis-nats) are rnas transcribed from the antisense strand of a gene locus, and are complementary to the rna transcribed from the sense strand. common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-nats in various eukaryotic organisms. genome-wide in silico analysis has identified a large number of cis-nats that may generate endogenous short interfering rnas (nat-sirnas), which particip ...201223259405
mkrn expression pattern during embryonic and post-embryonic organogenesis in rice (oryza sativa l. var. nipponbare).rice mkrn is a member of the makorin ring finger protein gene (mkrn) family, which encodes a protein with a characteristic array of zinc-finger motifs conserved in various eukaryotes. using non-radioactive in situ hybridization, we investigated the spatio-temporal gene expression pattern of rice mkrn during embryogenesis, imbibition, seminal and lateral root development of oryza sativa l. var. nipponbare. mkrn expression was ubiquitous during early organogenesis in the embryo along the apical-ba ...201323262670
rice glycosyltransferase1 encodes a glycosyltransferase essential for pollen wall formation.the pollen wall consists of an exine and an intine. the mechanism underlying its formation is not well understood. glycosyltransferases catalyze the modification of biological molecules by attaching a single or multiple sugars and play key roles in a wide range of biological processes. we examined the role of glycosyltransferase1 (osgt1) in pollen wall development in rice (oryza sativa). this gene is highly expressed in mature pollen, and plants containing alleles caused by transfer dna insertio ...201323263792
functional analysis of hsp70 superfamily proteins of rice (oryza sativa).heat stress results in misfolding and aggregation of cellular proteins. heat shock proteins (hsp) enable the cells to maintain proper folding of proteins, both in unstressed as well as stressed conditions. hsp70 genes encode for a group of highly conserved chaperone proteins across the living systems encompassing bacteria, plants, and animals. in the cellular chaperone network, hsp70 family proteins interconnect other chaperones and play a dominant role in various cell processes. to assess the f ...201323264228
long-term supplementation of high pigmented rice bran oil (oryza sativa l.) on amelioration of oxidative stress and histological changes in streptozotocin-induced diabetic rats fed a high fat diet; riceberry bran oil.diabetes is a serious health problem. searching for alternative natural antioxidants is considered important strategy to manage diabetes. this study evaluated the effect of riceberry bran oil (rbbo) supplementation on oxidative stress and organ histology in streptozotocin-induced diabetic rats fed a high fat (hf) diet. adult male sprague-dawley rats with hyperglycemia were divided into four groups: dm group fed a hf diet alone; dmrl group fed a hf diet and 5% rbbo; dmrm group fed a hf diet and 7 ...201323265517
plant secondary metabolite profiling evidences strain-dependent effect in the azospirillum-oryza sativa association.azospirillum is a plant growth-promoting rhizobacterium (pgpr) able to enhance growth and yield of cereals such as rice, maize and wheat. the growth-promoting ability of some azospirillum strains appears to be highly specific to certain plant species and cultivars. in order to ascertain the specificity of the associative symbiosis between rice and azospirillum, the physiological response of two rice cultivars, nipponbare and cigalon, inoculated with two rice-associated azospirillum was analyzed ...201223266268
soil to rice transfer factors for (226)ra, (228)ra, (210)pb, (40)k and (137)cs: a study on rice grown in india.india is the second largest producer of rice (oryza sativa l.) in the world and rice is an essential component of the diet for a majority of the population in india. however, detailed studies aimed at the evaluation of radionuclide transfer factors (f(v)) for the rice grown in india are almost non-existent. this paper presents the soil to rice transfer factors for natural ((226)ra, (228)ra, (40)k, and (210)pb) and artificial ((137)cs) radionuclides for rice grown in natural field conditions on t ...201323266913
whole genome identification and analysis of fk506-binding protein family genes in grapevine (vitis vinifera l.).in plant and animal species fk506-binding protein (fkbp) family genes are important conserved genes and it is defined as the receptors of fk506 and rapamycin, where they work as ppiase and protein folding chaperones. fkbp have been isolated from arabidopsis thaliana, oryza sativa, and zea mays. in grape, twenty-three genes containing the fk506-binding domain (fkbp_c) were first time identified by hmmer and blast research, they were classified into three groups and 17 out of the 23 genes were loc ...201323269629
antimicrobial activity and mechanism of action of a novel cationic α-helical dodecapeptide, a partial sequence of cyanate lyase from rice.cl(14-25), a dodecapeptide, that is a partial region near n-terminus of cyanate lyase (cl, ec 4.3.99.1) from rice (oryza sativa l. japonica), contains three arginine and two lysine residues. it was a novel cationic α-helical antimicrobial peptide. the antimicrobial activity of cl(14-25) against porphyromonas gingivalis, a periodontal pathogen, was quantitatively evaluated by a chemiluminescence method that measures atp derived from viable cells. the 50% growth-inhibitory concentration of cl(14-2 ...201223270672
transcription factor atbzip60 regulates expression of ca(2+)-dependent protein kinase genes in transgenic cells.the arabidopsis thaliana bzip60 (atbzip60) transcription factor regulates stress signaling. however, its molecular mechanism remains to be elucidated. in this investigation, cell suspension cultures of two different plant species rice (oryza sativa l.) and white pine (pinus strobes l.) were transformed using agrobacterium tumefaciens strain lba4404 harboring pbi-atzip60. integration of the atbzip60 gene into the genome of rice and white pine has been confirmed by polymerase chain reaction (pcr), ...201223275191
knockout of the vps22 component of the escrt-ii complex in rice (oryza sativa l.) causes chalky endosperm and early seedling lethality.in both yeast and mammals, the major constituent of the endosomal sorting complex required for transport-ii (escrt-ii) is the vps22/eap30 protein, which plays an important role in ubiquitin-mediated degradation of membrane proteins through the multivesicular body pathway. however, the functions of escrt-ii subunits in plants are largely unknown. in this work, we report the genetic analysis and phenotypic characterization of mutants in osvps22 gene, which encodes a functional vps22 homolog in ric ...201323275199
investigation of gold nanoparticles uptake and their tissue level distribution in rice plants by laser ablation-inductively coupled-mass spectrometry.the tissue level uptake and spatial distribution of gold nanoparticles (aunps) in rice (oryza sativa l.) roots and shoots under hydroponic conditions was investigated using laser ablation-inductively coupled plasma-mass spectrometry (la-icp-ms). rice plants were hydroponically exposed to positively, neutrally, and negatively charged aunps [aunp1(+), aunp2(0), aunp3(-)] with a core diameter of 2 nm. plants were exposed to aunps having 1.6 mg au/l for 5 days or 0.14 mg au/l for 3 months to elucida ...201323277326
indeterminate domain 10 regulates ammonium-mediated gene expression in rice roots.indeterminate domain (idd) genes are a family of plant transcriptional regulators that function in the control of development and metabolism during growth. here, the function of oryza sativa indeterminate domain 10 (osidd10) has been explored in rice plants. compared with wild-type roots, idd10 mutant roots are hypersensitive to exogenous ammonium. this work aims to define the action of idd10 on gene expression involved in ammonium uptake and nitrogen (n) metabolism. the ammonium induction of ke ...201323278238
antitumor effects of dietary black and brown rice brans in tumor-bearing mice: relationship to composition.feeding a diet supplemented with 10% (w/w) black and brown rice brans inhibited growth of transplanted tumors in mice.201223281142
development of genetic markers linked to straighthead resistance through fine mapping in rice (oryza sativa l.).straighthead, a physiological disorder characterized by sterile florets and distorted spikelets, causes significant yield losses in rice, and occurs in many countries. the current control method of draining paddies early in the season stresses plants, is costly, and wastes water. development of resistant cultivar is regarded as the most efficient way for its control. we mapped a qtl for straighthead resistance using two recombinant inbred line (ril) f(9) populations that were phenotyped over two ...201223285082
braving the attitude of altitude: caragana jubata at work in cold desert of himalaya.the present work was conducted to understand the basis of adaptation in caragana jubata in its niche environment at high altitude cold desert of himalaya. molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (lt), a major cue operative at high altitude. importantly, these genes expressed in c. jubata in its natural habitat. their homologues in arabidopsis thaliana, oryza sativa, and glycine max did not exhibit similar tre ...201323289064
oscyp2, a chaperone involved in degradation of auxin-responsive proteins, plays crucial roles in rice lateral root initiation.auxin plays a pivotal role in many facets of plant development. it acts by inducing the interaction between auxin-responsive [auxin (aux)/indole-3-acetic acid (iaa)] proteins and the ubiquitin protein ligase scf(tir) to promote the degradation of the aux/iaa proteins. other cofactors and chaperones that participate in auxin signaling remain to be identified. here, we characterized rice (oryza sativa) plants with mutations in a cyclophilin gene (oscyp2). cyp2 mutants showed defects in auxin respo ...201323289750
tiller number is altered in the ascorbic acid-deficient rice suppressed for l-galactono-1,4-lactone dehydrogenase.the tiller of rice (oryza sativa l.), which determines the panicle number per plant, is an important agronomic trait for grain production. ascorbic acid (asc) is a major plant antioxidant that serves many functions in plants. l-galactono-1,4-lactone dehydrogenase (gldh, ec 1.3.2.3) is an enzyme that catalyzes the last step of asc biosynthesis in plants. here we show that the gldh-suppressed transgenic rices, gi-1 and gi-2, which have constitutively low (between 30% and 50%) leaf asc content comp ...201323290459
potential value of a rice protein extract, containing proteinaceous inhibitors against cysteine proteinases from porphyromonas gingivalis, for managing periodontal diseases.arg-specific gingipain (rgp) is a major pathogenic determinant of porphyromonas gingivalis which is a major pathogen in periodontal disease. we prepared protein extracts with rgp-inhibitory activity from polished rice (oryza sativa) and evaluated the effects of these extracts on the growth and pathogenicity of p. gingivalis. the extracts inhibited the proteolytic degradation of human proteins by p. gingivalis proteinases, and repressed the growth and homotypic biofilm formation of p. gingivalis. ...201323291749
constitutive expression of a mir319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass.microrna319 (mir319) is one of the first characterized and conserved microrna families in plants and has been demonstrated to target tcp (for teosinte branched/cycloidea/proliferating cell factors [pcf]) genes encoding plant-specific transcription factors. mir319 expression is regulated by environmental stimuli, suggesting its involvement in plant stress response, although experimental evidence is lacking and the underlying mechanism remains elusive. this study investigates the role that mir319 ...201323292790
homologous expression of γ-glutamylcysteine synthetase increases grain yield and tolerance of transgenic rice plants to environmental stresses.various environmental stresses induce reactive oxygen species (ros), causing deleterious effects on plant cells. glutathione (gsh), a critical antioxidant, is used to combat ros. gsh is produced by γ-glutamylcysteine synthetase (γ-ecs) and glutathione synthetase (gs). to evaluate the functional roles of the oryza sativa l. japonica cv. ilmi ecs (osecs) gene, we generated transgenic rice plants overexpressing osecs under the control of an inducible promoter (rab21). when grown under saline condit ...201323294545
functional analyses of tahma2, a p(1b)-type atpase in wheat.currently, there are few studies concerning the function of heavy metal atpase 2 (hma2), particularly in monocotyledons, and the potential application of this protein in biofortification and phytoremediation. thus, we isolated and characterized the tahma2 gene from wheat (triticum aestivum l.). our results indicate that tahma2 is localized to the plasma membrane and stably expressed, except in the nodes, which showed relatively high expression. zinc/cadmium (zn/cd) resistance was observed in tah ...201323294838
ostzf1, a ccch-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes.ostzf1 is a member of the ccch-type zinc finger gene family in rice (oryza sativa). expression of ostzf1 was induced by drought, high-salt stress, and hydrogen peroxide. ostzf1 gene expression was also induced by abscisic acid, methyl jasmonate, and salicylic acid. histochemical activity of β-glucuronidase in transgenic rice plants containing the promoter of ostzf1 fused with β-glucuronidase was observed in callus, coleoptile, young leaf, and panicle tissues. upon stress, ostzf1-green fluorescen ...201323296688
genome-wide landscape of alternative splicing events in brachypodium distachyon.recently, brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (as) events spanning across 2021 putatively assembled transcripts generated from 941 genes. approximately, 6.3% of expressed genes are alternatively spliced in b. distachyon. we observed that a majority of the identified as events were related to reta ...201323297300
rice annotation project database (rap-db): an integrative and interactive database for rice genomics.the rice annotation project database (rap-db, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, oryza sativa (japonica group) cv. nipponbare. since the first release in 2005, rap-db has been updated several times along with the genome assembly updates. here, we present our newest rap-db based on the latest genome assembly, os-nipponbare-reference-irgsp-1.0 (irgsp-1.0), which was released in 2011. we detected 37,869 loci by ...201323299411
p5-type sulfhydryl oxidoreductase promotes the sorting of proteins to protein body i in rice endosperm cells.in rice (oryza sativa) endosperm cells, oxidative protein folding is necessary for the sorting of storage proteins to protein bodies, pb-i and pb-ii. here we examined the role of sulfhydryl oxidoreductase pdil2;3 (a human p5 ortholog) in the endoplasmic reticulum (er), using gfp-ab, a pb-i marker in which the n-terminal region (ab) of α-globulin is fused to green fluorescent protein (gfp). rnai knockdown of pdil2;3 inhibited the accumulation of gfp-ab in pb-i and promoted its exit from the er. w ...201323299424
osmads16 genetically interacts with osmads3 and osmads58 in specifying floral patterning in rice.rice (oryza sativa) has unique floral patterns that contribute to grain yield. however, the molecular mechanism underlying the specification of floral organ identities in rice, particularly the interaction among floral homeotic genes, remains poorly understood. here, we show that the floral homeotic gene osmads16 (also called superwoman1, spw1, a b-class gene) acts together with the rice c-class genes osmads3 and osmads58 in specifying floral organ patterning. osmads16 and the two c-class genes ...201323300256
structural insights into cellulolytic and chitinolytic enzymes revealing crucial residues of insect β-n-acetyl-d-hexosaminidase.the chemical similarity of cellulose and chitin supports the idea that their corresponding hydrolytic enzymes would bind β-1,4-linked glucose residues in a similar manner. a structural and mutational analysis was performed for the plant cellulolytic enzyme bglu1 from oryza sativa and the insect chitinolytic enzyme ofhex1 from ostrinia furnacalis. although bglu1 shows little amino-acid sequence or topological similarity with ofhex1, three residues (trp(490), glu(328), val(327) in ofhex1, and trp( ...201223300622
rice heterotrimeric g-protein alpha subunit (rga1): in silico analysis of the gene and promoter and its upregulation under abiotic stress.heterotrimeric g-protein complexes (gα, gβ and gγ) operate at the apex of diverse signal transduction systems along with their cognate transmembrane g-protein coupled receptors (gpcrs) and appropriate downstream effectors in the plant. rice gα in response to stress has not been well studied. here, we report the in silico analysis of gα subunit from oryza sativa cv. indica group swarna [rga1(i), accession number hq634688], its promoter and its transcript upregulation in response to abiotic stress ...201323313793
molecular cloning and functional analysis of a blue light receptor gene mdcry2 from apple (malus domestica).mdcry2 was isolated from apple fruit skin, and its function was analyzed in mdcry2 transgenic arabidopsis. the interaction between mdcry2 and atcop1 was found by yeast two-hybrid and bifc assays. cryptochromes are blue/ultraviolet-a (uv-a) light receptors involved in regulating various aspects of plant growth and development. investigations of the structure and functions of cryptochromes in plants have largely focused on arabidopsis (arabidopsis thaliana), tomato (solanum lycopersicum), pea (pis ...201323314496
stifdb2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in arabidopsis and rice.understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in th ...201323314754
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
gene body methylation is conserved between plant orthologs and is of evolutionary consequence.dna methylation is a common feature of eukaryotic genomes and is especially common in noncoding regions of plants. protein coding regions of plants are often methylated also, but the extent, function, and evolutionary consequences of gene body methylation remain unclear. here we investigate gene body methylation using an explicit comparative evolutionary approach. we generated bisulfite sequencing data from two tissues of brachypodium distachyon and compared genic methylation patterns to those o ...201323319627
oryza sativa coi homologues restore jasmonate signal transduction in arabidopsis coi1-1 mutants.coronatine insensitive 1 (coi1) encodes an e3 ubiquitin ligase complex component that interacts with jaz proteins and targets them for degradation in response to ja signaling. the arabidopsis genome has a single copy of coi1, but the oryza sativa genome has three closely related coi homologs. to examine the functions of the three oscois, we used yeast two-hybrid assays to examine their interactions with jaz proteins and found that oscois interacted with osjazs and with jazs, in a coronatine depe ...201323320078
transcriptomic analysis of rice (oryza sativa) endosperm using the rna-seq technique.the endosperm plays an important role in seed formation and germination, especially in rice (oryza sativa). we used a high-throughput sequencing technique (rna-seq) to reveal the molecular mechanisms involved in rice endosperm development. three cdna libraries were taken from rice endosperm at 3, 6 and 10 days after pollination (dap), which resulted in the detection of 21,596, 20,910 and 19,459 expressed gens, respectively. by erange, we identified 10,371 differentially expressed genes (log(2)ra ...201323322175
molecular breeding to improve salt tolerance of rice (oryza sativa l.) in the red river delta of vietnam.rice is a stable food in vietnam and plays a key role in the economy of the country. however, the production and the cultivating areas are adversely affected from the threats of devastation caused by the rise of sea level. using marker-assisted backcrossing (mabc) to develop a new salt tolerance rice cultivar is one of the feasible methods to cope with these devastating changes. to improve rice salt tolerance in bt7 cultivar, fl478 was used as a donor parent to introgress the saltol qtl conferri ...201223326259
insular organization of gene space in grass genomes.wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. the hypothesis is statistically tested here in four grass species differing in genome size, brachypodium distachyon, oryza sativa, sorghum bicolor, and aegilops tauschii. density functions obtained under a model where gene locations follow a homogeneous poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density ...201323326580
molecular control of flowering in response to day length in rice.flowering at the most appropriate times of the year requires careful monitoring of environmental conditions and correct integration of such information with an endogenous molecular network. rice (oryza sativa) is a facultative short day plant, and flowers quickly under short day lengths, as opposed to arabidopsis thaliana whose flowering is accelerated by longer days. despite these physiological differences, several genes controlling flowering in response to day length (or photoperiod) are conse ...201323331542
identification of a cis-element that mediates multiple pathways of the endoplasmic reticulum stress response in rice.the accumulation of unfolded proteins in the endoplasmic reticulum (er) lumen leads to er stress. intracellular signalling pathways are activated to alleviate the stress. the er stress sensor ire1 induces the active form of key transcription factors, such as xbp1 in mammals and bzip50 in oryza sativa (rice), by mediating the unconventional splicing of their mrnas. although the characterization of cis-elements that are recognized by these transcription factors is essential for understanding er st ...201323331932
atlazy1 is a signaling component required for gravitropism of the arabidopsis thaliana inflorescence.the present study identified a family of six a. thaliana genes that share five limited regions of sequence similarity with lazy1, a gene in oryza sativa (rice) shown to participate in the early gravity signaling for shoot gravitropism. a t-dna insertion into the arabidopsis gene (at5g14090) most similar to lazy1 increased the inflorescence branch angle to 81° from the wild type value of 42°. rna interference lines and molecular rescue experiments confirmed the linkage between the branch-angle ph ...201323331961
differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots.in rice seedlings, elongation of leaf sheaths is suppressed by light stimuli. the response is mediated by two classes of photoreceptors, phytochromes and cryptochromes. however, it remains unclear how these photoreceptors interact in the process. our recent study using phytochrome mutants and novel cryptochrome rnai lines revealed that cryptochromes and phytochromes function cooperatively, but independently to reduce active ga contents in seedlings in visible light. blue light captured by crypto ...201323333965
formin homology 1 (osfh1) regulates root-hair elongation in rice (oryza sativa).the outgrowth of root hairs from the epidermal cell layer is regulated by a strict genetic regulatory system and external growth conditions. rice plants cultivated in water-logged paddy land are exposed to a soil ecology that differs from the environment surrounding upland plants, such as arabidopsis and maize. to identify genes that play important roles in root-hair growth, a forward genetics approach was used to screen for short-root-hair mutants. a short-root-hair mutant was identified, and t ...201323334469
organ evolution in angiosperms driven by correlated divergences of gene sequences and expression patterns.the evolution of a species involves changes in its genome and its transcriptome. divergence in expression patterns may be more important than divergence in sequences for determining phenotypic changes, particularly among closely related species. we examined the relationships between organ evolution, sequence evolution, and expression evolution in arabidopsis thaliana, rice (oryza sativa), and maize (zea mays). we found correlated divergence of gene sequences and expression patterns, with distinc ...201323341336
genetic analysis and fine mapping of lh1 and lh2, a set of complementary genes controlling late heading in rice (oryza sativa l.).heading date in rice (oryza sativa l.) is a critical agronomic trait with a complex inheritance. to investigate the genetic basis and mechanism of gene interaction in heading date, we conducted genetic analysis on segregation populations derived from crosses among the indica cultivars bo b, yuefeng b and baoxuan 2. a set of dominant complementary genes controlling late heading, designated lh1 and lh2, were detected by molecular marker mapping. genetic analysis revealed that baoxuan 2 contains bo ...201223341744
osorc3 is required for lateral root development in rice.the origin recognition complex (orc) is a pivotal element in dna replication, heterochromatin assembly, checkpoint regulation and chromosome assembly. although the functions of the orc have been determined in yeast and model animals, they remain largely unknown in the plant kingdom. in this study, oryza sativa origin recognition complex subunit 3 (osorc3) was cloned using map-based cloning procedures, and functionally characterized using a rice (oryza sativa) orc3 mutant. the mutant showed a tem ...201323346890
translational downregulation of rbcl is operative in the coordinated expression of rubisco genes in senescent leaves in rice.rubisco gene expression was examined in detail in rice (oryza sativa l.) leaves at different positions, i.e. expanding, mature, and senescent leaves. rubisco small subunit (rbcs) synthesis and rbcs mrna levels were maximal in expanding leaves and gradually became lower in mature and senescent leaves, with declines in those of the large subunit (rbcl) being relatively slower. the amount of synthesized rbcl per unit level of rbcl mrna and polysome loading of rbcl mrna declined in senescent leaves, ...201323349140
genome-wide analysis of histone modifications: h3k4me2, h3k4me3, h3k9ac, and h3k27ac in oryza sativa l. japonica.while previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. this study used chromatin immunoprecipitation followed by high-throughput sequencing (chip-seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of h3k4 (h3k4me2 and h3k4me3) and acylation of h3k9 and h3k27 (h3k ...201323355544
more spikelets1 is required for spikelet fate in the inflorescence of brachypodium.grasses produce florets on a structure called a spikelet, and variation in the number and arrangement of both branches and spikelets contributes to the great diversity of grass inflorescence architecture. in brachypodium (brachypodium distachyon), the inflorescence is an unbranched spike with a terminal spikelet and a limited number of lateral spikelets. spikelets are indeterminate and give rise to a variable number of florets. here, we provide a detailed description of the stages of inflorescen ...201323355632
gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in oryza sativa (rice).whole-genome duplication (wgd) has been recurring and single-gene duplication is also widespread in angiosperms. recent whole-genome dna methylation maps indicate that gene body methylation (i.e. of coding regions) has a functional role. however, whether gene body methylation is related to gene origins and duplication modes has yet to be reported. in rice (oryza sativa), we computed a body methylation level (proportion of methylated cpg within coding regions) for each gene in five tissues. body ...201323356482
genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles.histone post-translational modifications (hptms) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. although solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (hms) in tomato are sketchy.201323356725
differential induction of mitochondrial machinery by light intensity correlates with changes in respiratory metabolism and photorespiration in rice leaves.the light responsiveness of mitochondrial function was investigated through changes in mitochondrial composition and metabolism in rice (oryza sativa) shoots. the mitochondrial proteome and metabolite abundances under low light, (ll, 100 μmol m(-2) s(-1) ), and high light (hl, 700 μmol m(-2) s(-1) ) were measured along with information on shoot photosynthetic, respiratory and photorespiratory activity. specific steps in mitochondrial tricarboxylic acid (tca) cycle metabolism were decreased under ...201323356873
functional characterization of a rice de novo dna methyltransferase, osdrm2, expressed in escherichia coli and yeast.dna methylation of cytosine nucleotides is an important epigenetic modification that occurs in most eukaryotic organisms and is established and maintained by various dna methyltransferases together with their co-factors. there are two major categories of dna methyltransferases: de novo and maintenance. here, we report the isolation and functional characterization of a de novo methyltransferase, named osdrm2, from rice (oryza sativa l.). the full-length coding region of osdrm2 was cloned and tran ...201323357425
the evolution and pathogenic mechanisms of the rice sheath blight pathogen.rhizoctonia solani is a major fungal pathogen of rice (oryza sativa l.) that causes great yield losses in all rice-growing regions of the world. here we report the draft genome sequence of the rice sheath blight disease pathogen, r. solani ag1 ia, assembled using next-generation illumina genome analyser sequencing technologies. the genome encodes a large and diverse set of secreted proteins, enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, which probabl ...201323361014
locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in arabidopsis and rice.whole-genome duplications (wgds) have recurred in the evolution of angiosperms, resulting in many duplicated chromosomal segments. local gene duplications are also widespread in angiosperms. wgd-derived duplicates, that is, ohnologs, and local duplicates often show contrasting patterns of gene retention and evolution. however, many genes in angiosperms underwent multiple gene duplication events, possibly by different modes, indicating that different modes of gene duplication are not mutually exc ...201323362157
stable mercury isotope variation in rice plants (oryza sativa l.) from the wanshan mercury mining district, sw china.to study the sources and transformations of hg in the rice plant ( oryza sativa l.), stable hg isotope variations in different tissues (foliage, root, stem, and seed) of rice which were collected from the wanshan mercury mine (wsmm, guizhou province, sw china) were investigated by multicollector inductively coupled plasma mass spectrometry (mc-icp-ms). in comparison, hg isotope compositions of paddy soil, lichen, and direct ambient air samples in wsmm were also analyzed. we observed that mass de ...201323363238
thai herbal formulas used for wound treatment: a study of their antibacterial potency, anti-inflammatory, antioxidant, and cytotoxicity effects.this present work was aimed to investigate wound healing-related biologic activities of traditional herbal formulas used for wound treatment in southern thailand.201323363309
effect of feeding piglets with different extruded and nonextruded cereals on the gut mucosa and microbiota during the first postweaning week.two trials were conducted to evaluate the effect of different cereals in piglet diets on the jejunal mucosa and the ileal and cecal microbiota during the first postweaning days. in trial 1, 48 newly weaned pigs (7.95 kg bw; 26 d of age) were individually housed and distributed among 3 experimental diets containing white rice (oryza sativa), naked oats (avena sativa), or barley (hordeum vulgare) as the cereal source. at the start of the trial (weaning; day 0), 12 piglets were slaughtered and samp ...201223365267
effect of feeding different cereal-based diets on the performance and gut health of weaned piglets with or without previous access to creep feed during lactation.a trial was conducted to evaluate the effect of different cereals on the performance, gut mucosa, and microbiota of weanling pigs with or without previous access to creep feed during lactation. a total of 108 newly weaned pigs (7.4 kg bw; 26 d of age; half with and half without creep feed) were used. piglets were distributed by bw into 36 pens according to a 2 × 6 factorial arrangement of treatments with previous access to creep feed (with or without) and cereal source in the experimental diet [ ...201223365275
prececal digestibility of various sources of starch in minipigs with or without experimentally induced exocrine pancreatic insufficiency.low prececal digestibility of starch leads to a higher starch flux into the hindgut, causing a forced microbial fermentation, energy losses, and meteorism. for exocrine pancreatic insufficiency (epi), lack of pancreatic amylase can be compensated mostly by hindgut fermentation of starch. even in pigs with complete loss of pancreatic secretion, starch digestibility over the entire tract is reaching levels of controls. to optimize diets for human patients with epi, the proportion of starch that is ...201223365290
comparison of standardized ileal amino acid digestibilities in protein supplements and cereal grains for weaned pigs.standardized ileal digestibility (sid) of aa in protein ingredients and grains was determined in weaned piglets (5 kg initial bw) using the difference method. animals were fitted with a simple ileal t-cannula on day 24 or 25 of age. a synthetic diet based on corn (zea mays) starch and casein was either supplemented with an extruded soybean (glycine max) meal (esm), rice (oryza sativa) protein concentrate (rpc), full fat heat-treated soybeans (sb), corn, barley (hordeum vulgare), or wheat (tritic ...201223365298
effects of pulses of elevated carbon dioxide concentration on stomatal conductance and photosynthesis in wheat and rice.systems for exposing plants to elevated concentrations of co₂ may expose plants to pulses of co₂ concentrations considerably above the control set point. the importance of such pulses to plant function is unknown. single leaves of wheat (triticum aestivum cv choptank) and rice (oryza sativa cv akitakomachi) were exposed for 30 minutes to pulses of elevated co₂ similar to the frequency, duration and magnitude of pulses observed in free-air co₂ enrichment systems. stomatal conductance decreased wi ...201323368841
heavy metal-associated isoprenylated plant protein (hipp): characterization of a family of proteins exclusive to plants.metallochaperones are key proteins for the safe transport of metallic ions inside the cell. hipps (heavy metal-associated isoprenylated plant proteins) are metallochaperones that contain a metal binding domain (hma) and a c-terminal isoprenylation motif. in this study, we provide evidence that proteins of this family are found only in vascular plants and may be separated into five distinct clusters. hipps may be involved in (a) heavy metal homeostasis and detoxification mechanisms, especially th ...201323368984
comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes.class 2 transposable elements (tes) are the predominant elements in and around plant genes where they generate significant allelic diversity. using the complete sequences of four grasses, we have performed a novel comparative analysis of class 2 tes. to ensure consistent comparative analyses, we re-annotated class 2 tes in brachypodium distachyon, oryza sativa (rice), sorghum bicolor and zea mays and assigned them to one of the five cut-and-paste superfamilies found in plant genomes (tc1/mariner ...201323369001
wuschel-related homeobox4 is involved in meristem maintenance and is negatively regulated by the cle gene fcp1 in rice.the shoot apical meristem is the ultimate source of the cells that constitute the entire aboveground portion of the plant body. in arabidopsis thaliana, meristem maintenance is regulated by the negative feedback loop of wuschel-clavata (wus-clv). although clv-like genes, such as floral organ number1 (fon1) and fon2, have been shown to be involved in maintenance of the reproductive meristems in rice (oryza sativa), current understanding of meristem maintenance remains insufficient. in this articl ...201323371950
expression and characterization of recombinant human alpha-antitrypsin in transgenic rice seed.human alpha-antitrypsin (aat) is the most abundant circulating protease inhibitor in the human plasma. it is produced in the liver and exerts a primary physiological role as inhibitor for the neutrophil elastase in the lung. individuals with one or several gene mutations in aat causing reduction of the protein are related to lung, liver and pancreatic emphysema diseases and are treated lifelong with infusions of human plasma-derived aat. due to shortage of plasma and low expression levels of rec ...201223376844
genome-wide identification and analysis of the b3 superfamily of transcription factors in brassicaceae and major crop plants.the plant-specific b3 superfamily of transcription factors has diverse functions in plant growth and development. using a genome-wide domain analysis, we identified 92, 187, 58, 90, 81, 55, and 77 b3 transcription factor genes in the sequenced genome of arabidopsis, brassica rapa, castor bean (ricinus communis), cocoa (theobroma cacao), soybean (glycine max), maize (zea mays), and rice (oryza sativa), respectively. the b3 superfamily has substantially expanded during the evolution in eudicots pa ...201323377560
lactobacillus oryzae sp. nov., isolated from fermented rice grain (oryza sativa l. subsp. japonica).the taxonomic position of three lactobacillus-like micro-organisms (strains sg293(t), sg296 and sg310) isolated from fermented rice grain (oryza sativa l. subsp. japonica) in japan was investigated. these heterofermentative lactic acid bacteria were gram-stain-positive, rod-shaped, facultatively anaerobic, non-motile, non-spore-forming and did not show catalase activity. 16s rrna gene sequence analysis of strain sg293(t) revealed that the type strains of lactobacillus malefermentans (98.3 %), la ...201323378109
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