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At least 127 records · Page 7Linked to original sources
PubMed2005

Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction.

To better understand the molecular basis of the defense response against the rice blast fungus (Magnaporthe grisea), a large-scale expressed sequence tag (EST) sequencing approach was used to identify genes involved in the early infection stages in rice (Oryza sativa). Six cDNA libraries were constructed using infected leaf tissues harvested from 6 conditions: resistant, partially resistant, and susceptible reactions at both 6 and 24 h after inoculation. Two additional libraries were constructed using uninoculated leaves and leaves from the lesion mimic mutant spl11. A total of 68,920 ESTs were generated from 8 libraries. Clustering and assembly analyses resulted in 13,570 unique sequences from 10,934 contigs and 2,636 singletons. Gene function classification showed that 42% of the ESTs were predicted to have putative gene function. Comparison of the pathogen-challenged libraries with the uninoculated control library revealed an increase in the percentage of genes in the functional categories of defense and signal transduction mechanisms and cell cycle control, cell division, and chromosome partitioning. In addition, hierarchical clustering analysis grouped the eight libraries based on their disease reactions. A total of 7,748 new and unique ESTs were identified from our collection compared with the KOME full-length cDNA collection. Interestingly, we found that rice ESTs are more closely related to sorghum (Sorghum bicolor) ESTs than to barley (Hordeum vulgare), wheat (Triticum aestivum), and maize (Zea mays) ESTs. The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies.

Disease Susceptibility↗
PubMed2005

The rice dwarf virus P2 protein interacts with ent-kaurene oxidases in vivo, leading to reduced biosynthesis of gibberellins and rice dwarf symptoms.

The mechanisms of viral diseases are a major focus of biology. Despite intensive investigations, how a plant virus interacts with host factors to cause diseases remains poorly understood. The Rice dwarf virus (RDV), a member of the genus Phytoreovirus, causes dwarfed growth phenotypes in infected rice (Oryza sativa) plants. The outer capsid protein P2 is essential during RDV infection of insects and thus influences transmission of RDV by the insect vector. However, its role during RDV infection within the rice host is unknown. By yeast two-hybrid and coimmunoprecipitation assays, we report that P2 of RDV interacts with ent-kaurene oxidases, which play a key role in the biosynthesis of plant growth hormones gibberellins, in infected plants. Furthermore, the expression of ent-kaurene oxidases was reduced in the infected plants. The level of endogenous GA1 (a major active gibberellin in rice vegetative tissues) in the RDV-infected plants was lower than that in healthy plants. Exogenous application of GA3 to RDV-infected rice plants restored the normal growth phenotypes. These results provide evidence that the P2 protein of RDV interferes with the function of a cellular factor, through direct physical interactions, that is important for the biosynthesis of a growth hormone leading to symptom expression. In addition, the interaction between P2 and rice ent-kaurene oxidase-like proteins may decrease phytoalexin biosynthesis and make plants more competent for virus replication. Moreover, P2 may provide a novel tool to investigate the regulation of GA metabolism for plant growth and development.

Amino Acid Sequence↗
PubMed1996

Rice allergenic protein and molecular-genetic approach for hypoallergenic rice.

Allergenic proteins with a molecular mass of about 14 to 16 kDa were isolated from a rice salt-soluble fraction based on the reactivity with IgE antibodies from patients allergic to rice. cDNA clones encoding these allergenic proteins were isolated from a cDNA library of maturing rice seeds, and the deduced amino acid sequences showed considerable similarity to wheat and barley alpha-amylase/trypsin inhibitors, which have recently been identified as major allergens associated with baker's asthma. An antisense RNA strategy was applied to repress the allergen gene expression in maturing rice seeds. Immunoblotting and ELISA analyses of the seeds using a monoclonal antibody to a 16-kDa allergen showed that allergen content of seeds from several transgenic rice plants was markedly lower than that of the seeds from parental wild type rice.

Allergens↗
PubMed2004

Enhanced resistance to blast fungus and bacterial blight in transgenic rice constitutively expressing OsSBP, a rice homologue of mammalian selenium-binding proteins.

The rice Oryza sativa selenium-binding protein homologue (OsSBP) gene encodes a homologue of mammalian selenium-binding proteins, and it has been isolated as one of the genes induced by treating a plant with a cerebroside elicitor from rice blast fungus. The possible role of OsSBP in plant defense was evaluated by using a transgenic approach. Plants overexpressing OsSBP showed enhanced resistance to a virulent strain of rice blast fungus as well as to rice bacterial blight. The expression of defense-related genes and the accumulation of phytoalexin after infection by rice blast fungus were accelerated in the OsSBP overexpressors. A higher level of H(2)O(2) accumulation and reduced activity of such scavenging enzymes as ascorbate peroxidase and catalase were seen when the OsSBP-overexpressing plants were treated with the protein phosphatase 1 inhibitor, calyculin A. These results suggest that the upregulation of OsSBP expression conferred enhanced tolerance to different pathogens, possibly by increasing plant sensitivity to endogenous defense responses. Additionally, the OsSBP protein might have a role in modulating the defense mechanism to biotic stress in rice.

Animals↗
PubMed2005

Studies on nutrient uptake of rice and characteristics of soil microorganisms in a long-term fertilization experiments for irrigated rice.

The ecosystem characteristics of soil microorganism and the nutrient uptake of irrigated rice were investigated in a split-block experiment with different fertilization treatments, including control (no fertilizer application), PK, NK, NP, NPK fertilization, in the main block, and conventional rice and hybrid rice comparison, in the sub block. Average data of five treatments in five years indicated that the indigenous N supply (INS) capacity ranged from 32.72 to 93.21 kg/ha; that indigenous P supply (IPS) capacity ranged from 7.42 to 32.25 kg/ha; and that indigenous K supply (IKS) capacity ranged from 16.24 to 140.51 kg/ha, which showed that soil available nutrient pool depletion might occur very fast and that P, K deficiency has become a constraint to increasing yields of consecutive crops grown without fertilizer application. It was found that soil nutrient deficiency and unbalanced fertilization to rice crop had negative effect on the diversity of the microbial community and total microbial biomass in the soil. The long-term fertilizer experiment (LTFE) also showed that balanced application of N, P and K promoted microbial biomass growth and improvement of community composition. Unbalanced fertilization reduced microbial N and increased C/N ratio of the microbial biomass. Compared with inbred rice, hybrid rice behavior is characterized by physiological advantage in nutrient uptake and lower internal K use efficiency.

Agriculture↗
PubMed1999

Application of restriction fragment fingerprinting with a rice microsatellite sequence to assembling rice YAC clones.

To refine the current physical map of rice, we have established a restriction fragment fingerprinting method for identifying overlap between pairs of rice yeast artificial chromosome (YAC) clones and defining the physical arrangement of YACs within contiguous fragments (contigs). In this method, Southern blots of rice YAC DNAs digested with a restriction endonuclease are probed with a rice microsatellite probe, (GGC)5. The probe produces a unique fingerprint profile characteristic of each YAC clone. The profile is then digitized, processed in a computer, and a statistic that represents the degree of overlap between two YACs is calculated. The statistics have been used to detect overlaps among YAC clones, thereby filling a gap between two neighbouring contigs and organizing overlapping rice YAC clones into contiguous fragments. We applied this method to rearranging YACs that had previously been assigned to rice chromosome 6 by anchoring with RFLP markers.

Chromosomes, Artificial, Yeast↗
PubMed2001

New evidence for the synteny of rice chromosome 1 and barley chromosome 3H from rice expressed sequence tags.

To provide improved access to the wealth of resources and genomic information that is presently being developed for rice a set of 88 rice expressed sequence tags (ESTs) previously mapped on rice chromosome I in the cross 'Nipponbare' x 'Kasalath' was used for comparative mapping in a cross of the barley cultivars 'Igri' and 'Franka'. As expected. most (89%) of the clones gave distinct banding patterns in barley of which about one-third was polymorphic between 'Igri' and 'Franka'. These polymorphisms were mapped, and most of these (56%) confirmed that rice chromosome 1 and barley chromosome 3H are syntenous. All single-copy markers identified conserved collinear positions, while markers with multiple copies did so in a few cases only. The markers that were not fitting in the collinear order were distributed randomly across the barley genome. The comparative maps of barley chromosome 3H and rice chromosome 1 comprise in total 26 common markers covering more than 95% of the genetic length of both chromosomes. A 30-fold reduction of recombination is seen around the barley centromere, and synteny may be interrupted in this region. However, the good overall synteny on a mesoscale (1-10 cM) justifies the use of rice as a platform for map-based cloning in barley.

Chromosome Mapping↗
PubMed1992

Effect of processing on availability of essential amino acids in rice flour and cooked rice.

The availability of nitrogen, lysine and nine essential amino acids was determined in rice flour and cooked rice. Lysine availability was determined by the growth response method using regression analysis of body weight gain or moisture gain against lysine consumed from rice flour and cooked rice. The results show a good correlation between lysine consumed and weight gain or moisture gain (r = 0.86 + 0.8) for rats fed cooked rice and fair correlation for those fed rice flour. The results of lysine availability show that cooking increases availability by both ways of calculation. The availability of nitrogen and of essential amino acids was also determined by the balance trial method with rats. Results of balance trial show that cooking has no significant effect on essential amino acids availability. Data for weight gain, food efficiency and PER were significantly decreased by cooking.

Amino Acids, Essential↗
PubMed2005

A hydroponic rice seedling culture model system for investigating proteome of salt stress in rice leaf.

By using an in vivo hydroponic rice seedling culture system, we investigated the physiological and biochemical responses of a model rice japonica cultivar Nipponbare to salt stress using proteomics and classical biochemical methods. Yoshida's nutrient solution (YS) was used to grow rice seedlings. YS-grown 18-day-old seedlings manifested highly stable and reproducible symptoms, prominently the wilting and browning of the 3rd leaf, reduced photosynthetic activity, inhibition in overall seedling growth, and failure to develop new (5th) leaf, when subjected to salt stress by transferring them to YS containing 130 mM NaCl for 4 days. As leaf response to salt stress is least investigated in rice by proteomics, we used the 3rd leaf as source material. A comparison of 2-DE protein profiles between the untreated control and salt-stressed 3rd leaves revealed 55 differentially expressed CBB-stained spots, where 47 spots were increased over the control. Of these changed spots, the identity of 33 protein spots (27 increased and 5 decreased) was determined by nESI-LC-MS/MS. Most of these identified proteins belonged to major metabolic processes like photosynthetic carbon dioxide assimilation and photorespiration, suggesting a good correlation between salt stress-responsive proteins and leaf morphology. Moreover, 2-DE immunoblot and enzymatic activity analyses of 3rd leaves revealed remarkable changes in the key marker enzymes associated with oxidative damage to salt stress: ascorbate peroxidase and lipid peroxidation were induced, and catalase was suppressed. These results demonstrate that hydroponic culture system is best suited for proteomics of salt stress in rice seedling.

Amino Acid Sequence↗
PubMed2003

New strategy for the determination of gliadins in maize- or rice-based foods matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: fractionation of gliadins from maize or rice prolamins by acidic treatment.

A procedure for determining small quantities of gliadins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) in gluten-free foods containing relatively large amounts of prolamin proteins from maize or rice is described. We report for the first time that gliadins, the ethanol-soluble wheat prolamin fraction, can be quantitatively solubilized in 1.0 M acetic acid, while the corresponding ethanol-soluble maize or rice prolamin fraction remains insoluble in acetic acid. We describe a methodology for the detection of gliadins in maize and rice foods based on a two-step procedure of extraction (60% aqueous ethanol followed by 1 M acetic acid). Subsequent MALDI-TOFMS analysis of the resulting acidic extract from these gluten-free foods clearly confirms the presence of a typical mass pattern corresponding to gliadin components, ranging from 30 to 45 kDa. Depending on the percentages of maize or rice flours employed in the elaboration of these foods, the combined procedure enables levels of gliadins from 100 to 400 ppm to be detected. The efficiency of this combined procedure corroborates enzyme-linked immunosorbent assay data for a large number of maize/rice gluten-free foods by means of direct visualization of the characteristic gliadin mass pattern in maize or rice foods.

Food Analysis↗
PubMed2006

Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb.

We have reported previously that introgression by Zizania latifolia resulted in extensive DNA methylation changes in the recipient rice genome, as detected by a set of pre-selected DNA segments. In this study, using the methylation-sensitive amplified polymorphism (MSAP) method, we globally assessed the extent and pattern of cytosine methylation alterations in three typical introgression lines relative to their rice parent at approximately 2,700 unbiased genomic loci each representing a recognition site cleaved by one or both of the isoschizomers, HpaII/MspI. Based on differential digestion by the isoschizomers, it is estimated that 15.9% of CCGG sites are either fully methylated at the internal Cs and/or hemi-methylated at the external Cs in the rice parental cultivar Matsumae. In comparison, a statistically significant increase in the overall level of both methylation types was detected in all three studied introgression lines (19.2, 18.6, 19.6%, respectively). Based on comparisons of MSAP profiles between the isoschizomers within the rice parent and between parent and the introgression lines, four major groups of MSAP banding patterns are recognized, which can be further divided into various subgroups as a result of inheritance of, or variation in, parental methylation patterns. The altered methylation patterns include hyper- and hypomethylation changes, as well as inter-conversion of hemi- to full-methylation, or vice versa, at the relevant CCGG site(s). Most alterations revealed by MSAP in low-copy loci can be validated by DNA gel blot analysis. The changed methylation patterns are uniform among randomly selected individuals for a given introgression line within or among selfed generations. Sequencing on 31 isolated fragments that showed different changing patterns in the introgression line(s) allowed their mapping onto variable regions on one or more of the 12 rice chromosomes. These segments include protein-coding genes, transposon/retrotransposons and sequences with no homology. Possible causes for the introgression-induced methylation changes and their implications for genome evolution and crop breeding are discussed.

Cytosine↗
PubMed2003

Characterization of two rice DNA methyltransferase genes and RNAi-mediated reactivation of a silenced transgene in rice callus.

Two genomic clones ( OsMET1-1, AF 462029 and OsMET1-2, TPA BK001405), each encoding a cytosine-5 DNA methyltransferase (MTase), were isolated from rice ( Oryza sativa L.) BAC libraries. OsMET1-1 has an open reading frame of 4,566 nucleotides with 12 exons and 11 introns while OsMET1-2 has an open reading frame of 4,491 nucleotides with 11 exons and 10 introns. Although OsMET1-1 and OsMET1-2 have high sequence similarity overall, they share only 24% identity in exon 1, and intron 3 of OsMET1-1 is absent from OsMET1-2. As for other eukaryotic DNA MTases of the Dnmt1/MET l class, the derived amino acid sequences of OsMET1-1 and OsMET1-2 suggest that they are comprised of two-thirds regulatory domain and one-third catalytic domain. Most functional domains identified for other MTases were present in the rice MET1 sequences. Amino acid sequence comparison indicated high similarity (56-75% identity) of rice MET1 proteins to other plant MET1 sequences but limited similarity (approx. 24% identity) to animal Dnmt1 proteins. Genomic blot and database analysis indicated the presence of a single copy of OsMET1-1 (on chromosome 3) and single copy of OsMET1-2 (on chromosome 7). Ribonuclease protection assays revealed expression of both OsMET1-1 and OsMET1-2 in highly dividing cells, but the steady-state level of OsMET1-2 was 7- to 12-fold higher than that for OsMET1-1 in callus, root and inflorescence. The functional involvement of the rice DNA MTases in gene silencing was investigated using an RNAi strategy. Inverted repeat constructs of either the N- or C-terminal regions of OsMET1-1 were supertransformed into calli derived from a rice line bearing a silenced 35S-uidA-nos transgene. Restoration of uidA expression in the bombarded calli was consistent with the inactivation of maintenance methylation and with previous evidence for the involvement of methylation in silencing of this line.

Base Sequence↗
PubMed2002

Detection of rice grassy stunt tenuivirus nonstructural proteins p2, p5 and p6 from infected rice plants and from viruliferous brown planthoppers.

The genome of Rice grassy stunt virus (RGSV) consists of 6 ambisense RNA segments, among which RNAs 1, 2, 5 and 6 are equivalent to RNAs 1, 2, 3 and 4, respectively, of Rice stripe virus, the type species of the genus Tenuivirus. The RGSV 36-kDa nucleocapsid protein (N) is encoded on the complementary strand of RNA 5. Here, we studied accumulation of three nonstructural proteins, a 23-kDa p2 protein encoded on vRNA 2 (virus genomic strand), a 22-kDa p5 protein encoded on vRNA 5, and a 21-kDa p6 protein encoded on vRNA 6, from RGSV-infected rice leaf tissues and from viruliferous vector insects (brown planthopper, Nilaparvata lugens) by Western blot analyses. p2, p5 and p6 were detected from RGSV-infected rice leaf homogenates; p2 was detected mostly in the cytoplasmic soluble fraction but also a small amount was detected in the cell-wall, organelle-enriched and crude membrane fractions; p5 and p6 were detected from the cytoplasmic soluble fraction in large amounts. Among individual nymphs of N. lugens raised on RGSV-infected rice leaves, only 20% of insects were positive with the N protein. A large amount of p5 was detected from all the N-positive insects. Small amounts of p2 and p6 were detected only from a subset of the N- and p5-positive insects. p5 may have an essential role in virus infection in both plant and insect hosts, whereas p2 may function in plants such as a cell-to-cell movement protein.

Animals↗
PubMed2005

Improvement of human lysozyme expression in transgenic rice grain by combining wheat (Triticum aestivum) puroindoline b and rice (Oryza sativa) Gt1 promoters and signal peptides.

Heterologous protein expression levels in transgenic plants are of critical importance in the production of plant-made pharmaceuticals (PMPs). We studied a puroindoline b promoter and signal peptide (Tapur) driving human lysozyme expression in rice endosperm. The results demonstrated that human lysozyme expressed under the control of the Tapur cassette is seed-specific, readily extractable, active, and properly processed. Immuno-electron microscopy indicated that lysozyme expressed from this cassette is localized in protein bodies I and II in rice endosperm cells, demonstrating that this non-storage promoter and signal peptide can be used for targeting human lysozyme to rice protein bodies. We successfully employed a strategy to improve the expression of human lysozyme in transgenic rice grain by combining the Tapur cassette with our well established Gt1 expression system. The results demonstrated that when the two expression cassettes were combined, the expression level of human lysozyme increased from 5.24 +/- 0.34 mg(-1) g flour for the best single cassette line to 9.24 +/- 0.06 mg(-1) g flour in the best double cassette line, indicating an additive effect on expression of human lysozyme in rice grain.

Base Sequence↗
PubMed2005

The impact of rice plant roots on the reducing conditions in flooded rice soils.

The impact of oxygen diffusion from plant roots on the soil redox in the root zone in flooded rice bays was investigated using two Australian rice growing soils. The rates of production of Fe(II) and Mn(II) in pore water resulting from the reduction of soil minerals was used to gauge the extent of development of anaerobic conditions and the time taken for equilibrium to establish. Soil concentrations of readily reducible Fe were 13-28 times greater than Mn, making Fe a more reliable indicator of redox conditions than Mn. In addition, Mn(II) concentrations reached equilibrium far more rapidly than Fe, which made the identification of any contribution to soil redox by oxygen diffusing from rice plant roots difficult to observe. Dissection of soil cores showed that more than 80% of the rice root mass occurred in the top 4 cm of soil, suggesting that any contribution roots may make to the redox potential of the flooded soils would occur in this region. However, studies conducted indicated that the diffusion of oxygen from the surface floodwater into soil pore water in the 2.5 cm layer of soil was so substantial that it would mask any contribution made by rice plant roots to the overall soil redox in this root zone.

Anaerobiosis↗
PubMed2005

Occurrence and daily intake of ochratoxin A of organic and non-organic rice and rice products.

Ochratoxin A (OTA) was extracted from 84 rice samples and rice products by using accelerated solvent extraction (ASE) and analysed with liquid chromatography coupled with fluorescence detection. Samples were collected from rice cultivars, local markets and supermarkets; 64 were of non-organic and 20 of organic production. 7.8% of non-organic samples had OTA levels from 4.3 to 27.3 microg/kg and in 30% of organic samples was detected the presence of this mycotoxin varying from 1.0 to 7.1 microg/kg. OTA presence was confirmed by methyl-ester derivatization. Rice and rice products labelled with denomination of origin (DO) were not detected OTA due to the fact that its production has implemented food safety measures such as good agricultural practices (GAPs), good manufacturing practices (GMPs), and the hazard analysis and critical control point (HACCP) system. Estimated daily intake of OTA was 0.17 ng/kg b.w./day. This value reflects that the analysed samples have a minimal contribution to toxicological risk.

Chromatography, Liquid↗
PubMed2000

Field evaluation of seed production, shattering, and dormancy in hybrid populations of transgenic rice (Oryza sativa) and the weed, red rice (Oryza sativa).

The genetic and agronomic consequences of transferring glufosinate (Liberty) herbicide resistance from transgenic rice (Oryza sativa L.) lines to the noxious weed red rice (Oryza sativa L.) were evaluated under field conditions. Replicated field trials in Louisiana (LA) and Arkansas (AR) were conducted in 1997 to evaluate ten vegetative and reproductive traits of eight F(2) populations produced from controlled crosses of two transgenic, glufosinate-resistant rice lines and four red rice biotypes. Plant vigor and plant density at both locations were similar among populations derived from either transgenic or non-transgenic parents. Significant differences in plant height and maturity were observed among LA populations produced from transgenic lines when compared to corresponding populations developed from non-transgenic material. However, values for these traits were not greater than those detected in the red rice biotypes. Seed dormancy and seed production were not significantly different at either location among transgenic and non-transgenic populations. Dominant Mendelian segregation of glufosinate resistance was detected in 40% of the populations evaluated. Results of this study indicated that those populations segregating for glufosinate resistance responded in a location-specific manner with respect to life history and fecundity traits.

Journal Article↗
PubMed2001

Quantification of the rice aroma compound, 2-acetyl-1-pyrroline, in uncooked Khao Dawk Mali 105 brown rice.

Volatile components of uncooked Khao Dawk Mali 105 brown rice were extracted using indirect steam distillation under reduced pressure and controlled temperature in order to prevent cooking. Analysis of the fresh extract by capillary gas chromatography-mass spectrometry revealed that there were >140 volatile constituents. Among these, 70 volatiles were identified, including 2-acetyl-1-pyrroline (2AP), a key aroma compound of cooked rice. Further study concentrated on an improved method for the quantification of 2AP in uncooked brown rice. The method was simplified by utilizing a solvent extraction procedure. Quantitative analysis was performed using a capillary gas chromatographic system employing a flame ionization detector with the aid of a more selective column, CP-Wax 51, for amines. This improved chromatographic system had remarkable detection sensitivity for 2AP in the rice extracts so that 2AP in an extract of only 0.5 g of uncooked Khao Dawk Mali 105 brown rice could be detected.

Capillary Action↗