相关论文
2014 - Toxins
Identification of Distinct Bacillus thuringiensis 4A4 Nematicidal Factors Using the Model Nematodes Pristionchus pacificus and Caenorhabditis elegans

Bacillus thuringiensis has been extensively used for the biological control of insect pests. Nematicidal B. thuringiensis strains have also been identified; however, virulence factors of such strains are poorly investigated. Here, we describe virulence factors of the nematicidal B. thuringiensis 4A4 strain, using the model nematodes Pristionchus pacificus and Caenorhabditis elegans. We show that B. thuringiensis 4A4 kills both nematodes via intestinal damage. Whole genome sequencing of B. thuringiensis 4A4 identified Cry21Ha, Cry1Ba, Vip1/Vip2 and β-exotoxin as potential nematicidal factors. Only Cry21Ha showed toxicity to C. elegans, while neither Cry nor Vip toxins were active against P. pacificus, when expressed in E. coli. Purified crystals also failed to intoxicate P. pacificus, while autoclaved spore-crystal mixture of B. thuringiensis 4A4 retained toxicity, suggesting that primary β-exotoxin is responsible for P. pacificus killing. In support of this, we found that a β-exotoxin-deficient variant of B. thuringiensis 4A4, generated by plasmid curing lost virulence to the nematodes. Thus, using two model nematodes we revealed virulence factors of the nematicidal strain B. thuringiensis 4A4 and showed the multifactorial nature of its virulence.

2006
Effect of tillage and irrigation on yield and soil properties under rice (Oryza sutiva)-wheat (Triticumz aestivum) system on a sandy clay loam soil of Uttaranchal

A field experiment was conducted for 2 years (2001-02 to 2002-03) to study the tillage (conventional and zero) and irrigations effects on direct seeded rice (Oryza Sativa L.) wheat (Triticulil aestivunl L. emend. Fiori & Paol.)productivity and soil physical conditions after ricc and wheat harvest. Tl~crew as a reduction up to 6% in soil organic carbon with conventional tillage both aftcr rice and wheat halvest. Soil organic carbon increased (data) significant with incrcase in levels of irrigation for both tlie crops and the hiegst average value of organic carbon obtained in the most frequently irrigated plots. Soil bulk density decreased significantly with conventional tillage ( 1.34 and 1.36 MgIm3 at 0-1 5 and 15-30 cm soil depth respectively) at both the soil depths and after botli rice and wheat crop. But plant available water capacity was significantly higher in zero tilled plots (5.07 and 4.86 cnu' 30 c ns~o il layer after rice and wheat crop respectively) tlian the conventionally tilled plots (4.23 and 4.21 cni 130 cm soil layer after rice and wheat crop respectively). There was a significant increase in labo~.atorye stimated saturated hydraulic conductivity ~ncasurcdu ndcr zero-tilled plots (1 .I3 and 1.07 cn~ihart 0-15 and 15-30 cm soil layer respectively) after rice harvest. Pooled yield data sliowcd that the performance of conventionally and zcro-tilled direct seeded rice was at par but botli rice and wheat yields were 1 and 4's higher respcctively in conventionaliy tilled plots.

2001 - Applied and Environmental Microbiology
Plasmid Transfer between Bacillus thuringiensis subsp.israelensis Strains in Laboratory Culture, River Water, and Dipteran Larvae

ABSTRACT Plasmid transfer between strains of Bacillus thuringiensis subsp. israelensis was studied under a range of environmentally relevant laboratory conditions in vitro, in river water, and in mosquito larvae. Mobilization of pBC16 was detected in vitro at a range of temperatures, pH values, and available water conditions, and the maximum transfer ratio was 10−3transconjugant per recipient under optimal conditions. Transfer of conjugative plasmid pXO16∷Tn5401 was also detected under this range of conditions. However, a maximum transfer ratio of 1.0 transconjugant per recipient was attained, and every recipient became a transconjugant. In river water, transfer of pBC16 was not detected, probably as a result of the low transfer frequency for this plasmid and the formation of spores by the introduced donor and recipient strains. In contrast, transfer of plasmid pXO16∷Tn5401 was detected in water, but at a lower transfer ratio (ca. 10−2transconjugant per donor). The number of transconjugants increased over the first 7 days, probably as a result of new transfer events between cells, since growth of both donor and recipient cells in water was not detected. Mobilization of pBC16 was not detected in killed mosquito larvae, but transfer of plasmid pXO16::Tn5401 was evident, with a maximum rate of 10−3 transconjugant per donor. The reduced transfer rate in insects compared to broth cultures may be accounted for by competition from the background bacterial population present in the mosquito gut and diet or by the maintenance of a large population of B. thuringiensis spores in the insects.

2004 - Journal of Clinical Microbiology
Detection of the Bacillus anthracis gyrA Gene by Using a Minor Groove Binder Probe

ABSTRACT Identification of chromosomal markers for rapid detection of Bacillus anthracis is difficult because significant chromosomal homology exists among B. anthracis, Bacillus cereus, and Bacillus thuringiensis. We evaluated the bacterial gyrA gene as a potential chromosomal marker for B. anthracis. A real-time PCR assay was developed for the detection of B. anthracis. After analysis of the unique nucleotide sequence of the B. anthracis gyrA gene, a fluorescent 3′ minor groove binding probe was tested with 171 organisms from 29 genera of bacteria, including 102 Bacillus strains. The assay was found to be specific for all 43 strains of B. anthracis tested. In addition, a test panel of 105 samples was analyzed to evaluate the potential diagnostic capability of the assay. The assay showed 100% specificity, demonstrating the usefulness of the gyrA gene as a specific chromosomal marker for B. anthracis.

2012 - Crop Protection
Changes in the weed seed bank over 9 consecutive years of rice–duck farming

Abstract Rice–duck farming (RDF), a form of organic farming, has been widely adopted in rice production in East Asia. In RDF, it is believed that ducks can control weeds effectively. Since the weed seed bank determines the weed community in the following crop, a better understanding of the seed bank could provide useful insights into the long-term effects of RDF adopted for weed control. Nine consecutive years' field experiments were conducted to study the characteristics of the weed seed bank under RDF and evaluate the weed control effect of RDF. After 9 years under RDF, the number of weed species in the weed seed bank declined from 38 to 21 and the density of both the weed seed bank and the above-ground weed decreased by more than 90%. RDF resulted in a more uniform vertical distribution of the weed seed bank both quantitatively and qualitatively. The ecological indices point to a gradual change towards fewer species, lower density, and lower diversity following continued RDF. The dominant species in the weed seed bank shifted from Lindernia procumbens, Mazus japonicus, Cardamine hirsuta, and Alopecurus aequalis at the beginning of this experiment in 1999 to A. aequalis, Rotala indica, M. japonicus, and Cyperus difformis in 2008. The results provide concrete evidence for the efficacy of RDF in depleting the weed seed bank and as a weed management approach without any herbicides.

2000 - International Journal of Plant Sciences
Low Levels of Genetic Diversity within Populations and High Differentiation among Populations of a Wild Rice, Oryza granulata Nees et Arn. ex Watt., from China

To characterize genetic diversity within and among populations of Oryza granulata Nees et Arn. ex Watt., allozyme variation was assayed for 17 loci in 15 natural populations from Hainan and Yunnan provinces, China, using starch gel electrophoresis. A low level of genetic variability within populations (the mean \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$A=1.09$$ \end{document} , \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$p=6.33\% $$ \end{document} , \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$H_{\mathrm{e}\,}=0.016$$ \end{document} , and \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$H_{\mathrm{o}\,}=0.009$$ \end{document} ), but high genetic differentiation ( \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$F_{\mathrm{ST}\,}$$ \end{document} ) among populations was observed. The low amount of genetic variability of the species may be strongly affected by founder effect because of the marginal nature of the populations in China. The results also indicate that the restricted gene flow occuring between the two regions as well as the characteristics of O. granulata as a colonizing plant species are probably of significance in shaping the observed population genetic structure. Finally, an appropriate strategy for sampling more populations, but fewer individuals within populations, was proposed for the conservation of O. granulata in China.

2002
Effect of Seed Hardening on the Seedling Emergence and α-amylase Activity in the Grains of Wheat and Rice Sown in Dry Soil

Seed hardening, wetting and redrying of the seed before sowing, increases the rates of germination and seedling emergence of wheat and rice sown in dry soil. We examined the effect of the seed hardening on the water potential of seed, a driving force of water absorption from soil, and the activity of α-amylase, a key enzyme for soluble carbohydrate supply. In wheat variety Norin-61, the water and osmotic potentials at the time of sowing were -7.2 and -12.3 MPa, respectively, in the hardened seed, and was -4.8 and -9.9 MPa, respectively, in non-hardened seed. However, in rice variety Nipponbare, neither water nor osmotic potential was clearly affected by seed hardening. In hardened seeds, the activity of α-amylase at 12 hours after sowing in dry soil was 2.7 and 2.8 times as high as that in non-hardened seeds in both Norin-61 and Nipponbare, respectively. In several other Japanese varieties and Korean native varieties also, seedling emergence rate in dry soil and α-amylase activity before sowing were increased by hardening treatment, and α-amylase activity of hardened seedsbefore sowing was 1.9∼8.3 times as high as that of non-hardened seeds. It was assumed that the rates of germination and seedling emergence in dry soil were increased by seed hardening through the increase of soluble carbohydrate supply owing to increased α-amylase activity. However, hardening treatment did not decrease osmotic potential of rice seed. Redrying during the hardening treatment may have kept the activities of some enzymes in addition to α-amylase at the levels just before germination, and thus promoted germination.

2005 - Plant Molecular Biology
Microarray Analysis of Gene Expression Involved in Anther Development in rice (Oryza sativa L.)

In flowering plants, anthers bear male gametophytes whose development is regulated by the elaborate coordination of many genes. In addition, both gibberellic acid (GA3) and jasmonic acid (JA) play important roles in anther development and pollen fertility. To facilitate the analysis of anther development genes and how GA3 and JA regulate anther development, we performed microarray experiments using a 10-K cDNA microarray with probes derived from seedlings, meiotic anthers, mature anthers and GA3- or JA-treated suspension cells of rice. The expression level change of 2155 genes was significantly (by 2-fold or greater) detected in anthers compared with seedlings. Forty-seven genes, representing genes with potential function in cell cycle and cell structure regulation, hormone response, photosynthesis, stress resistance and metabolism, were differentially expressed in meiotic and mature anthers. Moreover, 314 genes responded to either GA3 or JA treatment, and 24 GA3- and 82 JA-responsive genes showed significant changes in expression between meiosis and the mature anther stages. RT-PCR demonstrated that gene y656d05 was not only highly expressed in meiotic anthers but also induced by GA3. Strong RNA signals of y656d05 were detected in pollen mother cells and tapetum in in situ hybridization. Further characterization of these candidate genes can contribute to the understanding of the molecular mechanism of anther development and the involvement of JA and GA3 signals in the control of anther development in rice.

2005 - Proceedings of the National Academy of Sciences of the United States of America
Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.

The three-dimensional structure of the N-acyl-l-homoserine lactone hydrolase (AHL lactonase) from Bacillus thuringiensis has been determined, by using single-wavelength anomalous dispersion (SAD) phasing, to 1.6-angstroms resolution. AHLs are produced by many Gram-negative bacteria as signaling molecules used in quorum-sensing pathways that indirectly sense cell density and regulate communal behavior. Because of their importance in pathogenicity, quorum-sensing pathways have been suggested as potential targets for the development of novel therapeutics. Quorum-sensing can be disrupted by enzymes evolved to degrade these lactones, such as AHL lactonases. These enzymes are members of the metallo-beta-lactamase superfamily and contain two zinc ions in their active sites. The zinc ions are coordinated to a number of ligands, including a single oxygen of a bridging carboxylate and a bridging water/hydroxide ion, thought to be the nucleophile that hydrolyzes the AHLs to ring-opened products, which can no longer act as quorum signals.

2002 - Journal of Bacteriology
Requirement of flhA for Swarming Differentiation, Flagellin Export, and Secretion of Virulence-Associated Proteins in Bacillus thuringiensis

ABSTRACT Bacillus thuringiensis is being used worldwide as a biopesticide, although increasing evidence suggests that it is emerging as an opportunistic human pathogen. While phospholipases, hemolysins, and enterotoxins are claimed to be responsible for B. thuringiensis virulence, there is no direct evidence to indicate that the flagellum-driven motility plays a role in parasite-host interactions. This report describes the characterization of a mini-Tn10 mutant of B. thuringiensis that is defective in flagellum filament assembly and in swimming and swarming motility as well as in the production of hemolysin BL and phosphatidylcholine-preferring phospholipase C. The mutant strain was determined to carry the transposon insertion in flhA, a flagellar class II gene encoding a protein of the flagellar type III export apparatus. Interestingly, the flhA mutant of B. thuringiensis synthesized flagellin but was impaired in flagellin export. Moreover, a protein similar to the anti-sigma factor FlgM that acts in regulating flagellar class III gene transcription was not detectable in B. thuringiensis, thus suggesting that the flagellar gene expression hierarchy of B. thuringiensis differs from that described for Bacillus subtilis. The flhA mutant of B. thuringiensis was also defective in the secretion of hemolysin BL and phosphatidylcholine-preferring phospholipase C, although both of these virulence factors were synthesized by the mutant. Since complementation of the mutant with a plasmid harboring the flhA gene restored swimming and swarming motility as well as secretion of toxins, the overall results indicate that motility and virulence in B. thuringiensis may be coordinately regulated by flhA, which appears to play a crucial role in the export of flagellar as well as nonflagellar proteins.

2010 - PLoS Genetics
The APETALA-2-Like Transcription Factor OsAP2-39 Controls Key Interactions between Abscisic Acid and Gibberellin in Rice

The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants. Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses. Controlling the expression level of OsAP2-39 which includes an APETALA 2 (AP2) domain leads to phenotypic changes in rice. Overexpression of OsAP2-39 leads to a reduction in yield by decreasing the biomass and the number of seeds in the transgenic rice lines. Global transcriptome analysis of the OsAP2-39 overexpression transgenic rice revealed the upregulation of a key Abscisic Acid (ABA) biosynthetic gene OsNCED-I which codes for 9-cis-epoxycarotenoid dioxygenase and leads to an increase in the endogenous ABA level. In addition to OsNCED-1, the gene expression analysis revealed the upregulation of a gene that codes for the Elongation of Upper most Internode (EUI) protein, an enzyme that catalyzes 16α, 17-epoxidation of non-13-hydroxylated GAs, which has been shown to deactivate gibberellins (GAs) in rice. The exogenous application of GA restores the wild-type phenotype in the transgenic line and ABA application induces the expression of EUI and suppresses the expression of OsAP2-39 in the wild-type line. These observations clarify the antagonistic relationship between ABA and GA and illustrate a mechanism that leads to homeostasis of these hormones. In vivo and in vitro analysis showed that the expression of both OsNCED-1 and EUI are directly controlled by OsAP2-39. Together, these results reveal a novel mechanism for the control of the ABA/GA balance in rice which is regulated by OsAP2-39 that in turn regulates plant growth and seed production.

2014 - Proceedings of the National Academy of Sciences
Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs

Significance Strigolactones are a new class of plant hormones regulating plant shoot and root architecture in response to the environment. Also present in root exudates, strigolactones stimulate the germination of parasitic plant seeds. This report describes a genomic polymorphism—associated with the Indica/Japonica subspecies divide in rice that has a major impact on the biosynthesis of strigolactones, plant tillering, and germination of the parasitic plant Striga hermonthica—consisting of the deletion of two strigolactone biosynthetic genes orthologous to Arabidopsis MAX1. Both of these genes rescued the Arabidopsis max1-1 highly branched mutant phenotype and increased the strigolactone level when overexpressed in the Indica rice variety Bala. This finding is of great interest for plant physiologists, plant evolutionary biologists, and breeders. Rice (Oryza sativa) cultivar Azucena—belonging to the Japonica subspecies—exudes high strigolactone (SL) levels and induces high germination of the root parasitic plant Striga hermonthica. Consistent with the fact that SLs also inhibit shoot branching, Azucena is a low-tillering variety. In contrast, Bala, an Indica cultivar, is a low-SL producer, stimulates less Striga germination, and is highly tillered. Using a Bala × Azucena F6 population, a major quantitative trait loci—qSLB1.1—for the exudation of SL, tillering, and induction of Striga germination was detected on chromosome 1. Sequence analysis of the corresponding locus revealed a rearrangement of a 51- to 59-kbp stretch between 28.9 and 29 Mbp in the Bala genome, resulting in the deletion of two cytochrome P450 genes—SLB1 and SLB2—with high homology to the Arabidopsis SL biosynthesis gene, MAX1. Both rice genes rescue the Arabidopsis max1-1 highly branched mutant phenotype and increase the production of the SL, ent-2′-epi-5-deoxystrigol, when overexpressed in Bala. Furthermore, analysis of this region in 367 cultivars of the publicly available Rice Diversity Panel population shows that the rearrangement at this locus is a recurrent natural trait associated with the Indica/Japonica divide in rice.

2001
Locating Genes Controlling Allelopathic Effects against Barnyardgrass in Upland Rice

To understand the genetic control of allelopathy in rice (Oryza saliva L.), quantitative trait loci (QTL) mapping was performed using a population of 142 recombinant inbred lines derived from a cross between cultivar IAC 165 (japonica upland variety) and cultivar CO 39 (indica irrigated variety). The map contained 140 DNA markers. The relay seeding technique, which is a laboratory bioassay measuring the inhibition in weed root growth due to the presence of rice seedlings, was used to evaluate the allelopathic effect of the rice lines. Cultivar IAC 165 showed strong and consistent allelopathic activity against barnyardgrass [Echinochloa crus-galli (L.) Beauv.], whereas CO 39 was weakly allelopathic. Transgressive segregation for allelopathic activity in both directions was observed in the population. No significant correlation was found between root morphology of the lines and their allelopathic potential, suggesting that allelopathy in rice was under genetic control independent from root morphology. Four main-effect QTLs located on three chromosomes were identified, which collectively explained 35% of the total phenotypic variation of the allelopathic activity in the population. One pair of digenic epistatic loci, not involving any of the main-effect loci, was also detected. Once confirmed, these QTLs may be useful for genetic improvement of allelopathy in rice using marker-assisted selection.

2007 - Journal of experimental botany
Short, direct repeats (SDRs)-mediated post-transcriptional processing of a transcription factor gene OsVP1 in rice (Oryza sativa).

The various degrees of preharvest sprouting occurring in hybrid rice is a limiting factor in the propagation and production of hybrid rice seeds. The phenotype of sprouted rice is very similar to that of the maize (Zea mays) seed-specific mutation viviparous 1. VP1 has been shown to be a transcription factor essential for seed maturation and dormancy induction. In this study, numerous truncated transcripts of OsVP1 resulting from an unusual post-transcriptional processing, were detected in four rice (Oryza sativa) cultivars. The observed events took place at a region spanning exons 1 to 5, and led to a variety of deletions that resulted in the loss of functional domain and frame-shifts with premature termination by introducing a stop codon. Various proportions of the transcripts expressed in both immature and mature embryos were observed to be incorrectly processed and associated with the genetic variation of preharvest sprouting rates among various rice varieties. In sprouting-susceptible rice cultivars, G46B and HeiB, many more incorrectly processed OsVP1 transcripts were expressed in immature than in mature embryos, indicating that the unusual post-transcriptional processing of the OsVP1 gene was developmentally regulated. In addition, comprehensive sequence analyses demonstrated the presence of paired short direct repeats (SDRs) at the junctions of the unusual excision sites in exons of OsVP1 gene. Site selection for the deletion of exon materials was altered along with the genotypes and developmental stages.

2019 - International Journal of Pure & Applied Bioscience
Combining Ability Analysis in Rice (Oryza sativa L.)

Combining ability in rice was studied with a set of 4 lines and 10 testers and their 40 hybrids. The magnitudes of gea variances were higher than sea variances for all the characters which indicated that additive gene action was predominant in the expression of traits. The estimation of gea effects for parents revealed that females, Acharmati, Pusa Sugandha-5 and males IET-1934 7, GR-4 and GNR-2 were good general combiners for yield and yield contributing characters. The best specific cross combinations obtained through poor x good and poor x average combining parents respectively for grain yield per plant.

2002 - Plant Physiology
Gramene, a Tool for Grass Genomics

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.

2003 - Nature
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis

Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or emetic syndromes. It is closely related to the animal and human pathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, the former being used as a biological weapon and the latter as a pesticide. B. anthracis and B. thuringiensis are readily distinguished from B. cereus by the presence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) and capsule (B. anthracis). But phylogenetic studies based on the analysis of chromosomal genes bring controversial results, and it is unclear whether B. cereus, B. anthracis and B. thuringiensis are varieties of the same species or different species. Here we report the sequencing and analysis of the type strain B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 enables us to perform comparative analysis, and hence to identify the genes that are conserved between B. cereus and B. anthracis, and the genes that are unique for each species. We use the former to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers.

2005 - BMC Plant Biology
Bmc Plant Biology Molecular Characterization and Differential Expression of Cytokinin-responsive Type-a Response Regulators in Rice (oryza Sativa)

BackgroundThe response regulators represent the elements of bacterial two-component system and have been characterized from dicot plants like Arabidopsis but little information is available on the monocots, including the cereal crops. The aim of this study was to characterize type-A response regulator genes from rice, and to investigate their expression in various organs as well as in response to different hormones, including cytokinin, and environmental stimuli.ResultsBy analysis of the whole genome sequence of rice, we have identified ten genes encoding type-A response regulators based upon their high sequence identity within the receiver domain. The exon-intron organization, intron-phasing as well as chromosomal location of all the RT-PCR amplified rice (Oryza sativa) response regulator (OsRR) genes have been analyzed. The transcripts of OsRR genes could be detected by real-time PCR in all organs of the light- and dark-grown rice seedlings/plants, although there were quantitative differences. The steady-state transcript levels of most of the OsRR genes increased rapidly (within 15 min) on exogenous cytokinin application even in the presence of cycloheximide. Moreover, the expression of the OsRR6 gene was enhanced in rice seedlings exposed to salinity, dehydration and low temperature stress.ConclusionTen type-A response regulator genes identified in rice, the model monocot plant, show overlapping/differential expression patterns in various organs and in response to light. The induction of OsRR genes by cytokinin even in the absence of de novo protein synthesis qualifies them to be primary cytokinin response genes. The induction of OsRR6 in response to different environmental stimuli indicates its role in cross-talk between abiotic stress and cytokinin signaling. These results provide a foundation for further investigations on specific as well as overlapping cellular functions of type-A response regulators in rice.

1984 - Plant physiology
Influence of Osmotic Adjustment on Leaf Rolling and Tissue Death in Rice (Oryza sativa L.).

Osmotic adjustment, measured by the lowering of the osmotic potential at full turgor, and its influence on leaf rolling and leaf death was assessed in the lowland rice (Oryza sativa L.) cultivar IR36 in both the greenhouse and field. The degree of osmotic adjustment varied with the degree and duration of stress, but was usually 0.5 to 0.6 megapascal (maximally 0.8 to 0.9 megapascal) under severe stress conditions. In leaves in which osmotic adjustment was 0.5 to 0.6 megapascal, leaf rolling and leaf death occurred at lower leaf water potentials in adjusted than in nonadjusted leaves. We conclude that osmotic adjustment aids in the drought resistance of rice by delaying leaf rolling, thereby maintaining gas exchange, and by delaying leaf death.

2000
Germination behaviour of red rice (Oryza sativa L.) seeds in field and laboratory conditions.

Two experiments were carried out in 1996-1998 to study (1) the germination behaviour of red rice seeds kept for different periods of time in field and laboratory conditions, and (2) the weed emergence behaviour in response to different burial depths. The first experiment was carried out considering mature red rice seeds of two biotypes which were exposed to field conditions and to 20 °C, for different periods of time, and then tested for their germinability over 6 months. The time required for red rice seed to germinate in petri dishes depended on the storage conditions and proved to be inversely related to the storage duration. Immediately after harvesting, the red rice seeds required 180 days of permanence in petri dishes to germinate. This time was reduced to 20 days when the seeds were exposed for 30 days at 20 °C or for 160 days in field conditions. The second experiment was conducted both in the greenhouse and in the field, placing seeds at different depths from 0 to 13 cm, in saturated and flooded soil conditions, and in loamy and clayey soil. The emergence was affected both by the depth of burial and the presence of a water layer on the soil sur- face, and occurred from a maximum depth of 10 cm. Most of the emergences were recorded in the 0-5 cm soil layer in saturated loamy soil (92-45%).

Nondestructive determination of transgenic Bacillus thuringiensis rice seeds (Oryza sativa L.) using multispectral imaging and chemometric methods.

Wei Liu
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Lei Zheng
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Wei Chen
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Changhong Liu
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Changhong Liu
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Wei Liu
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X. Lu
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Wei Chen
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Jianbo Yang
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Lei Zheng
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Xuzhong Lu
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Jianbo Yang

Abstract:Crop-to-crop transgene flow may affect the seed purity of non-transgenic rice varieties, resulting in unwanted biosafety consequences. The feasibility of a rapid and nondestructive determination of transgenic rice seeds from its non-transgenic counterparts was examined by using multispectral imaging system combined with chemometric data analysis. Principal component analysis (PCA), partial least squares discriminant analysis (PLSDA), least squares-support vector machines (LS-SVM), and PCA-back propagation neural network (PCA-BPNN) methods were applied to classify rice seeds according to their genetic origins. The results demonstrated that clear differences between non-transgenic and transgenic rice seeds could be easily visualized with the nondestructive determination method developed through this study and an excellent classification (up to 100% with LS-SVM model) can be achieved. It is concluded that multispectral imaging together with chemometric data analysis is a promising technique to identify transgenic rice seeds with high efficiency, providing bright prospects for future applications.

参考文献

[1]  Marc Loose,et al.  Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods , 2004, Analytical and bioanalytical chemistry.

[2]  L. Duponchel,et al.  Support vector machines (SVM) in near infrared (NIR) spectroscopy: Focus on parameters optimization and model interpretation , 2009 .

[3]  E. Hinchliffe,et al.  Improving the nutritional value of Golden Rice through increased pro-vitamin A content , 2005, Nature Biotechnology.

[4]  Zhuo Zhang,et al.  Unintended compositional changes in transgenic rice seeds ( Oryza sativa L.) studied by spectral and chromatographic analysis coupled with chemometrics methods. , 2010, Journal of agricultural and food chemistry.

[5]  A. Snow,et al.  Gene Flow from Genetically Modified Rice and Its Environmental Consequences , 2005 .

[6]  F. J. Acevedo,et al.  Classification of wines produced in specific regions by UV-visible spectroscopy combined with support vector machines. , 2007, Journal of agricultural and food chemistry.

[7]  Myoung-Gun Choung,et al.  Nondestructive determination of herbicide-resistant genetically modified soybean seeds using near-infrared reflectance spectroscopy , 2011 .

[8]  Lijuan Xie,et al.  Classification of tomatoes with different genotypes by visible and short-wave near-infrared spectroscopy with least-squares support vector machines and other chemometrics. , 2009 .

[9]  R. Lu.  Multispectral imaging for predicting firmness and soluble solids content of apple fruit , 2004 .

[10]  Rapid analysis of genetically modified organisms by in‐house developed capillary electrophoresis chip and laser‐induced fluorescence system , 2004, Electrophoresis.

[11]  Corinna Cortes,et al.  Support-Vector Networks , 1995, Machine Learning.

[12]  Friedrich Spener,et al.  PCR-ELISA for the CaMV-35S promoter as a screening method for genetically modified Roundup Ready soybeans , 2001 .

[13]  Jikun Huang,et al.  Insect-Resistant GM Rice in Farmers' Fields: Assessing Productivity and Health Effects in China , 2005, Science.

[14]  A. Mohanty,et al.  Recent advances in rice biotechnology--towards genetically superior transgenic rice. , 2005, Plant biotechnology journal.

[15]  M. Long,et al.  Liquid-phase hybridization based PCR-ELISA for detection of genetically modified organisms in food , 2004 .

[16]  Yankun Peng,et al.  Prediction of apple fruit firmness and soluble solids content using characteristics of multispectral scattering images , 2007 .

[17]  Hu Wei-qun,et al.  Measurement of Rice Leaf Chlorophyll and Seed Nitrogen Contents by Using Multi-Spectral Imagine , 2008 .

[18]  Yankun Peng,et al.  Improving apple fruit firmness predictions by effective correction of multispectral scattering images , 2006 .

[19]  Zhiping Song,et al.  Low frequency of transgene flow from Bt/CpTI rice to its non-transgenic counterparts planted at close spacing. , 2005, The New phytologist.

[20]  Urs Pauli,et al.  Event Specific Transgene Detection in Bt11 Corn by Quantitative PCR at the Integration Site , 2000 .

[21]  M. Ruiz-Altisent,et al.  Multispectral images of peach related to firmness and maturity at harvest , 2009 .

[22]  I. Nishida,et al.  An increase in unsaturation of fatty acids in phosphatidylglycerol from leaves improves the rates of photosynthesis and growth at low temperatures in transgenic rice seedlings. , 2002, Plant & cell physiology.

[23]  B. R. MacKay,et al.  Applications of Canonical Discriminant Analysis in Horticultural Research , 1994 .

[24]  T. Kobayashi,et al.  Detection of rice panicle blast with multispectral radiometer and the potential of using airborne multispectral scanners. , 2001, Phytopathology.

[25]  Colm P. O'Donnell,et al.  Hyperspectral imaging – an emerging process analytical tool for food quality and safety control , 2007 .

[26]  Xin Lu,et al.  Metabolic profiling of transgenic rice with cryIAc and sck genes: an evaluation of unintended effects at metabolic level by using GC-FID and GC-MS. , 2009, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[27]  Zhihao Qin,et al.  Detection of rice sheath blight for in-season disease management using multispectral remote sensing , 2005 .

[28]  L. Grohmann,et al.  Detection of genetically modified rice: a construct-specific real-time PCR method based on DNA sequences from transgenic Bt rice , 2006 .

[29]  Stina Frosch,et al.  Multispectral Imaging for Determination of Astaxanthin Concentration in Salmonids , 2011, PloS one.

[30]  Jens Michael Carstensen,et al.  Using Multispectral Imaging for Spoilage Detection of Pork Meat , 2013, Food and Bioprocess Technology.

[31]  Merete Edelenbos,et al.  Color and textural quality of packaged wild rocket measured by multispectral imaging , 2013 .

[32]  K. Chen,et al.  Predicting beef tenderness using color and multispectral image texture features. , 2012, Meat science.

[33]  M. S. Kim,et al.  MULTISPECTRAL DETECTION OF FECAL CONTAMINATION ON APPLES BASED ON HYPERSPECTRAL IMAGERY: PART I. APPLICATION OF VISIBLE AND NEAR–INFRARED REFLECTANCE IMAGING , 2002 .

[34]  Jinheng Zhang,et al.  Predicting Nitrogen Status of Rice Using Multispectral Data at Canopy Scale , 2006 .

[35]  Da-Wen Sun,et al.  Application of Hyperspectral Imaging in Food Safety Inspection and Control: A Review , 2012, Critical reviews in food science and nutrition.

[36]  Joseph Wang.  SURVEY AND SUMMARY From DNA biosensors to gene chips , 2000 .

[37]  Xiaping Fu,et al.  Discrimination of transgenic tomatoes based on visible/near-infrared spectra. , 2007, Analytica chimica acta.

[38]  A. C. Chang,et al.  Construction of biologically functional bacterial plasmids in vitro. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[39]  M. Darvishi,et al.  Metabolome Comparison of Transgenic and Non-transgenic Rice by Statistical Analysis of FTIR and NMR Spectra , 2009 .

[40]  A. Bakshi.  Potential Adverse Health Effects of Genetically Modified Crops , 2003, Journal of toxicology and environmental health. Part B, Critical reviews.

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