Biological event extraction with Turku system
I am quite interested in bioinformatics data mining and knowledge discovery. Recently, I am focusing a lot on bioNLP (Biomedical natural language process) and Turku system application. I am trying to explore the potential effectiveness of features used in this system, and aiming to improve it. In the meantime, by using Turku system, paper abstracts from PubMed are analyzed and related events are extracted. The paper we choose is rice-research paper.
---- This research is supported and financially sponsored by Dr.Fang's Dialogue System Group, City University of Hong Kong. ----
My student Zhang, Z.H is also helping me to transfer huge amount of pdf files to texts to give another search. The results are under prepared.
For the format of results reports, please see below examples. (Collected by Yang, L.). The whole results could be fetched via email inquiry.
I am quite interested in bioinformatics data mining and knowledge discovery. Recently, I am focusing a lot on bioNLP (Biomedical natural language process) and Turku system application. I am trying to explore the potential effectiveness of features used in this system, and aiming to improve it. In the meantime, by using Turku system, paper abstracts from PubMed are analyzed and related events are extracted. The paper we choose is rice-research paper.
---- This research is supported and financially sponsored by Dr.Fang's Dialogue System Group, City University of Hong Kong. ----
My student Zhang, Z.H is also helping me to transfer huge amount of pdf files to texts to give another search. The results are under prepared.
For the format of results reports, please see below examples. (Collected by Yang, L.). The whole results could be fetched via email inquiry.
Turku System is the best event extraction tool in BioNLP Shared tasks. For further information of BioNLP and Turku sytem, please
Click here.
Original ID: 22270237
Abstract: Expression and characterization of a novel metagenome-derived cellulase Exo2b and its application to improve cellulase activity in Trichoderma reesei . A metagenomic fosmid library containing 1 x 10 ( 5 ) clones was constructed from a biogas digester fed with pig ordure and rice straw . In total , 121 clones with activity of 4-methylumbelliferyl-cellobiosidase were screened from the metagenomic library . A novel GH5 cellulase gene exo2b was identified from a sequenced clone EXO02C10 and expressed in Escherichia coli BL21 . The corresponding recombinant Exo2b protein showed high specific activity toward both carboxymethylcellulose ( CMC ; 260 U/mg protein ) and beta-D : - glucan from barley ( 849 U/mg ) , with an optimal pH and temperature of 7.5 and 58 degrees C , respectively . Exo2b showed stable activity at a wide pH range from 5.5 to 9.0 and was highly thermostable at 60 degrees C in the presence of 60 mM cysteine . Residual activity was maintained at nearly 100 % when Exo2b was incubated at 60 degrees C for 15 h. A thin-layer chromatography analysis of the hydrolysis products confirmed that Exo2b was an endo-beta-1 ,4 - glucanase and it could also produce oligosaccharide smaller than cellotetraose . The fragment encoding the Exo2b catalytic domain was then fused with the cbh1 gene from Trichoderma reesei , and the fused gene was successfully expressed in T. reesei Rut-C30 . Compared to that of the parent strain , the filter paper activity and CMCase activity of the secreted proteins of a selected transformant A1 increased by 24 % and 18 % , respectively . Besides , the glucose concentration from the hydrolysis of pretreated corn stover by the A1 secreted proteins increased by 19.8 % . The present study demonstrated the potential application of metagenome originated cellulase genes to modify cellulase producing fungi .
Sentence: Besides , the glucose concentration from the hydrolysis of pretreated corn stover by the A1 secreted proteins increased by 19.8 % .
Simple Events:
ID: E1 Type: Localization Trigger: secreted Theme: A1
Original ID: 22228180
Abstract: Activation of rice Yellow Stripe1-Like 16 ( OsYSL16 ) enhances iron efficiency . Graminaceous plants release ferric-chelating phytosiderophores that bind to iron . These ferric-phytosiderophore complexes are transported across the plasma membrane by a protein produced from Yellow Stripe 1 ( YS1 ) . Here , we report the characterization of OsYSL16 , one of the YS1-like genes in rice . Real-time analysis revealed that this gene is constitutively expressed irrespective of metal status . Promoter fusions of OsYSL16 to beta-glucuronidase ( GUS ) showed that OsYSL16 was highly expressed in the vascular tissues of the root , leaf , and spikelet , and in leaf mesophyll cells . The OsYSL16-green fluorescence protein ( GFP ) fusion protein was localized to the plasma mem-brane . From a pool of rice T-DNA insertional lines , we identified two independent activation-tagging mutants in OsYSL16 . On an Fe-deficient medium , those mutants re-tained relatively high chlorophyll concentrations com-pared with the wild-type ( WT ) controls , indicating that they are more tolerant to a lack of iron . The Fe concentration in shoots was also higher in the OsYSL16 activation lines than in the WT . During germination , the rate of Fe-utili-zation from the seeds was higher in the OsYSL16 activa-tion lines than in the WT seeds . Our results suggest that the function of OsYSL16 in Fe-homeostasis is to enable distribution of iron within a plant .
Sentence: Here , we report the characterization of OsYSL16 , one of the YS1-like genes in rice .
Simple Events:
Original ID: 22228180
Abstract: Activation of rice Yellow Stripe1-Like 16 ( OsYSL16 ) enhances iron efficiency . Graminaceous plants release ferric-chelating phytosiderophores that bind to iron . These ferric-phytosiderophore complexes are transported across the plasma membrane by a protein produced from Yellow Stripe 1 ( YS1 ) . Here , we report the characterization of OsYSL16 , one of the YS1-like genes in rice . Real-time analysis revealed that this gene is constitutively expressed irrespective of metal status . Promoter fusions of OsYSL16 to beta-glucuronidase ( GUS ) showed that OsYSL16 was highly expressed in the vascular tissues of the root , leaf , and spikelet , and in leaf mesophyll cells . The OsYSL16-green fluorescence protein ( GFP ) fusion protein was localized to the plasma mem-brane . From a pool of rice T-DNA insertional lines , we identified two independent activation-tagging mutants in OsYSL16 . On an Fe-deficient medium , those mutants re-tained relatively high chlorophyll concentrations com-pared with the wild-type ( WT ) controls , indicating that they are more tolerant to a lack of iron . The Fe concentration in shoots was also higher in the OsYSL16 activation lines than in the WT . During germination , the rate of Fe-utili-zation from the seeds was higher in the OsYSL16 activa-tion lines than in the WT seeds . Our results suggest that the function of OsYSL16 in Fe-homeostasis is to enable distribution of iron within a plant .
Sentence: Here , we report the characterization of OsYSL16 , one of the YS1-like genes in rice .
Simple Events:
ID: E1 Type: Binding Trigger: characterization Theme: OsYSL16
Sentence: Promoter fusions of OsYSL16 to beta-glucuronidase ( GUS ) showed that OsYSL16 was highly expressed in the vascular tissues of the root , leaf , and spikelet , and in leaf mesophyll cells .
Simple Events:
Sentence: Promoter fusions of OsYSL16 to beta-glucuronidase ( GUS ) showed that OsYSL16 was highly expressed in the vascular tissues of the root , leaf , and spikelet , and in leaf mesophyll cells .
Simple Events:
ID: E2 Type: Gene_expression Trigger: expressed Theme: OsYSL16
Original ID: 22306743
Abstract: Expression of an Acidothermus cellulolyticus endoglucanase in transgenic rice seeds . The thermostable endo-1 ,4 - beta-glucanase ( E1 ) from Acidothermus cellulolyticus , is a useful enzyme for commercial hydrolysis of cellulose into glucose . A codon-optimized synthetic gene encoding this enzyme was transformed into rice ( Oryza sativa L. ssp . japonica ) under the control of the rice seed storage protein Gt1 promoter . The transgenic line C19 was identified as the one with the highest endoglucanase activity among the total of 36 independent transgenic lines obtained . The cellulase activity in the C19 seeds was estimated at about 830U/g of dried seeds using CMC as substrate . The enzymes produced in the seeds had an optimum pH of 5.0 and optimum temperature of 80 degrees C , which is similar to the enzymes produced by the native bacterium host . This study demonstrates that the transgenic rice seeds could be used as a bioreactor for production of enzymes for cellulosic biomass conversion .
Sentence: japonica ) under the control of the rice seed storage protein Gt1 promoter .
Simple Events:
Original ID: 22306743
Abstract: Expression of an Acidothermus cellulolyticus endoglucanase in transgenic rice seeds . The thermostable endo-1 ,4 - beta-glucanase ( E1 ) from Acidothermus cellulolyticus , is a useful enzyme for commercial hydrolysis of cellulose into glucose . A codon-optimized synthetic gene encoding this enzyme was transformed into rice ( Oryza sativa L. ssp . japonica ) under the control of the rice seed storage protein Gt1 promoter . The transgenic line C19 was identified as the one with the highest endoglucanase activity among the total of 36 independent transgenic lines obtained . The cellulase activity in the C19 seeds was estimated at about 830U/g of dried seeds using CMC as substrate . The enzymes produced in the seeds had an optimum pH of 5.0 and optimum temperature of 80 degrees C , which is similar to the enzymes produced by the native bacterium host . This study demonstrates that the transgenic rice seeds could be used as a bioreactor for production of enzymes for cellulosic biomass conversion .
Sentence: japonica ) under the control of the rice seed storage protein Gt1 promoter .
Simple Events:
ID: E1 Type: Regulation Trigger: control Theme: Gt1
Original ID: 22253868
Abstract: OsTIR1 and OsAFB2 Downregulation via OsmiR393 Overexpression Leads to More Tillers , Early Flowering and Less Tolerance to Salt and Drought in Rice . The microRNA miR393 has been shown to play a role in plant development and in the stress response by targeting mRNAs that code for the auxin receptors in Arabidopsis . In this study , we verified that two rice auxin receptor gene homologs ( OsTIR1 and OsAFB2 ) could be targeted by OsmiR393 ( Os for Oryza sativa ) . Two new phenotypes ( increased tillers and early flowering ) and two previously observed phenotypes ( reduced tolerance to salt and drought and hyposensitivity to auxin ) were observed in the OsmiR393-overexpressing rice plants . The OsmiR393-overexpressing rice demonstrated hyposensitivity to synthetic auxin-analog treatments . These data indicated that the phenotypes of OsmiR393-overexpressing rice may be caused through hyposensitivity to the auxin signal by reduced expression of two auxin receptor genes ( OsTIR1 and OsAFB2 ) . The expression of an auxin transporter ( OsAUX1 ) and a tillering inhibitor ( OsTB1 ) were downregulated by overexpression of OsmiR393 , which suggested that a gene chain from OsmiR393 to rice tillering may be from OsTIR1 and OsAFB2 to OsAUX1 , which affected the transportation of auxin , then to OsTB1 , which finally controlled tillering . The positive phenotypes ( increased tillers and early flowering ) and negative phenotypes ( reduced tolerance to salt and hyposensitivity to auxin ) of OsmiR393-overexpressing rice present a dilemma for molecular breeding .
Sentence: The expression of an auxin transporter ( OsAUX1 ) and a tillering inhibitor ( OsTB1 ) were downregulated by overexpression of OsmiR393 , which suggested that a gene chain from OsmiR393 to rice tillering may be from OsTIR1 and OsAFB2 to OsAUX1 , which affected the transportation of auxin , then to OsTB1 , which finally controlled tillering .
Simple Events:
Original ID: 22248149
Abstract: Biochemical identification of the OsMKK6-OsMPK3 signaling pathway for chilling stress tolerance in rice . Mitogen-activated protein kinase ( MAPK ) pathways have been implicated in stress signaling in plants . In this study , we performed yeast two-hybrid screening to identify partner MAPKs for OsMKK6 , a rice MAPK kinase , and revealed specific interactions of OsMKK6 with OsMPK3 and OsMPK6 . OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro . A MBP kinase assay of the immunoprecipitation complex indicated that OsMPK3 and OsMPK6 were activated in response to a moderately low temperature ( 12 degrees C ) but a severely low temperature ( 4 degrees C ) in rice seedlings . A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro . OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 . Enhanced chilling tolerance was observed in the transgenic plants overexpressing OsMKK6DD . Taken together , our data suggest that OsMKK6 and OsMPK3 constitute a moderately low-temperature signaling pathway and regulate cold stress tolerance in rice .
Sentence: In this study , we performed yeast two-hybrid screening to identify partner MAPKs for OsMKK6 , a rice MAPK kinase , and revealed specific interactions of OsMKK6 with OsMPK3 and OsMPK6 .
Simple Events:
Original ID: 22253868
Abstract: OsTIR1 and OsAFB2 Downregulation via OsmiR393 Overexpression Leads to More Tillers , Early Flowering and Less Tolerance to Salt and Drought in Rice . The microRNA miR393 has been shown to play a role in plant development and in the stress response by targeting mRNAs that code for the auxin receptors in Arabidopsis . In this study , we verified that two rice auxin receptor gene homologs ( OsTIR1 and OsAFB2 ) could be targeted by OsmiR393 ( Os for Oryza sativa ) . Two new phenotypes ( increased tillers and early flowering ) and two previously observed phenotypes ( reduced tolerance to salt and drought and hyposensitivity to auxin ) were observed in the OsmiR393-overexpressing rice plants . The OsmiR393-overexpressing rice demonstrated hyposensitivity to synthetic auxin-analog treatments . These data indicated that the phenotypes of OsmiR393-overexpressing rice may be caused through hyposensitivity to the auxin signal by reduced expression of two auxin receptor genes ( OsTIR1 and OsAFB2 ) . The expression of an auxin transporter ( OsAUX1 ) and a tillering inhibitor ( OsTB1 ) were downregulated by overexpression of OsmiR393 , which suggested that a gene chain from OsmiR393 to rice tillering may be from OsTIR1 and OsAFB2 to OsAUX1 , which affected the transportation of auxin , then to OsTB1 , which finally controlled tillering . The positive phenotypes ( increased tillers and early flowering ) and negative phenotypes ( reduced tolerance to salt and hyposensitivity to auxin ) of OsmiR393-overexpressing rice present a dilemma for molecular breeding .
Sentence: The expression of an auxin transporter ( OsAUX1 ) and a tillering inhibitor ( OsTB1 ) were downregulated by overexpression of OsmiR393 , which suggested that a gene chain from OsmiR393 to rice tillering may be from OsTIR1 and OsAFB2 to OsAUX1 , which affected the transportation of auxin , then to OsTB1 , which finally controlled tillering .
Simple Events:
ID:E3 Type: Gene_expression Trigger: expression Theme: OsTB1
Relevant Mixed Events:
ID: E1 Type: Negative_regulation Trigger: inhibitor Theme: E3
ID: E2 Type: Negative_regulation Trigger: downregulated Theme: E3
Original ID: 22248149
Abstract: Biochemical identification of the OsMKK6-OsMPK3 signaling pathway for chilling stress tolerance in rice . Mitogen-activated protein kinase ( MAPK ) pathways have been implicated in stress signaling in plants . In this study , we performed yeast two-hybrid screening to identify partner MAPKs for OsMKK6 , a rice MAPK kinase , and revealed specific interactions of OsMKK6 with OsMPK3 and OsMPK6 . OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro . A MBP kinase assay of the immunoprecipitation complex indicated that OsMPK3 and OsMPK6 were activated in response to a moderately low temperature ( 12 degrees C ) but a severely low temperature ( 4 degrees C ) in rice seedlings . A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro . OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 . Enhanced chilling tolerance was observed in the transgenic plants overexpressing OsMKK6DD . Taken together , our data suggest that OsMKK6 and OsMPK3 constitute a moderately low-temperature signaling pathway and regulate cold stress tolerance in rice .
Sentence: In this study , we performed yeast two-hybrid screening to identify partner MAPKs for OsMKK6 , a rice MAPK kinase , and revealed specific interactions of OsMKK6 with OsMPK3 and OsMPK6 .
Simple Events:
ID: E1 Type: Binding Trigger: interactions Theme1: OsMKK6Theme2: OsMPK6
Sentence: In this study , we performed yeast two-hybrid screening to identify partner MAPKs for OsMKK6 , a rice MAPK kinase , and revealed specific interactions of OsMKK6 with OsMPK3 and OsMPK6 .
Simple Events:
Sentence: In this study , we performed yeast two-hybrid screening to identify partner MAPKs for OsMKK6 , a rice MAPK kinase , and revealed specific interactions of OsMKK6 with OsMPK3 and OsMPK6 .
Simple Events:
ID: E2 Type: Binding Trigger: interactions Theme1: OsMKK6Theme2: OsMPK3
Sentence: OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro .
Simple Events:
Sentence: OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro .
Simple Events:
ID: E3 Type: Phosphorylation Trigger: phosphorylated Theme: OsMKK6
Sentence: OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro .
Simple Events:
Sentence: OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro .
Simple Events:
ID: E4 Type: Gene_expression Trigger: OsMPK3 Theme: OsMPK6
Sentence: OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro .
Simple Events:
Sentence: OsMPK3 and OsMPK6 each co-immunoprecipitated OsMKK6 , and both were directly phosphorylated by OsMKK6 in vitro .
Simple Events:
ID: E5 Type: Gene_expression Trigger: OsMPK3 Theme: OsMKK6
Sentence: A MBP kinase assay of the immunoprecipitation complex indicated that OsMPK3 and OsMPK6 were activated in response to a moderately low temperature ( 12 degrees C ) but a severely low temperature ( 4 degrees C ) in rice seedlings .
Simple Events:
Sentence: A MBP kinase assay of the immunoprecipitation complex indicated that OsMPK3 and OsMPK6 were activated in response to a moderately low temperature ( 12 degrees C ) but a severely low temperature ( 4 degrees C ) in rice seedlings .
Simple Events:
ID: E6 Type: Positive_regulation Trigger: activated Theme: OsMPK3
Sentence: A MBP kinase assay of the immunoprecipitation complex indicated that OsMPK3 and OsMPK6 were activated in response to a moderately low temperature ( 12 degrees C ) but a severely low temperature ( 4 degrees C ) in rice seedlings .
Simple Events:
Sentence: A MBP kinase assay of the immunoprecipitation complex indicated that OsMPK3 and OsMPK6 were activated in response to a moderately low temperature ( 12 degrees C ) but a severely low temperature ( 4 degrees C ) in rice seedlings .
Simple Events:
ID: E7 Type: Positive_regulation Trigger: activated Theme: OsMPK6
Sentence: A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro .
Simple Events:
Sentence: A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro .
Simple Events:
ID: E8 Type: Phosphorylation Trigger: phosphorylation Theme: OsMPK6
Sentence: A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro .
Simple Events:
Sentence: A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro .
Simple Events:
ID: E9 Type: Phosphorylation Trigger: phosphorylation Theme: OsMKK6
Sentence: A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro .
Simple Events:
Sentence: A constitutively active form of OsMKK6 , OsMKK6DD , showed elevated phosphorylation activity against OsMPK3 and OsMPK6 in vitro .
Simple Events:
ID: E10 Type: Phosphorylation Trigger: phosphorylation Theme: OsMPK3
Sentence: OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 .
Simple Events:
Sentence: OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 .
Simple Events:
ID: E11 Type: Positive_regulation Trigger: activated Theme: OsMPK6
Sentence: OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 .
Simple Events:
Sentence: OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 .
Simple Events:
ID: E12 Type: Localization Trigger: target Theme: OsMPK3
Sentence: OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 .
Simple Events:
Sentence: OsMPK3 , but not OsMPK6 , was constitutively activated in transgenic plants overexpressing OsMKK6DD , indicating that OsMPK3 is an in vivo target of OsMKK6 .
Simple Events:
ID: E13 Type: Localization Trigger: target Theme: OsMKK6
Original ID: 22270358
Abstract: Regulation of a proteinaceous elicitor-induced Ca2 + influx and production of phytoalexins by a putative voltage-gated cation channel , OsTPC1 , in cultured rice cells . Pathogen/microbe - or plant-derived signaling molecules ( PAMPs/MAMPs/DAMPs ) or elicitors induce increases in the cytosolic concentration of free Ca ( 2 + ) followed by a series of defense responses including biosynthesis of antimicrobial secondary metabolites called phytoalexins ; however the molecular links and regulatory mechanisms of the phytoalexin biosynthesis remains largely unknown . A putative voltage-gated cation channel , OsTPC1 has been shown to play a critical role in hypersensitive cell death induced by a fungal xylanase protein ( TvX ) in suspension-cultured rice cells . Here we show that TvX induced a prolonged increase in cytosolic Ca ( 2 + ) , mainly due to a Ca ( 2 + ) influx through the plasma membrane . Membrane fractionation by two-phase partitioning and immunoblot analyses revealed that OsTPC1 is localized predominantly at the plasma membrane . In retrotransposon-insertional Ostpc1 knockout cell lines harboring a Ca ( 2 + ) - sensitive photoprotein , aequorin , TvX - induced Ca ( 2 + ) elevation was significantly impaired , which was restored by expression of OsTPC1 . TvX-induced production of major diterpenoid phytoalexins and the expression of a series of diterpene cyclase genes involved in phytoalexin biosynthesis were also impaired in the Ostpc1 cells . Whole cell patch clamp analyses of OsTPC1 heterologously expressed in HEK293T cells showed its voltage-dependent Ca ( 2 + ) - permeability . These results suggest that OsTPC1 plays a crucial role in TvX-induced Ca ( 2 + ) influx as a plasma membrane Ca ( 2 + ) - permeable channel consequently required for the regulation of phytoalexin biosynthesis in cultured rice cells .
Sentence: Membrane fractionation by two-phase partitioning and immunoblot analyses revealed that OsTPC1 is localized predominantly at the plasma membrane .
Simple Events:
Original ID: 22270358
Abstract: Regulation of a proteinaceous elicitor-induced Ca2 + influx and production of phytoalexins by a putative voltage-gated cation channel , OsTPC1 , in cultured rice cells . Pathogen/microbe - or plant-derived signaling molecules ( PAMPs/MAMPs/DAMPs ) or elicitors induce increases in the cytosolic concentration of free Ca ( 2 + ) followed by a series of defense responses including biosynthesis of antimicrobial secondary metabolites called phytoalexins ; however the molecular links and regulatory mechanisms of the phytoalexin biosynthesis remains largely unknown . A putative voltage-gated cation channel , OsTPC1 has been shown to play a critical role in hypersensitive cell death induced by a fungal xylanase protein ( TvX ) in suspension-cultured rice cells . Here we show that TvX induced a prolonged increase in cytosolic Ca ( 2 + ) , mainly due to a Ca ( 2 + ) influx through the plasma membrane . Membrane fractionation by two-phase partitioning and immunoblot analyses revealed that OsTPC1 is localized predominantly at the plasma membrane . In retrotransposon-insertional Ostpc1 knockout cell lines harboring a Ca ( 2 + ) - sensitive photoprotein , aequorin , TvX - induced Ca ( 2 + ) elevation was significantly impaired , which was restored by expression of OsTPC1 . TvX-induced production of major diterpenoid phytoalexins and the expression of a series of diterpene cyclase genes involved in phytoalexin biosynthesis were also impaired in the Ostpc1 cells . Whole cell patch clamp analyses of OsTPC1 heterologously expressed in HEK293T cells showed its voltage-dependent Ca ( 2 + ) - permeability . These results suggest that OsTPC1 plays a crucial role in TvX-induced Ca ( 2 + ) influx as a plasma membrane Ca ( 2 + ) - permeable channel consequently required for the regulation of phytoalexin biosynthesis in cultured rice cells .
Sentence: Membrane fractionation by two-phase partitioning and immunoblot analyses revealed that OsTPC1 is localized predominantly at the plasma membrane .
Simple Events:
ID: E1 Type: Localization Trigger: localized Theme: OsTPC1
Sentence: In retrotransposon-insertional Ostpc1 knockout cell lines harboring a Ca ( 2 + ) - sensitive photoprotein , aequorin , TvX - induced Ca ( 2 + ) elevation was significantly impaired , which was restored by expression of OsTPC1 .
Simple Events:
Sentence: In retrotransposon-insertional Ostpc1 knockout cell lines harboring a Ca ( 2 + ) - sensitive photoprotein , aequorin , TvX - induced Ca ( 2 + ) elevation was significantly impaired , which was restored by expression of OsTPC1 .
Simple Events:
ID: E2 Type: Gene_expression Trigger: expression Theme: OsTPC1
Sentence: Whole cell patch clamp analyses of OsTPC1 heterologously expressed in HEK293T cells showed its voltage-dependent Ca ( 2 + ) - permeability .
Simple Events:
Sentence: Whole cell patch clamp analyses of OsTPC1 heterologously expressed in HEK293T cells showed its voltage-dependent Ca ( 2 + ) - permeability .
Simple Events:
ID: E3 Type: Gene_expression Trigger: expressed Theme: OsTPC1
Original ID: 22325870
Abstract: Functional conservation and diversification between rice OsMADS22/OsMADS55 and Arabidopsis SVP proteins . MADS-box transcription factors play pivotal roles in several aspects of plant growth and development . The Arabidopsis SHORT VEGETATIVE PHASE ( SVP ) protein mediates the integration of signals involved in the control of flowering time and flower development by interacting with MADS-box proteins . In the rice genome , three SVP-like genes ( OsMADS22 , OsMADS47 , and OsMADS55 ) are present . To investigate the functional conservation of these SVP-like genes in rice and Arabidopsis , the phenotypes of transgenic Arabidopsis plants overexpressing OsMADS22 and OsMADS55 were analyzed . Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) . Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC . Overexpression of OsMADS55 , but not OsMADS22 , complemented the early flowering phenotype and ambient temperature-insensitive flowering phenotype seen in svp mutants , suggesting that OsMADS55 regulates flowering time associated with ambient temperature responses in Arabidopsis . Taken together , our data are consistent with functional conservation and diversification between Arabidopsis and rice SVP-like genes involved in controlling flowering time and flower development .
Sentence: To investigate the functional conservation of these SVP-like genes in rice and Arabidopsis , the phenotypes of transgenic Arabidopsis plants overexpressing OsMADS22 and OsMADS55 were analyzed .
Simple Events:
Sentence: To investigate the functional conservation of these SVP-like genes in rice and Arabidopsis , the phenotypes of transgenic Arabidopsis plants overexpressing OsMADS22 and OsMADS55 were analyzed .
Simple Events:
Sentence: Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) .
Simple Events:
Original ID: 22325870
Abstract: Functional conservation and diversification between rice OsMADS22/OsMADS55 and Arabidopsis SVP proteins . MADS-box transcription factors play pivotal roles in several aspects of plant growth and development . The Arabidopsis SHORT VEGETATIVE PHASE ( SVP ) protein mediates the integration of signals involved in the control of flowering time and flower development by interacting with MADS-box proteins . In the rice genome , three SVP-like genes ( OsMADS22 , OsMADS47 , and OsMADS55 ) are present . To investigate the functional conservation of these SVP-like genes in rice and Arabidopsis , the phenotypes of transgenic Arabidopsis plants overexpressing OsMADS22 and OsMADS55 were analyzed . Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) . Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC . Overexpression of OsMADS55 , but not OsMADS22 , complemented the early flowering phenotype and ambient temperature-insensitive flowering phenotype seen in svp mutants , suggesting that OsMADS55 regulates flowering time associated with ambient temperature responses in Arabidopsis . Taken together , our data are consistent with functional conservation and diversification between Arabidopsis and rice SVP-like genes involved in controlling flowering time and flower development .
Sentence: To investigate the functional conservation of these SVP-like genes in rice and Arabidopsis , the phenotypes of transgenic Arabidopsis plants overexpressing OsMADS22 and OsMADS55 were analyzed .
Simple Events:
ID:E3 Type: Gene_expression Trigger: overexpressing Theme: OsMADS55
Relevant Mixed Events:
ID: E2 Type: Positive_regulation Trigger: overexpressing Theme: E3
Sentence: To investigate the functional conservation of these SVP-like genes in rice and Arabidopsis , the phenotypes of transgenic Arabidopsis plants overexpressing OsMADS22 and OsMADS55 were analyzed .
Simple Events:
ID:E4 Type: Gene_expression Trigger: overexpressing Theme: OsMADS22
Relevant Mixed Events:
ID: E1 Type: Positive_regulation Trigger: overexpressing Theme: E4
Sentence: Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) .
Simple Events:
ID: E5 Type: Gene_expression Trigger: expression Theme: OsMADS55
Sentence: Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) .
Simple Events:
Sentence: Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) .
Simple Events:
Sentence: Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC .
Simple Events:
Sentence: Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) .
Simple Events:
ID:E8 Type: Gene_expression Trigger: Overexpression Theme: OsMADS55
Relevant Mixed Events:
ID: E7 Type: Positive_regulation Trigger: Overexpression Theme: E8
Sentence: Overexpression of OsMADS22 and OsMADS55 led to abnormal floral morphologies including leaf-like sepals , whereas only OsMADS55 expression caused delayed flowering via downregulation of FLOWERING LOCUS T ( FT ) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) .
Simple Events:
ID:E9 Type: Gene_expression Trigger: Overexpression Theme: OsMADS22
Relevant Mixed Events:
ID: E6 Type: Positive_regulation Trigger: Overexpression Theme: E9
Sentence: Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC .
Simple Events:
ID: E10 Type: Binding Trigger: interacted Theme: OsMADS55
Sentence: Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC .
Simple Events:
Sentence: Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC .
Simple Events:
ID: E11 Type: Binding Trigger: interacted Theme: OsMADS22
Sentence: Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC .
Simple Events:
Sentence: Yeast two-hybrid assays revealed that OsMADS22 and OsMADS55 interacted with Arabidopsis AGL24 and AP1 , but only OsMADS55 interacted with FLC .
Simple Events:
ID: E12 Type: Binding Trigger: interacted Theme: OsMADS55
Sentence: Overexpression of OsMADS55 , but not OsMADS22 , complemented the early flowering phenotype and ambient temperature-insensitive flowering phenotype seen in svp mutants , suggesting that OsMADS55 regulates flowering time associated with ambient temperature responses in Arabidopsis .
Simple Events:
Sentence: Overexpression of OsMADS55 , but not OsMADS22 , complemented the early flowering phenotype and ambient temperature-insensitive flowering phenotype seen in svp mutants , suggesting that OsMADS55 regulates flowering time associated with ambient temperature responses in Arabidopsis .
Simple Events:
Original ID: 22196946
Abstract: Involvement of hydrogen peroxide in heat shock - and cadmium-induced expression of ascorbate peroxidase and glutathione reductase in leaves of rice seedlings . Hydrogen peroxide ( H ( 2 ) O ( 2 ) ) is considered a signal molecule inducing cellular stress . Both heat shock ( HS ) and Cd can increase H ( 2 ) O ( 2 ) content . We investigated the involvement of H ( 2 ) O ( 2 ) in HS - and Cd-mediated changes in the expression of ascorbate peroxidase ( APX ) and glutathione reductase ( GR ) in leaves of rice seedlings . HS treatment increased the content of H ( 2 ) O ( 2 ) before it increased activities of APX and GR in rice leaves . Moreover , HS-induced H ( 2 ) O ( 2 ) production and APX and GR activities could be counteracted by the NADPH oxidase inhibitors dipehenylene iodonium ( DPI ) and imidazole ( IMD ) . HS-induced OsAPX2 gene expression was associated with HS-induced APX activity but was not regulated by H ( 2 ) O ( 2 ) . Cd-increased H ( 2 ) O ( 2 ) content and APX and GR activities were lower with than without HS . Cd did not increase the expression of OsAPX and OsGR without HS treatment . Cd increased H ( 2 ) O ( 2 ) content by Cd before it increased APX and GR activities without HS . Treatment with DPI and IMD effectively inhibited Cd-induced H ( 2 ) O ( 2 ) production and APX and GR activities . Moreover , the effects of DPI and IMD could be rescued with H ( 2 ) O ( 2 ) treatment . H ( 2 ) O ( 2 ) may be involved in the regulation of HS - and Cd-increased APX and GR activities in leaves of rice seedlings .
Sentence: HS-induced OsAPX2 gene expression was associated with HS-induced APX activity but was not regulated by H ( 2 ) O ( 2 ) .
Simple Events:
Original ID: 22218926
Abstract: Molecular Basis Underlying the S5-Dependent Reproductive Isolation and Compatibility of Indica/Japonica Rice Hybrids . The S5 locus regulates spikelet fertility of indica/japonica hybrid rice . There are three alleles at the S5 locus , including an indica allele ( S5i ) , a japonica allele ( S5j ) , and a wide-compatibility allele ( S5n ) . This study analyzed the molecular basis for S5-dependent reproductive isolation and compatibility of indica/japonica rice hybrids . Three S5 alleles were expressed at extremely low levels , and only in the ovary . S5n was more similar to S5i in both RNA and protein expression profiles . The S5 locus was not essential for embryo-sac development , although deleterious interactions between S5i and S5j resulted in reduced rates of spikelet fertility . The yeast two-hybrid system was used to test direct interactions between S5-encoded proteins . The results indicated that the S5i - and S5j-encoded eukaryotic aspartyl proteases formed both homo - and heterodimers , whereas the S5n-encoded aspartyl protease was incapable of dimerization . Site-directed mutagenesis revealed that a single amino-acid difference between S5i - and S5j-encoded aspartyl proteases ( Phe/Leu at residue 273 ) was primarily responsible for embryo-sac abortion . The S5 locus may have promoted sub-speciation of indica and japonica , but it also enables gene flow between them .
Sentence: Three S5 alleles were expressed at extremely low levels , and only in the ovary .
Simple Events:
Sentence: Overexpression of OsMADS55 , but not OsMADS22 , complemented the early flowering phenotype and ambient temperature-insensitive flowering phenotype seen in svp mutants , suggesting that OsMADS55 regulates flowering time associated with ambient temperature responses in Arabidopsis .
Simple Events:
ID:E15 Type: Gene_expression Trigger: Overexpression Theme: OsMADS55
Relevant Mixed Events:
ID: E13 Type: Positive_regulation Trigger: Overexpression Theme: E15
Sentence: Overexpression of OsMADS55 , but not OsMADS22 , complemented the early flowering phenotype and ambient temperature-insensitive flowering phenotype seen in svp mutants , suggesting that OsMADS55 regulates flowering time associated with ambient temperature responses in Arabidopsis .
Simple Events:
ID:E16 Type: Gene_expression Trigger: Overexpression Theme: OsMADS22
Relevant Mixed Events:
ID: E14 Type: Positive_regulation Trigger: Overexpression Theme: E16
Original ID: 22196946
Abstract: Involvement of hydrogen peroxide in heat shock - and cadmium-induced expression of ascorbate peroxidase and glutathione reductase in leaves of rice seedlings . Hydrogen peroxide ( H ( 2 ) O ( 2 ) ) is considered a signal molecule inducing cellular stress . Both heat shock ( HS ) and Cd can increase H ( 2 ) O ( 2 ) content . We investigated the involvement of H ( 2 ) O ( 2 ) in HS - and Cd-mediated changes in the expression of ascorbate peroxidase ( APX ) and glutathione reductase ( GR ) in leaves of rice seedlings . HS treatment increased the content of H ( 2 ) O ( 2 ) before it increased activities of APX and GR in rice leaves . Moreover , HS-induced H ( 2 ) O ( 2 ) production and APX and GR activities could be counteracted by the NADPH oxidase inhibitors dipehenylene iodonium ( DPI ) and imidazole ( IMD ) . HS-induced OsAPX2 gene expression was associated with HS-induced APX activity but was not regulated by H ( 2 ) O ( 2 ) . Cd-increased H ( 2 ) O ( 2 ) content and APX and GR activities were lower with than without HS . Cd did not increase the expression of OsAPX and OsGR without HS treatment . Cd increased H ( 2 ) O ( 2 ) content by Cd before it increased APX and GR activities without HS . Treatment with DPI and IMD effectively inhibited Cd-induced H ( 2 ) O ( 2 ) production and APX and GR activities . Moreover , the effects of DPI and IMD could be rescued with H ( 2 ) O ( 2 ) treatment . H ( 2 ) O ( 2 ) may be involved in the regulation of HS - and Cd-increased APX and GR activities in leaves of rice seedlings .
Sentence: HS-induced OsAPX2 gene expression was associated with HS-induced APX activity but was not regulated by H ( 2 ) O ( 2 ) .
Simple Events:
ID:E4 Type: Gene_expression Trigger: expression Theme: OsAPX2
Relevant Mixed Events:
ID: E1 Type: Positive_regulation Trigger: HS-induced Theme: E4
ID: E2 Type: Regulation Trigger: regulated Theme: E4
Original ID: 22218926
Abstract: Molecular Basis Underlying the S5-Dependent Reproductive Isolation and Compatibility of Indica/Japonica Rice Hybrids . The S5 locus regulates spikelet fertility of indica/japonica hybrid rice . There are three alleles at the S5 locus , including an indica allele ( S5i ) , a japonica allele ( S5j ) , and a wide-compatibility allele ( S5n ) . This study analyzed the molecular basis for S5-dependent reproductive isolation and compatibility of indica/japonica rice hybrids . Three S5 alleles were expressed at extremely low levels , and only in the ovary . S5n was more similar to S5i in both RNA and protein expression profiles . The S5 locus was not essential for embryo-sac development , although deleterious interactions between S5i and S5j resulted in reduced rates of spikelet fertility . The yeast two-hybrid system was used to test direct interactions between S5-encoded proteins . The results indicated that the S5i - and S5j-encoded eukaryotic aspartyl proteases formed both homo - and heterodimers , whereas the S5n-encoded aspartyl protease was incapable of dimerization . Site-directed mutagenesis revealed that a single amino-acid difference between S5i - and S5j-encoded aspartyl proteases ( Phe/Leu at residue 273 ) was primarily responsible for embryo-sac abortion . The S5 locus may have promoted sub-speciation of indica and japonica , but it also enables gene flow between them .
Sentence: Three S5 alleles were expressed at extremely low levels , and only in the ovary .
Simple Events:
ID: E1 Type: Gene_expression Trigger: expressed Theme: S5
Original ID: 22189955
Abstract: bZIP transcription factor OsbZIP52/RISBZ5 : a potential negative regulator of cold and drought stress response in rice . OsbZIP52/RISBZ5 is a member of the basic leucine zipper ( bZIP ) transcription factor ( TF ) family in rice ( Oryza sativa ) isolated from rice ( Zhonghua11 ) panicles . Expression of the OsbZIP52 gene was strongly induced by low temperature ( 4 degrees C ) but not by drought , PEG , salt , or ABA . The subcellular localization of OsbZIP52-GFP in onion ( Allium cepa ) epidermis cells revealed that OsbZIP52 is a nuclear localized protein . A transactivation assay in yeast demonstrated that OsbZIP52 functions as a transcriptional activator and can specifically bind to the G-box promoter motif . In a yeast two-hybrid ( Y-2-H ) experiment , OsbZIP52 was able to form homodimeric complexes . Rice plants overexpressing OsbZIP52 showed significantly increased sensitivity to cold and drought stress . Real-time PCR analysis revealed that some abiotic stress-related genes , such as OsLEA3 , OsTPP1 , Rab25 , gp1 precursor , beta-gal , LOC_Os05g11910 and LOC_Os05g39250 , were down-regulated in OsbZIP52 overexpression lines . These results suggest that OsbZIP52/RISBZ5 could function as a negative regulator in cold and drought stress environments .
Sentence: Real-time PCR analysis revealed that some abiotic stress-related genes , such as OsLEA3 , OsTPP1 , Rab25 , gp1 precursor , beta-gal , LOC_Os05g11910 and LOC_Os05g39250 , were down-regulated in OsbZIP52 overexpression lines .
Simple Events:
Original ID: 22189955
Abstract: bZIP transcription factor OsbZIP52/RISBZ5 : a potential negative regulator of cold and drought stress response in rice . OsbZIP52/RISBZ5 is a member of the basic leucine zipper ( bZIP ) transcription factor ( TF ) family in rice ( Oryza sativa ) isolated from rice ( Zhonghua11 ) panicles . Expression of the OsbZIP52 gene was strongly induced by low temperature ( 4 degrees C ) but not by drought , PEG , salt , or ABA . The subcellular localization of OsbZIP52-GFP in onion ( Allium cepa ) epidermis cells revealed that OsbZIP52 is a nuclear localized protein . A transactivation assay in yeast demonstrated that OsbZIP52 functions as a transcriptional activator and can specifically bind to the G-box promoter motif . In a yeast two-hybrid ( Y-2-H ) experiment , OsbZIP52 was able to form homodimeric complexes . Rice plants overexpressing OsbZIP52 showed significantly increased sensitivity to cold and drought stress . Real-time PCR analysis revealed that some abiotic stress-related genes , such as OsLEA3 , OsTPP1 , Rab25 , gp1 precursor , beta-gal , LOC_Os05g11910 and LOC_Os05g39250 , were down-regulated in OsbZIP52 overexpression lines . These results suggest that OsbZIP52/RISBZ5 could function as a negative regulator in cold and drought stress environments .
Sentence: Real-time PCR analysis revealed that some abiotic stress-related genes , such as OsLEA3 , OsTPP1 , Rab25 , gp1 precursor , beta-gal , LOC_Os05g11910 and LOC_Os05g39250 , were down-regulated in OsbZIP52 overexpression lines .
Simple Events:
ID: E2 Type: Negative_regulation Trigger: down-regulated Theme: OsTPP1
Sentence: Real-time PCR analysis revealed that some abiotic stress-related genes , such as OsLEA3 , OsTPP1 , Rab25 , gp1 precursor , beta-gal , LOC_Os05g11910 and LOC_Os05g39250 , were down-regulated in OsbZIP52 overexpression lines .
Simple Events:
Original ID: 22218673
Abstract: Gene silencing using the recessive rice bacterial blight resistance gene xa13 as a new paradigm in plant breeding . Resistant germplasm resources are valuable for developing resistant varieties in agricultural production . However , recessive resistance genes are usually overlooked in hybrid breeding . Compared with dominant traits , however , they may confer resistance to different pathogenic races or pest biotypes with different mechanisms of action . The recessive rice bacterial blight resistance gene xa13 , also involved in pollen development , has been cloned and its resistance mechanism has been recently characterized . This report describes the conversion of bacterial blight resistance mediated by the recessive xa13 gene into a dominant trait to facilitate its use in a breeding program . This was achieved by knockdown of the corresponding dominant allele Xa13 in transgenic rice using recently developed artificial microRNA technology . Tissue-specific promoters were used to exclude most of the expression of artificial microRNA in the anther to ensure that Xa13 functioned normally during pollen development . A battery of highly bacterial blight resistant transgenic plants with normal seed setting rates were acquired , indicating that highly specific gene silencing had been achieved . Our success with xa13 provides a paradigm that can be adapted to other recessive resistance genes .
Sentence: Our success with xa13 provides a paradigm that can be adapted to other recessive resistance genes .
Simple Events:
Sentence: Real-time PCR analysis revealed that some abiotic stress-related genes , such as OsLEA3 , OsTPP1 , Rab25 , gp1 precursor , beta-gal , LOC_Os05g11910 and LOC_Os05g39250 , were down-regulated in OsbZIP52 overexpression lines .
Simple Events:
ID:E5 Type: Gene_expression Trigger: overexpression Theme: OsTPP1
Relevant Mixed Events:
ID: E1 Type: Negative_regulation Trigger: down-regulated Theme: E5
ID: E4 Type: Positive_regulation Trigger: overexpression Theme: E5
Original ID: 22218673
Abstract: Gene silencing using the recessive rice bacterial blight resistance gene xa13 as a new paradigm in plant breeding . Resistant germplasm resources are valuable for developing resistant varieties in agricultural production . However , recessive resistance genes are usually overlooked in hybrid breeding . Compared with dominant traits , however , they may confer resistance to different pathogenic races or pest biotypes with different mechanisms of action . The recessive rice bacterial blight resistance gene xa13 , also involved in pollen development , has been cloned and its resistance mechanism has been recently characterized . This report describes the conversion of bacterial blight resistance mediated by the recessive xa13 gene into a dominant trait to facilitate its use in a breeding program . This was achieved by knockdown of the corresponding dominant allele Xa13 in transgenic rice using recently developed artificial microRNA technology . Tissue-specific promoters were used to exclude most of the expression of artificial microRNA in the anther to ensure that Xa13 functioned normally during pollen development . A battery of highly bacterial blight resistant transgenic plants with normal seed setting rates were acquired , indicating that highly specific gene silencing had been achieved . Our success with xa13 provides a paradigm that can be adapted to other recessive resistance genes .
Sentence: Our success with xa13 provides a paradigm that can be adapted to other recessive resistance genes .
Simple Events:
ID: E1 Type: Binding Trigger: success Theme: xa13
Original ID: 22212404
Abstract: The arbuscular mycorrhizal symbiosis promotes the systemic induction of regulatory defence-related genes in rice leaves and confers resistance to pathogen infection . Arbuscular mycorrhizal ( AM ) symbioses are mutualistic associations between soil fungi and most vascular plants . Their association benefits the host plant by improving nutrition , mainly phosphorus nutrition , and by providing increased capability to cope with adverse conditions . In this study , we investigated the transcriptional changes triggered in rice leaves as a result of AM symbiosis , focusing on the relevance of the plant defense response . We showed that root colonization by the AM fungus Glomus intraradices is accompanied by the systemic induction of genes that play a regulatory role in the host defense response , such as OsNPR1 , OsAP2 , OsEREBP and OsJAmyb . Genes involved in signal transduction processes ( OsDUF26 and OsMPK6 ) and genes that function in calcium-mediated signalling processes ( OsCBP , OsCaM and OsCML4 ) are also up-regulated in leaves of mycorrhizal rice plants in the absence of pathogen infection . In addition , the mycorrhizal rice plants exhibit a stronger induction of defense marker genes ( i.e. pathogenesis-related ( PR ) genes ) in their leaves in response to infection by the blast fungus Magnaporthe oryzae . Evidence indicates that mycorrhizal rice plants show enhanced resistance to the rice blast fungus . Overall , these results suggest that the protective effect of the AM symbiosis in rice plants relies on both the systemic activation of defense regulatory genes in the absence of pathogen challenge and the priming for stronger expression of defense effector genes during pathogen infection . The possible mechanisms involved in the mycorrhiza-induced resistance to M. oryzae infection are discussed .
Sentence: Genes involved in signal transduction processes ( OsDUF26 and OsMPK6 ) and genes that function in calcium-mediated signalling processes ( OsCBP , OsCaM and OsCML4 ) are also up-regulated in leaves of mycorrhizal rice plants in the absence of pathogen infection .
Simple Events:
Original ID: 22212404
Abstract: The arbuscular mycorrhizal symbiosis promotes the systemic induction of regulatory defence-related genes in rice leaves and confers resistance to pathogen infection . Arbuscular mycorrhizal ( AM ) symbioses are mutualistic associations between soil fungi and most vascular plants . Their association benefits the host plant by improving nutrition , mainly phosphorus nutrition , and by providing increased capability to cope with adverse conditions . In this study , we investigated the transcriptional changes triggered in rice leaves as a result of AM symbiosis , focusing on the relevance of the plant defense response . We showed that root colonization by the AM fungus Glomus intraradices is accompanied by the systemic induction of genes that play a regulatory role in the host defense response , such as OsNPR1 , OsAP2 , OsEREBP and OsJAmyb . Genes involved in signal transduction processes ( OsDUF26 and OsMPK6 ) and genes that function in calcium-mediated signalling processes ( OsCBP , OsCaM and OsCML4 ) are also up-regulated in leaves of mycorrhizal rice plants in the absence of pathogen infection . In addition , the mycorrhizal rice plants exhibit a stronger induction of defense marker genes ( i.e. pathogenesis-related ( PR ) genes ) in their leaves in response to infection by the blast fungus Magnaporthe oryzae . Evidence indicates that mycorrhizal rice plants show enhanced resistance to the rice blast fungus . Overall , these results suggest that the protective effect of the AM symbiosis in rice plants relies on both the systemic activation of defense regulatory genes in the absence of pathogen challenge and the priming for stronger expression of defense effector genes during pathogen infection . The possible mechanisms involved in the mycorrhiza-induced resistance to M. oryzae infection are discussed .
Sentence: Genes involved in signal transduction processes ( OsDUF26 and OsMPK6 ) and genes that function in calcium-mediated signalling processes ( OsCBP , OsCaM and OsCML4 ) are also up-regulated in leaves of mycorrhizal rice plants in the absence of pathogen infection .
Simple Events:
ID: E1 Type: Positive_regulation Trigger: up-regulated Theme: OsMPK6
Original ID: 22290495
Abstract: Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress . The pre-mRNA processing ( Prp1 ) gene encodes a spliceosomal protein . It was firstly identified in fission yeast and plays a regular role during spliceosome activation and cell cycle . Plant Prp1 genes have only been identified from rice , Sorghum and Arabidopsis thaliana . In this study , we reported the identification and isolation of a novel Prp1 gene from barley , and further explored its expressional pattern by using real-time quantitative RT-PCR , promoter prediction and analysis of microarray data . The putative barley Prp1 protein has a similar primary structure features to those of other known Prp1 protein in this family . The results of amino acid comparison indicated that Prp1 protein of barley and other plant species has a highly conserved 3 ' termnal region while their 5 ' sequences greatly varied . The results of expressional analysis revealed that the expression level of barley Prp1 gene is always stable in different vegetative tissues , except it is up-regulated at the mid - and late stages of seed development or under the condition of cold stress . This kind of expressional pattern for barley Prp1 is also supported by our results of comparison of microarray data from barley , rice and Arabidopsis . For the molecular mechanism of its expressional pattern , we conclude that the expression of Prp1 gene may be up-regulated by the increase of pre-mRNAs and not be constitutive or ubiquitous .
Sentence: Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress .
Simple Events:
Original ID: 22290495
Abstract: Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress . The pre-mRNA processing ( Prp1 ) gene encodes a spliceosomal protein . It was firstly identified in fission yeast and plays a regular role during spliceosome activation and cell cycle . Plant Prp1 genes have only been identified from rice , Sorghum and Arabidopsis thaliana . In this study , we reported the identification and isolation of a novel Prp1 gene from barley , and further explored its expressional pattern by using real-time quantitative RT-PCR , promoter prediction and analysis of microarray data . The putative barley Prp1 protein has a similar primary structure features to those of other known Prp1 protein in this family . The results of amino acid comparison indicated that Prp1 protein of barley and other plant species has a highly conserved 3 ' termnal region while their 5 ' sequences greatly varied . The results of expressional analysis revealed that the expression level of barley Prp1 gene is always stable in different vegetative tissues , except it is up-regulated at the mid - and late stages of seed development or under the condition of cold stress . This kind of expressional pattern for barley Prp1 is also supported by our results of comparison of microarray data from barley , rice and Arabidopsis . For the molecular mechanism of its expressional pattern , we conclude that the expression of Prp1 gene may be up-regulated by the increase of pre-mRNAs and not be constitutive or ubiquitous .
Sentence: Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress .
Simple Events:
ID: E1 Type: Regulation Trigger: Characterization Theme: Prp1
Sentence: Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress .
Simple Events:
Sentence: In this study , we reported the identification and isolation of a novel Prp1 gene from barley , and further explored its expressional pattern by using real-time quantitative RT-PCR , promoter prediction and analysis of microarray data .
Simple Events:
Sentence: Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress .
Simple Events:
ID:E3 Type: Gene_expression Trigger: expression Theme: Prp1
Relevant Mixed Events:
ID: E2 Type: Regulation Trigger: Characterization Theme: E3
Sentence: In this study , we reported the identification and isolation of a novel Prp1 gene from barley , and further explored its expressional pattern by using real-time quantitative RT-PCR , promoter prediction and analysis of microarray data .
Simple Events:
ID: E4 Type: Gene_expression Trigger: expressional Theme: Prp1
Sentence: The results of expressional analysis revealed that the expression level of barley Prp1 gene is always stable in different vegetative tissues , except it is up-regulated at the mid - and late stages of seed development or under the condition of cold stress .
Simple Events:
Sentence: The results of expressional analysis revealed that the expression level of barley Prp1 gene is always stable in different vegetative tissues , except it is up-regulated at the mid - and late stages of seed development or under the condition of cold stress .
Simple Events:
ID: E5 Type: Gene_expression Trigger: expression Theme: Prp1
Sentence: This kind of expressional pattern for barley Prp1 is also supported by our results of comparison of microarray data from barley , rice and Arabidopsis .
Simple Events:
Sentence: This kind of expressional pattern for barley Prp1 is also supported by our results of comparison of microarray data from barley , rice and Arabidopsis .
Simple Events:
ID: E6 Type: Gene_expression Trigger: expressional Theme: Prp1
Sentence: For the molecular mechanism of its expressional pattern , we conclude that the expression of Prp1 gene may be up-regulated by the increase of pre-mRNAs and not be constitutive or ubiquitous .
Simple Events:
Original ID: 22228185
Abstract: Activation of Rice nicotianamine synthase 2 ( OsNAS2 ) enhances iron availability for biofortification . Because micronutrients in human diets ultimately come from plant sources , malnutrition of essential minerals is a significant public health concern . By increasing the expression of nicotianamine synthase ( NAS ) , we fortified the level of bioavailable iron in rice seeds . Activation of iron deficiency-inducible OsNAS2 resulted in a rise in Fe content ( 3.0-fold ) in mature seeds . Its ectopic expression also increased that content . Enhanced expression led to higher tolerance of Fe deficiency and better growth under elevated pH. . Mice fed with OsNAS2-D1 seeds recovered more rapidly from anemia , indicating that bioavailable Fe contents were improved by this increase in OsNAS2 expression .
Sentence: Mice fed with OsNAS2-D1 seeds recovered more rapidly from anemia , indicating that bioavailable Fe contents were improved by this increase in OsNAS2 expression .
Simple Events:
Original ID: 22247270
Abstract: CYP701A8 : A rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism . All higher plants contain an ent-kaurene oxidase ( KO ) , as such a cytochrome P450 CYP701 family member is required for gibberellin ( GA ) phytohormone biosynthesis . While gene expansion and functional diversification of GA biosynthesis derived diterpene synthases into more specialized metabolism has been demonstrated , no functionally divergent KO/CYP701 homologs have been previously identified . Rice ( Oryza sativa ) contains five CYP701A sub-family members in its genome , despite the fact that only one ( OsKO2/CYP701A6 ) is required for GA biosynthesis . Here we demonstrate that one of the other rice CYP701A sub-family members , OsKOL4/CYP701A8 , does not catalyze the prototypical conversion of the ent-kaurene C4alpha-methyl to a carboxylic acid , but instead carries out hydroxylation at the nearby C3alpha position in a number of related diterpenes . In particular , under conditions where OsKO2 catalyzes the expected conversion of ent-kaurene to ent-kaurenoic acid required for GA biosynthesis , OsKOL4 instead efficiently reacts with ent-sandaracopimaradiene and ent-cassadiene to produce the corresponding C3alpha-hydroxylated diterpenoids . These compounds are expected intermediates in biosynthesis of the oryzalexin and phytocassane families of rice antifungal phytoalexins , respectively , and can be detected in rice plants under the appropriate conditions . Thus , it appears that OsKOL4 plays a role in the more specialized diterpenoid metabolism of rice , and our results provide novel evidence for divergence of a KO/CYP701 family member from GA biosynthesis . This further expands the range of enzymes recruited from the ancestral GA primary pathway to the more complex and specialized labdane-related diterpenoid metabolic network found in rice .
Sentence: In particular , under conditions where OsKO2 catalyzes the expected conversion of ent-kaurene to ent-kaurenoic acid required for GA biosynthesis , OsKOL4 instead efficiently reacts with ent-sandaracopimaradiene and ent-cassadiene to produce the corresponding C3alpha-hydroxylated diterpenoids .
Simple Events:
Sentence: For the molecular mechanism of its expressional pattern , we conclude that the expression of Prp1 gene may be up-regulated by the increase of pre-mRNAs and not be constitutive or ubiquitous .
Simple Events:
ID:E7 Type: Gene_expression Trigger: expression Theme: Prp1
Relevant Mixed Events:
ID: E8 Type: Positive_regulation Trigger: up-regulated Theme: E7
Original ID: 22228185
Abstract: Activation of Rice nicotianamine synthase 2 ( OsNAS2 ) enhances iron availability for biofortification . Because micronutrients in human diets ultimately come from plant sources , malnutrition of essential minerals is a significant public health concern . By increasing the expression of nicotianamine synthase ( NAS ) , we fortified the level of bioavailable iron in rice seeds . Activation of iron deficiency-inducible OsNAS2 resulted in a rise in Fe content ( 3.0-fold ) in mature seeds . Its ectopic expression also increased that content . Enhanced expression led to higher tolerance of Fe deficiency and better growth under elevated pH. . Mice fed with OsNAS2-D1 seeds recovered more rapidly from anemia , indicating that bioavailable Fe contents were improved by this increase in OsNAS2 expression .
Sentence: Mice fed with OsNAS2-D1 seeds recovered more rapidly from anemia , indicating that bioavailable Fe contents were improved by this increase in OsNAS2 expression .
Simple Events:
ID:E2 Type: Gene_expression Trigger: expression Theme: OsNAS2
Relevant Mixed Events:
ID: E1 Type: Positive_regulation Trigger: increase Theme: E2
Original ID: 22247270
Abstract: CYP701A8 : A rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism . All higher plants contain an ent-kaurene oxidase ( KO ) , as such a cytochrome P450 CYP701 family member is required for gibberellin ( GA ) phytohormone biosynthesis . While gene expansion and functional diversification of GA biosynthesis derived diterpene synthases into more specialized metabolism has been demonstrated , no functionally divergent KO/CYP701 homologs have been previously identified . Rice ( Oryza sativa ) contains five CYP701A sub-family members in its genome , despite the fact that only one ( OsKO2/CYP701A6 ) is required for GA biosynthesis . Here we demonstrate that one of the other rice CYP701A sub-family members , OsKOL4/CYP701A8 , does not catalyze the prototypical conversion of the ent-kaurene C4alpha-methyl to a carboxylic acid , but instead carries out hydroxylation at the nearby C3alpha position in a number of related diterpenes . In particular , under conditions where OsKO2 catalyzes the expected conversion of ent-kaurene to ent-kaurenoic acid required for GA biosynthesis , OsKOL4 instead efficiently reacts with ent-sandaracopimaradiene and ent-cassadiene to produce the corresponding C3alpha-hydroxylated diterpenoids . These compounds are expected intermediates in biosynthesis of the oryzalexin and phytocassane families of rice antifungal phytoalexins , respectively , and can be detected in rice plants under the appropriate conditions . Thus , it appears that OsKOL4 plays a role in the more specialized diterpenoid metabolism of rice , and our results provide novel evidence for divergence of a KO/CYP701 family member from GA biosynthesis . This further expands the range of enzymes recruited from the ancestral GA primary pathway to the more complex and specialized labdane-related diterpenoid metabolic network found in rice .
Sentence: In particular , under conditions where OsKO2 catalyzes the expected conversion of ent-kaurene to ent-kaurenoic acid required for GA biosynthesis , OsKOL4 instead efficiently reacts with ent-sandaracopimaradiene and ent-cassadiene to produce the corresponding C3alpha-hydroxylated diterpenoids .
Simple Events:
ID: E1 Type: Binding Trigger: reacts Theme: OsKOL4
Sentence: In particular , under conditions where OsKO2 catalyzes the expected conversion of ent-kaurene to ent-kaurenoic acid required for GA biosynthesis , OsKOL4 instead efficiently reacts with ent-sandaracopimaradiene and ent-cassadiene to produce the corresponding C3alpha-hydroxylated diterpenoids .
Simple Events:
Sentence: In particular , under conditions where OsKO2 catalyzes the expected conversion of ent-kaurene to ent-kaurenoic acid required for GA biosynthesis , OsKOL4 instead efficiently reacts with ent-sandaracopimaradiene and ent-cassadiene to produce the corresponding C3alpha-hydroxylated diterpenoids .
Simple Events:
ID: E2 Type: Gene_expression Trigger: produce Theme: OsKOL4
Original ID: 22268147
Abstract: Overexpression of the aspartic protease ASPG1 gene confers drought avoidance in Arabidopsis . Drought is one of the most severe environmental stresses affecting plant growth and limiting crop production . Although many genes involved in adaptation to drought stress have been disclosed , the relevant molecular mechanisms are far from understood . This study describes an Arabidopsis gene , ASPG1 ( ASPARTIC PROTEASE IN GUARD CELL 1 ) , that may function in drought avoidance through abscisic acid ( ABA ) signalling in guard cells . Overexpression of the ASPG1 gene enhanced ABA sensitivity in guard cells and reduced water loss in ectopically overexpressing ASPG1 ( ASPG1-OE ) transgenic plants . In ASPG1-OE plants , some downstream targets in ABA and/or drought-signalling pathways were altered at various levels , suggesting the involvement of ASPG1 in ABA-dependent drought avoidance in Arabidopsis . By analyzing the activities of several antioxidases including superoxide dismutase and catalase in ASPG1-OE plants , the existence was demonstrated of an effective detoxification system for drought avoidance in these plants . Analysis of ProASPG1-GUS lines showed a predominant guard cell expression pattern in various aerial tissues . Moreover , the protease activity of ASPG1 was characterized in vitro , and two aspartic acid sites , D180 and D379 , were found to be key residues for ASPG1 aspartic protease activity in response to ABA . In summary , these findings suggest that functional ASPG1 may be involved in ABA-dependent responsiveness and that overexpression of the ASPG1 gene can confer drought avoidance in Arabidopsis .
Sentence: Moreover , the protease activity of ASPG1 was characterized in vitro , and two aspartic acid sites , D180 and D379 , were found to be key residues for ASPG1 aspartic protease activity in response to ABA .
Simple Events:
Original ID: 22268147
Abstract: Overexpression of the aspartic protease ASPG1 gene confers drought avoidance in Arabidopsis . Drought is one of the most severe environmental stresses affecting plant growth and limiting crop production . Although many genes involved in adaptation to drought stress have been disclosed , the relevant molecular mechanisms are far from understood . This study describes an Arabidopsis gene , ASPG1 ( ASPARTIC PROTEASE IN GUARD CELL 1 ) , that may function in drought avoidance through abscisic acid ( ABA ) signalling in guard cells . Overexpression of the ASPG1 gene enhanced ABA sensitivity in guard cells and reduced water loss in ectopically overexpressing ASPG1 ( ASPG1-OE ) transgenic plants . In ASPG1-OE plants , some downstream targets in ABA and/or drought-signalling pathways were altered at various levels , suggesting the involvement of ASPG1 in ABA-dependent drought avoidance in Arabidopsis . By analyzing the activities of several antioxidases including superoxide dismutase and catalase in ASPG1-OE plants , the existence was demonstrated of an effective detoxification system for drought avoidance in these plants . Analysis of ProASPG1-GUS lines showed a predominant guard cell expression pattern in various aerial tissues . Moreover , the protease activity of ASPG1 was characterized in vitro , and two aspartic acid sites , D180 and D379 , were found to be key residues for ASPG1 aspartic protease activity in response to ABA . In summary , these findings suggest that functional ASPG1 may be involved in ABA-dependent responsiveness and that overexpression of the ASPG1 gene can confer drought avoidance in Arabidopsis .
Sentence: Moreover , the protease activity of ASPG1 was characterized in vitro , and two aspartic acid sites , D180 and D379 , were found to be key residues for ASPG1 aspartic protease activity in response to ABA .
Simple Events:
ID: E1 Type: Positive_regulation Trigger: residues Theme: D180
Original ID: 22196800
Abstract: Functional complementation of dwf4 mutants of Arabidopsis by overexpression of CYP724A1 . An essential step in the biosynthesis of bioactive brassinosteroids ( BRs ) in plants is the hydroxylation at C-22 , a reaction catalyzed by P450 enzymes of the CYP90B and CYP724B subfamilies . Genes for both types of enzymes are present in many species , and in rice ( Oryza sativa ) and tomato ( Solanum lycopersicum ) both CYP90B and CYP724B enzymes contribute to C-22 hydroxylation . In Arabidopsis ( Arabidopsis thaliana ) , C-22 hydroxylation of BRs is catalyzed by CYP90B1 ( encoded by DWF4 ) and null dwf4 mutants show severe symptoms of BR-deficiency . CYP724A1 ( At5g14400 ) , an Arabidopsis gene of unknown function and limited expression , encodes a P450 sharing less than 55 % sequence identity to CYP724B proteins . We used transgenic plants of the null mutants dwf4-102 and a novel allele , bashful ( bsf ) , ectopically expressing the CYP724A1 gene to investigate the potential activity of CYP724A1 as a C-22 hydroxylase of BRs . Defects associated with BR deficiency were reversed and a normal growth habit restored in transgenic dwf4-102 and bsf plants overexpressing CYP724A1 . The vegetative phase was prolonged and the transgenic plants were on average larger than wild type plants with respect to several morphometric parameters . Fertility was restored in the transgenic plants but individual siliques yielded fewer and heavier seeds than those of wild type plants . The implications of these findings with regard to the functions of CYP724A1 and the activity of its encoded enzyme are discussed .
Sentence: Functional complementation of dwf4 mutants of Arabidopsis by overexpression of CYP724A1 .
Simple Events:
Original ID: 22312119
Abstract: QTL Analysis for Grain Quality Traits in 2 BC2F2 Populations Derived from Crosses between Oryza sativa cv Swarna and 2 Accessions of O. nivara . The appearance and cooking quality of rice determine its acceptability and price to a large extent . Quantitative trait loci ( QTLs ) for 12 grain quality traits were mapped in 2 mapping populations derived from Oryza sativa cv Swarna x O. nivara . The BC ( 2 ) F ( 2 ) population of the cross Swarna x O. nivara IRGC81848 ( population 1 ) was evaluated during 2005 and that from Swarna x O. nivara IRGC81832 ( population 2 ) was evaluated during 2006 . Linkage maps were constructed using 100 simple sequence repeat ( SSR ) markers in population 1 and 75 SSR markers in population 2 . In all , 21 QTLs were identified in population 1 ( 43 % from O. nivara ) and 37 in population 2 ( 38 % QTLs from O. nivara ) . The location of O. nivara-derived QTLs mp1 .2 for milling percent , kw6 .1 for kernel width , and klac12 .1 for kernel length after cooking coincided in the 2 populations and appear to be useful for Marker Assisted Selection ( MAS ) . Four QTLs for milling percent , 1 QTL each for amylose content , water uptake , elongation ratio , 2 QTLs for kernel width , and 3 QTLs for gel consistency , each explained more than 20 % phenotypic variance . Three QTL clusters for grain quality traits were close to the genes/QTLs for shattering and seed dormancy . QTLs for 4 quality traits were associated with 5 of the 7 major yield QTLs reported in the same 2 mapping populations . Useful introgression lines have been developed for several agronomic traits . It emerges that 40 % O. nivara alleles were trait enhancing in both populations , and QTLs for grain quality overlapped with yield meta-QTLs and QTLs for dormancy and seed shattering .
Sentence: The location of O. nivara-derived QTLs mp1 .
Simple Events:
Original ID: 22196800
Abstract: Functional complementation of dwf4 mutants of Arabidopsis by overexpression of CYP724A1 . An essential step in the biosynthesis of bioactive brassinosteroids ( BRs ) in plants is the hydroxylation at C-22 , a reaction catalyzed by P450 enzymes of the CYP90B and CYP724B subfamilies . Genes for both types of enzymes are present in many species , and in rice ( Oryza sativa ) and tomato ( Solanum lycopersicum ) both CYP90B and CYP724B enzymes contribute to C-22 hydroxylation . In Arabidopsis ( Arabidopsis thaliana ) , C-22 hydroxylation of BRs is catalyzed by CYP90B1 ( encoded by DWF4 ) and null dwf4 mutants show severe symptoms of BR-deficiency . CYP724A1 ( At5g14400 ) , an Arabidopsis gene of unknown function and limited expression , encodes a P450 sharing less than 55 % sequence identity to CYP724B proteins . We used transgenic plants of the null mutants dwf4-102 and a novel allele , bashful ( bsf ) , ectopically expressing the CYP724A1 gene to investigate the potential activity of CYP724A1 as a C-22 hydroxylase of BRs . Defects associated with BR deficiency were reversed and a normal growth habit restored in transgenic dwf4-102 and bsf plants overexpressing CYP724A1 . The vegetative phase was prolonged and the transgenic plants were on average larger than wild type plants with respect to several morphometric parameters . Fertility was restored in the transgenic plants but individual siliques yielded fewer and heavier seeds than those of wild type plants . The implications of these findings with regard to the functions of CYP724A1 and the activity of its encoded enzyme are discussed .
Sentence: Functional complementation of dwf4 mutants of Arabidopsis by overexpression of CYP724A1 .
Simple Events:
ID:E2 Type: Gene_expression Trigger: overexpression Theme: dwf4
Relevant Mixed Events:
ID: E1 Type: Positive_regulation Trigger: overexpression Theme: E2
Original ID: 22312119
Abstract: QTL Analysis for Grain Quality Traits in 2 BC2F2 Populations Derived from Crosses between Oryza sativa cv Swarna and 2 Accessions of O. nivara . The appearance and cooking quality of rice determine its acceptability and price to a large extent . Quantitative trait loci ( QTLs ) for 12 grain quality traits were mapped in 2 mapping populations derived from Oryza sativa cv Swarna x O. nivara . The BC ( 2 ) F ( 2 ) population of the cross Swarna x O. nivara IRGC81848 ( population 1 ) was evaluated during 2005 and that from Swarna x O. nivara IRGC81832 ( population 2 ) was evaluated during 2006 . Linkage maps were constructed using 100 simple sequence repeat ( SSR ) markers in population 1 and 75 SSR markers in population 2 . In all , 21 QTLs were identified in population 1 ( 43 % from O. nivara ) and 37 in population 2 ( 38 % QTLs from O. nivara ) . The location of O. nivara-derived QTLs mp1 .2 for milling percent , kw6 .1 for kernel width , and klac12 .1 for kernel length after cooking coincided in the 2 populations and appear to be useful for Marker Assisted Selection ( MAS ) . Four QTLs for milling percent , 1 QTL each for amylose content , water uptake , elongation ratio , 2 QTLs for kernel width , and 3 QTLs for gel consistency , each explained more than 20 % phenotypic variance . Three QTL clusters for grain quality traits were close to the genes/QTLs for shattering and seed dormancy . QTLs for 4 quality traits were associated with 5 of the 7 major yield QTLs reported in the same 2 mapping populations . Useful introgression lines have been developed for several agronomic traits . It emerges that 40 % O. nivara alleles were trait enhancing in both populations , and QTLs for grain quality overlapped with yield meta-QTLs and QTLs for dormancy and seed shattering .
Sentence: The location of O. nivara-derived QTLs mp1 .
Simple Events:
ID: E1 Type: Positive_regulation Trigger: nivara-derived Theme: mp1
Original ID: 22266099
Abstract: Identification of an E-box motif responsible for the expression of jasmonic acid-induced chitinase gene OsChia4a in rice . The plant hormone jasmonic acid ( JA ) is known to be involved in multiple defense responses against pathogens , which include the production of pathogenesis-related ( PR ) proteins . In order to investigate the induction mechanism of the rice defense responses by JA , we performed transcriptome analyses and focused on a chitinase gene , OsChia4a , which was identified to be one of the highest JA-inductive genes . The recombinant protein of His-tagged OsChia4a exhibited an inhibitory effect against the spore germination and hyphal growth of Magnaporthe oryzae . The promoter analysis of OsChia4a revealed that the region from -515 bp to -265 bp upstream of the ATG translation initiation site was required for the responsiveness to JA . A subsequent mutation analysis indicated that an E-box ( CANNTG ) in this region act as a JA-responsive cis element . These results imply that a basic helix-loop-helix transcription factor is likely to be involved in the regulation of the OsChia4a expression in a JA-dependent manner .
Sentence: Identification of an E-box motif responsible for the expression of jasmonic acid-induced chitinase gene OsChia4a in rice .
Simple Events:
Sentence: These results imply that a basic helix-loop-helix transcription factor is likely to be involved in the regulation of the OsChia4a expression in a JA-dependent manner .
Simple Events:
Original ID: 22207572
Abstract: Positive Autoregulation of a KNOX Gene Is Essential for Shoot Apical Meristem Maintenance in Rice . Self-maintenance of the shoot apical meristem ( SAM ) , from which aerial organs are formed throughout the life cycle , is crucial in plant development . Class I Knotted1-like homeobox ( KNOX ) genes restrict cell differentiation and play an indispensable role in maintaining the SAM . However , the mechanism that positively regulates their expression is unknown . Here , we show that expression of a rice ( Oryza sativa ) KNOX gene , Oryza sativa homeobox1 ( OSH1 ) , is positively regulated by direct autoregulation . Interestingly , loss-of-function mutants of OSH1 lose the SAM just after germination but can be rescued to grow until reproductive development when they are regenerated from callus . Double mutants of osh1 and d6 , a loss-of-function mutant of OSH15 , fail to establish the SAM both in embryogenesis and regeneration . Expression analyses in these mutants reveal that KNOX gene expression is positively regulated by the phytohormone cytokinin and by KNOX genes themselves . We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance . Thus , the maintenance of the indeterminate state mediated by positive autoregulation of a KNOX gene is an indispensable mechanism of self-maintenance of the SAM .
Sentence: Here , we show that expression of a rice ( Oryza sativa ) KNOX gene , Oryza sativa homeobox1 ( OSH1 ) , is positively regulated by direct autoregulation .
Simple Events:
Sentence: We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance .
Simple Events:
Original ID: 22266099
Abstract: Identification of an E-box motif responsible for the expression of jasmonic acid-induced chitinase gene OsChia4a in rice . The plant hormone jasmonic acid ( JA ) is known to be involved in multiple defense responses against pathogens , which include the production of pathogenesis-related ( PR ) proteins . In order to investigate the induction mechanism of the rice defense responses by JA , we performed transcriptome analyses and focused on a chitinase gene , OsChia4a , which was identified to be one of the highest JA-inductive genes . The recombinant protein of His-tagged OsChia4a exhibited an inhibitory effect against the spore germination and hyphal growth of Magnaporthe oryzae . The promoter analysis of OsChia4a revealed that the region from -515 bp to -265 bp upstream of the ATG translation initiation site was required for the responsiveness to JA . A subsequent mutation analysis indicated that an E-box ( CANNTG ) in this region act as a JA-responsive cis element . These results imply that a basic helix-loop-helix transcription factor is likely to be involved in the regulation of the OsChia4a expression in a JA-dependent manner .
Sentence: Identification of an E-box motif responsible for the expression of jasmonic acid-induced chitinase gene OsChia4a in rice .
Simple Events:
ID:E2 Type: Gene_expression Trigger: expression Theme: OsChia4a
Relevant Mixed Events:
ID: E1 Type: Regulation Trigger: responsible Theme: E2
Sentence: These results imply that a basic helix-loop-helix transcription factor is likely to be involved in the regulation of the OsChia4a expression in a JA-dependent manner .
Simple Events:
ID:E4 Type: Gene_expression Trigger: expression Theme: OsChia4a
Relevant Mixed Events:
ID: E3 Type: Regulation Trigger: regulation Theme: E4
Original ID: 22207572
Abstract: Positive Autoregulation of a KNOX Gene Is Essential for Shoot Apical Meristem Maintenance in Rice . Self-maintenance of the shoot apical meristem ( SAM ) , from which aerial organs are formed throughout the life cycle , is crucial in plant development . Class I Knotted1-like homeobox ( KNOX ) genes restrict cell differentiation and play an indispensable role in maintaining the SAM . However , the mechanism that positively regulates their expression is unknown . Here , we show that expression of a rice ( Oryza sativa ) KNOX gene , Oryza sativa homeobox1 ( OSH1 ) , is positively regulated by direct autoregulation . Interestingly , loss-of-function mutants of OSH1 lose the SAM just after germination but can be rescued to grow until reproductive development when they are regenerated from callus . Double mutants of osh1 and d6 , a loss-of-function mutant of OSH15 , fail to establish the SAM both in embryogenesis and regeneration . Expression analyses in these mutants reveal that KNOX gene expression is positively regulated by the phytohormone cytokinin and by KNOX genes themselves . We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance . Thus , the maintenance of the indeterminate state mediated by positive autoregulation of a KNOX gene is an indispensable mechanism of self-maintenance of the SAM .
Sentence: Here , we show that expression of a rice ( Oryza sativa ) KNOX gene , Oryza sativa homeobox1 ( OSH1 ) , is positively regulated by direct autoregulation .
Simple Events:
ID:E2 Type: Gene_expression Trigger: expression Theme: OSH1
Relevant Mixed Events:
ID: E1 Type: Regulation Trigger: regulated Theme: E2
Sentence: We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance .
Simple Events:
ID: E3 Type: Gene_expression Trigger: including Theme: OSH15
Sentence: We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance .
Simple Events:
Sentence: We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance .
Simple Events:
ID: E4 Type: Gene_expression Trigger: including Theme: OSH1
Sentence: We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance .
Simple Events:
Sentence: We demonstrate that OSH1 directly binds to five KNOX loci , including OSH1 and OSH15 , through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance .
Simple Events:
ID: