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Score: 11.00
Title: Infrared photodissociation of a water molecule from a flexible molecule-H ( 2 ) O complex : Rates and conformational product yields following XH stretch excitation .
Author: Clarkson JR Herbert JM Zwier TS .
Journal: Citation: V : 126 ( 13 ) P : 134306 Year: 2007 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub17430031 Accession (PMID): 17430031
Abstract: Infrared-ultraviolet hole-burning and hole-filling spectroscopies have been used to study IR-induced dissociation of the tryptamineH ( 2 ) O and tryptamineD ( 2 ) O complexes . Upon complexation of a single water molecule , the seven conformational isomers of tryptamine collapse to a single structure that retains the same ethylamine side chain conformation present in the most highly populated conformer of tryptamine monomer . Infrared excitation of the tryptamineH ( 2 ) O complex was carried out using a series of infrared absorptions spanning the range of 2470-3715 cm ( -1 ) . The authors have determined the conformational product yield over this range and the dissociation rate near threshold , where it is slow enough to be measured by our methods . The observed threshold for dissociation occurred at 2872 cm ( -1 ) in tryptamineH ( 2 ) O and at 2869 cm ( -1 ) in tryptamineD ( 2 ) O , with no dissociation occurring on the time scale of the experiment ( approximately 2 mus ) at 2745 cm ( -1 ) . The dissociation time constants varied from approximately 200 ns for the 2869 cm ( -1 ) band of tryptamineD ( 2 ) O to approximately 25 ns for the 2872 cm ( -1 ) band of tryptamineH ( 2 ) O This large isotope dependence is associated with a zero-point energy effect that increases the binding energy of the deuterated complex by approximately 190 cm ( -1 ) , thereby reducing the excess energy available at the same excitation energy . At all higher energies , the dissociation lifetime was shorter than the pulse duration of our lasers ( 8 ns ) . At all wavelengths , the observed products in the presence of collisions are dominated by conformers A and B of tryptamine monomer , with small contributions from the other minor conformers . In addition , right at threshold ( 2869 cm ( -1 ) ) , tryptamineD ( 2 ) O dissociates exclusively to conformer A in the absence of collisions with helium , while both A and B conformational products are observed in the presence of collisions with helium . Using resolution-of-identity approximation to second-order Moller-Plesset binding energies extrapolated to the complete basis set limit and harmonic vibrational frequencies and transition states calculated at the density functional limit B3LYP6-31+G ( * ) level of theory , Rice-Ramsperger-Kassel-Marcus ( RRKM ) predictions for the dissociation , isomerization , and water shuttling rates as a function of energy are made . At threshold , the experimental dissociation rate is almost 10 ( 3 ) faster than RRKM predictions . Reasons for this apparent non-RRKM behavior will be discussed .
Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Infrared-ultraviolet hole-burning and hole-filling spectroscopies have been used to study IR-induced dissociation of the tryptamineH ( 2 ) O and tryptamineD ( 2 ) O complexes .
[ Sen. 2, subscore: 2.00 ]: Upon complexation of a single water molecule , the seven conformational isomers of tryptamine collapse to a single structure that retains the same ethylamine side chain conformation present in the most highly populated conformer of tryptamine monomer .
[ Sen. 5, subscore: 2.00 ]: The observed threshold for dissociation occurred at 2872 cm ( -1 ) in tryptamineH ( 2 ) O and at 2869 cm ( -1 ) in tryptamineD ( 2 ) O , with no dissociation occurring on the time scale of the experiment ( approximately 2 mus ) at 2745 cm ( -1 ) .
[ Sen. 6, subscore: 2.00 ]: The dissociation time constants varied from approximately 200 ns for the 2869 cm ( -1 ) band of tryptamineD ( 2 ) O to approximately 25 ns for the 2872 cm ( -1 ) band of tryptamineH ( 2 ) O This large isotope dependence is associated with a zero-point energy effect that increases the binding energy of the deuterated complex by approximately 190 cm ( -1 ) , thereby reducing the excess energy available at the same excitation energy .
[ Sen. 3, subscore: 1.00 ]: Infrared excitation of the tryptamineH ( 2 ) O complex was carried out using a series of infrared absorptions spanning the range of 2470-3715 cm ( -1 ) .
[ Sen. 8, subscore: 1.00 ]: At all wavelengths , the observed products in the presence of collisions are dominated by conformers A and B of tryptamine monomer , with small contributions from the other minor conformers .
[ Sen. 9, subscore: 1.00 ]: In addition , right at threshold ( 2869 cm ( -1 ) ) , tryptamineD ( 2 ) O dissociates exclusively to conformer A in the absence of collisions with helium , while both A and B conformational products are observed in the presence of collisions with helium .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 10.00
Title: In vitro inhibition of the activation of Pro-matrix Metalloproteinase 1 ( Pro-MMP-1 ) and Pro-matrix metalloproteinase 9 ( Pro-MMP-9 ) by rice and soybean Bowman-Birk inhibitors .
Author: Bawadi HA Antunes TM Shih F Losso JN .
Journal: J Agric . Food Chem . Citation: V : 52 ( 15 ) P : 4730-6 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15264907 Accession (PMID): 15264907
Abstract: The in vitro inhibitory activity of the rice Bowman-Birk inhibitor ( rBBI ) or soybean Bowman-Birk inhibitor ( sBBI ) against trypsin-catalyzed activation of pro-matrix metalloproteinase 1 or 9 ( pro-MMP-1 or pro-MMP-9 ) , respectively , was investigated using electrophoresis with silver staining , heparin-enhanced zymography , biotinylated gelatin , Biotrak assay , and fluorescence quenched substrate hydrolysis . rBBI at concentrations of 0 . 08-0 . 352 mg/mL dose-dependently inhibited the in vitro activation of 45 microg/mL pro-MMP-1 by trypsin . Heparin-enhanced zymography analysis of pro-MMP-1 , trypsin-activated MMP-1 , and a mixture of pro-MMP-1-trypsin-rBBI showed clear zones associated with trypsin-activated MMP-1 and the absence of clear zones in lanes containing pro-MMP-1 or a mixture of pro-MMP-1 , trypsin , and rBBI . The results of the Biotrak assay also indicated that rBBI dose-dependently suppressed the activation of pro-MMP-1 by trypsin . sBBI dose-dependently inhibited the activation of 100 microg/mL of pro-MMP-9 by trypsin . Biotinylated gelatin assays demonstrated that pro-MMP-9 or pro-MMP-9 in the presence of trypsin and BBI did not hydrolyze gelatin , whereas p-aminophenylmercury acetate ( APMA ) -activated MMP-9 and trypsin-activated MMP-9 caused significant hydrolysis of gelatin . Quenched fluorescence substrate hydrolysis for total MMP activity showed that pro-MMP-1 or pro-MMP-9 did not hydrolyze the substrate Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 ; active MMP-1 or MMP-9 hydrolyzed the substrate , but lower substrate hydrolysis was obtained when pro-MMP-1 or pro-MMP-9 was incubated with trypsin in the presence of increasing concentrations of rBBI . The results are discussed in light of the role of MMP-1 and MMP-9 in the process of angiogenesis and the potential of rBBI or sBBI as a functional food ingredient .
Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: Heparin-enhanced zymography analysis of pro-MMP-1 , trypsin-activated MMP-1 , and a mixture of pro-MMP-1-trypsin-rBBI showed clear zones associated with trypsin-activated MMP-1 and the absence of clear zones in lanes containing pro-MMP-1 or a mixture of pro-MMP-1 , trypsin , and rBBI .
[ Sen. 1, subscore: 2.00 ]: The in vitro inhibitory activity of the rice Bowman-Birk inhibitor ( rBBI ) or soybean Bowman-Birk inhibitor ( sBBI ) against trypsin-catalyzed activation of pro-matrix metalloproteinase 1 or 9 ( pro-MMP-1 or pro-MMP-9 ) , respectively , was investigated using electrophoresis with silver staining , heparin-enhanced zymography , biotinylated gelatin , Biotrak assay , and fluorescence quenched substrate hydrolysis . rBBI at concentrations of 0 . 08-0 . 352 mg/mL dose-dependently inhibited the in vitro activation of 45 microg/mL pro-MMP-1 by trypsin .
[ Sen. 3, subscore: 2.00 ]: The results of the Biotrak assay also indicated that rBBI dose-dependently suppressed the activation of pro-MMP-1 by trypsin . sBBI dose-dependently inhibited the activation of 100 microg/mL of pro-MMP-9 by trypsin .
[ Sen. 4, subscore: 2.00 ]: Biotinylated gelatin assays demonstrated that pro-MMP-9 or pro-MMP-9 in the presence of trypsin and BBI did not hydrolyze gelatin , whereas p-aminophenylmercury acetate ( APMA ) -activated MMP-9 and trypsin-activated MMP-9 caused significant hydrolysis of gelatin .
[ Sen. 5, subscore: 1.00 ]: Quenched fluorescence substrate hydrolysis for total MMP activity showed that pro-MMP-1 or pro-MMP-9 did not hydrolyze the substrate Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 ; active MMP-1 or MMP-9 hydrolyzed the substrate , but lower substrate hydrolysis was obtained when pro-MMP-1 or pro-MMP-9 was incubated with trypsin in the presence of increasing concentrations of rBBI .
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Score: 10.00
Title: Probing the role of tryptophan-derived secondary metabolism in defense responses against Bipolaris oryzae infection in rice leaves by a suicide substrate of tryptophan decarboxylase .
Author: Ishihara A Nakao T Mashimo Y Murai M Ichimaru N Tanaka C Nakajima H Wakasa K Miyagawa H
Journal: Phytochemistry Citation: V : 72 P : 7-13 Year: 2011 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub21112065 Accession (PMID): 21112065
Abstract: Tryptophan-derived secondary metabolites , including serotonin and its hydroxycinnamic acid amides , markedly accumulate in rice leaves in response to pathogen attack . These compounds have been implicated in the physical defense system against pathogen invasion by being deposited in cell walls . Serotonin is biosynthesized from tryptophan via tryptamine , and tryptophan decarboxylase ( TDC ) catalyzes the first committed reaction . In this study , ( S ) -alpha- ( fluoromethyl ) tryptophan ( S-alphaFMT ) was utilized to investigate the effects of the inhibition of TDC on the defense responses of rice leaves . S-alphaFMT , enantiospecifically synthesized from L-tryptophan , effectively inhibited TDC activity extracted from rice leaves infected by Bipolaris oryzae . The inhibition rate increased dependently on the incubation time , indicating that S-alphaFMT served as a suicide substrate . Treatment of rice seedlings with S-alphaFMT suppressed accumulation of serotonin , tryptamine , and hydroxycinnamic acid amides of serotonin in a dose-dependent manner in B oryzae-inoculated leaves . The lesions formed on seedlings treated with S-alphaFMT lacked deposition of brown materials , and those leaves were severely damaged in comparison with leaves without S-alphaFMT treatment . Administrating tryptamine to S-alphaFMT-treated leaves restored accumulation of tryptophan-derived secondary metabolites as well as deposition of brown material In addition , tryptamine administration reduced damage caused by fungal infection . Accordingly , the accumulation of tryptophan-derived secondary metabolites was suggested to be part of the effective defense mechanism of rice .
Matching Sentences:
[ Sen. 3, subscore: 3.00 ]: Serotonin is biosynthesized from tryptophan via tryptamine , and tryptophan decarboxylase ( TDC ) catalyzes the first committed reaction .
[ Sen. 9, subscore: 3.00 ]: Administrating tryptamine to S-alphaFMT-treated leaves restored accumulation of tryptophan-derived secondary metabolites as well as deposition of brown material In addition , tryptamine administration reduced damage caused by fungal infection .
[ Sen. 1, subscore: 1.00 ]: Tryptophan-derived secondary metabolites , including serotonin and its hydroxycinnamic acid amides , markedly accumulate in rice leaves in response to pathogen attack .
[ Sen. 4, subscore: 1.00 ]: In this study , ( S ) -alpha- ( fluoromethyl ) tryptophan ( S-alphaFMT ) was utilized to investigate the effects of the inhibition of TDC on the defense responses of rice leaves .
[ Sen. 7, subscore: 1.00 ]: Treatment of rice seedlings with S-alphaFMT suppressed accumulation of serotonin , tryptamine , and hydroxycinnamic acid amides of serotonin in a dose-dependent manner in B oryzae-inoculated leaves .
[ Sen. 10, subscore: 1.00 ]: Accordingly , the accumulation of tryptophan-derived secondary metabolites was suggested to be part of the effective defense mechanism of rice .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 7.00
Title: Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis .
Author: Hirasawa T Yoshikawa K Nakakura Y Nagahisa K Furusawa C Katakura Y Shimizu H Shioya S
Journal: J Biotechnol Citation: V : 131 P : 34-44 Year: 2007 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17604866 Accession (PMID): 17604866
Abstract: During industrial production process using yeast , cells are exposed to the stress due to the accumulation of ethanol , which affects the cell growth activity and productivity of target products , thus , the ethanol stress-tolerant yeast strains are highly desired . To identify the target gene ( s ) for constructing ethanol stress tolerant yeast strains , we obtained the gene expression profiles of two strains of Saccharomyces cerevisiae , namely , a laboratory strain and a strain used for brewing Japanese rice wine ( sake ) , in the presence of 5% ( v/v ) ethanol , using DNA microarray . For the selection of target genes for breeding ethanol stress tolerant strains , clustering of DNA microarray data was performed . For further selection , the ethanol sensitivity of the knockout mutants in each of which the gene selected by DNA microarray analysis is deleted , was also investigated . The integration of the DNA microarray data and the ethanol sensitivity data of knockout strains suggests that the enhancement of expression of genes related to tryptophan biosynthesis might confer the ethanol stress tolerance to yeast cells . Indeed , the strains overexpressing tryptophan biosynthesis genes showed a stress tolerance to 5% ethanol . Moreover , the addition of tryptophan to the culture medium and overexpression of tryptophan permease gene conferred ethanol stress tolerance to yeast cells . These results indicate that overexpression of the genes for trypophan biosynthesis increases the ethanol stress tolerance . Tryptophan supplementation to culture and overexpression of the tryptophan permease gene are also effective for the increase in ethanol stress tolerance . Our methodology for the selection of target genes for constructing ethanol stress tolerant strains , based on the data of DNA microarray analysis and phenotypes of knockout mutants , was validated .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: Moreover , the addition of tryptophan to the culture medium and overexpression of tryptophan permease gene conferred ethanol stress tolerance to yeast cells .
[ Sen. 9, subscore: 2.00 ]: Tryptophan supplementation to culture and overexpression of the tryptophan permease gene are also effective for the increase in ethanol stress tolerance .
[ Sen. 5, subscore: 1.00 ]: The integration of the DNA microarray data and the ethanol sensitivity data of knockout strains suggests that the enhancement of expression of genes related to tryptophan biosynthesis might confer the ethanol stress tolerance to yeast cells .
[ Sen. 6, subscore: 1.00 ]: Indeed , the strains overexpressing tryptophan biosynthesis genes showed a stress tolerance to 5% ethanol .
[ Sen. 8, subscore: 1.00 ]: These results indicate that overexpression of the genes for trypophan biosynthesis increases the ethanol stress tolerance .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 7.00
Title: Serotonin accumulation in transgenic rice by over-expressing tryptophan decarboxylase results in a dark brown phenotype and stunted growth .
Author: Kanjanaphachoat P Wei BY Lo SF Wang IW Wang CS Yu SM Yen ML Chiu SH Lai CC Chen LJ
Journal: Plant Mol Biol Citation: V : 78 P : 525-43 Year: 2012 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub22297847 Accession (PMID): 22297847
Abstract: A mutant M47286 with a stunted growth , low fertility and dark-brown phenotype was identified from a T-DNA-tagged rice mutant library . This mutant contained a copy of the T-DNA tag inserted at the location where the expression of two putative tryptophan decarboxylase genes , TDC-1 and TDC-3 , were activated . Enzymatic assays of both recombinant proteins showed tryptophan decarboxylase activities that converted tryptophan to tryptamine , which could be converted to serotonin by a constitutively expressed tryptamine 5 hydroxylase ( T5H ) in rice plants . Over-expression of TDC-1 and TDC-3 in transgenic rice recapitulated the stunted growth , darkbrown phenotype and resulted in a low fertility similar to M47286 . The degree of stunted growth and dark-brown color was proportional to the expression levels of TDC-1 and TDC-3 . The levels of tryptamine and serotonin accumulation in these transgenic rice lines were also directly correlated with the expression levels of TDC-1 and TDC-3 . A mass spectrometry assay demonstrated that the darkbrown leaves and hulls in the TDC-overexpressing transgenic rice were caused by the accumulation of serotonin dimer and that the stunted growth and low fertility were also caused by the accumulation of serotonin and serotonin dimer , but not tryptamine . These results represent the first evidence that over-expression of TDC results in stunted growth , low fertility and the accumulation of serotonin , which when converted to serotonin dimer , leads to a dark brown plant color .
Matching Sentences:
[ Sen. 3, subscore: 4.00 ]: Enzymatic assays of both recombinant proteins showed tryptophan decarboxylase activities that converted tryptophan to tryptamine , which could be converted to serotonin by a constitutively expressed tryptamine 5 hydroxylase ( T5H ) in rice plants .
[ Sen. 2, subscore: 1.00 ]: This mutant contained a copy of the T-DNA tag inserted at the location where the expression of two putative tryptophan decarboxylase genes , TDC-1 and TDC-3 , were activated .
[ Sen. 6, subscore: 1.00 ]: The levels of tryptamine and serotonin accumulation in these transgenic rice lines were also directly correlated with the expression levels of TDC-1 and TDC-3 .
[ Sen. 7, subscore: 1.00 ]: A mass spectrometry assay demonstrated that the darkbrown leaves and hulls in the TDC-overexpressing transgenic rice were caused by the accumulation of serotonin dimer and that the stunted growth and low fertility were also caused by the accumulation of serotonin and serotonin dimer , but not tryptamine .
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