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| Title: Evolutionary dynamics of Ty1-copia group retrotransposons in grass shown by reverse transcriptase domain analysis .
| | Author: Matsuoka Y Tsunewaki K | | Journal: Mol . Biol . Evol Citation: V : 16 ( 2 ) P : 208-17 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10028288 Accession (PMID): 10028288 | | Abstract: The evolutionary dynamics of Ty1-copia group retrotransposons in grass were examined by reverse transcriptase ( RT ) domain analysis .
Twenty-three rice RT sequences were newly determined for this report .
Phylogenetic analysis of 177 RT sequences , mostly derived from wheat , rice , and , maize , showed four distinct families , which were designated G1 , G2 , G3 , and G4 .
Three of these families have elements obtained from distantly related species , indicative of origins prior to the radiation of grass species .
Results of Southern hybridization and detailed comparisons between the wheat and rice sequences indicated that each of the families had undergone a distinct pattern of evolution .
Multiple families appear to have evolved in parallel in a host species .
Analyses of synonymous and nonsynonymous substitutions suggested that there is a low percentage of elements carrying functional RT domains in the G4 family , indicating that the production of new G4 elements has been controlled by a small number of elements carrying functional RT domains . | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: The evolutionary dynamics of Ty1-copia group retrotransposons in grass were examined by reverse transcriptase ( RT ) domain analysis . Twenty-three rice RT sequences were newly determined for this report . Phylogenetic analysis of 177 RT sequences , mostly derived from wheat , rice , and , maize , showed four distinct families , which were designated G1 , G2 , G3 , and G4 . Three of these families have elements obtained from distantly related species , indicative of origins prior to the radiation of grass species . Results of Southern hybridization and detailed comparisons between the wheat and rice sequences indicated that each of the families had undergone a distinct pattern of evolution . Multiple families appear to have evolved in parallel in a host species . Analyses of synonymous and nonsynonymous substitutions suggested that there is a low percentage of elements carrying functional RT domains in the G4 family , indicating that the production of new G4 elements has been controlled by a small number of elements carrying functional RT domains .
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Score: 3.00 |
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| Title: Survey of fungal counts and natural occurrence of aflatoxins in Malaysian starch-based foods .
| | Author: Abdullah N Nawawi A Othman I | | Journal: Mycopathologia Citation: V : 143 ( 1 ) P : 53-8 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10205885 Accession (PMID): 10205885 | | Abstract: In a survey of starch-based foods sampled from retail outlets in Malaysia , fungal colonies were mostly detected in wheat flour ( 100% ) , followed by rice flour ( 74% ) , glutinous rice grains ( 72% ) , ordinary rice grains ( 60% ) , glutinous rice flour ( 48% ) and corn flour ( 26% ) .
All positive samples of ordinary rice and glutinous rice grains had total fungal counts below 10 ( 3 ) cfu/g sample , while among the positive rice flour , glutinous rice flour and corn flour samples , the highest total fungal count was more than 10 ( 3 ) but less than 10 ( 4 ) cfu/g sample respectively .
However , in wheat flour samples total fungal count ranged from 10 ( 2 ) cfu/g sample to slightly more than 10 ( 4 ) cfu/g sample .
Aflatoxigenic colonies were mostly detected in wheat flour ( 20% ) , followed by ordinary rice grains ( 4% ) , glutinous rice grains ( 4% ) and glutinous rice flour ( 2% ) .
No aflatoxigenic colonies were isolated from rice flour and corn flour samples .
Screening of aflatoxin B1 , aflatoxin B2 , aflatoxin G1 and aflatoxin G2 using reversed-phase HPLC were carried out on 84 samples of ordinary rice grains and 83 samples of wheat flour .
Two point four percent ( 2 . 4% ) of ordinary rice grains were positive for aflatoxin G1 and 3 . 6% were positive for aflatoxin G2 .
All the positive samples were collected from private homes at concentrations ranging from 3 . 69-77 . 50 micrograms/kg .
One point two percent ( 1 . 2% ) of wheat flour samples were positive for aflatoxin B1 at a concentration of 25 . 62 micrograms/kg , 4 . 8% were positive for aflatoxin B2 at concentrations ranging from 11 . 25-252 . 50 micrograms/kg , 3 . 6% were positive for aflatoxin G1 at concentrations ranging from 25 . 00-289 . 38 micrograms/kg and 13 . 25% were positive for aflatoxin G2 at concentrations ranging from 16 . 25-436 . 25 micrograms/kg .
Similarly , positive wheat flour samples were mostly collected from private homes .
| Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: In a survey of starch-based foods sampled from retail outlets in Malaysia , fungal colonies were mostly detected in wheat flour ( 100% ) , followed by rice flour ( 74% ) , glutinous rice grains ( 72% ) , ordinary rice grains ( 60% ) , glutinous rice flour ( 48% ) and corn flour ( 26% ) . All positive samples of ordinary rice and glutinous rice grains had total fungal counts below 10 ( 3 ) cfu/g sample , while among the positive rice flour , glutinous rice flour and corn flour samples , the highest total fungal count was more than 10 ( 3 ) but less than 10 ( 4 ) cfu/g sample respectively . However , in wheat flour samples total fungal count ranged from 10 ( 2 ) cfu/g sample to slightly more than 10 ( 4 ) cfu/g sample . Aflatoxigenic colonies were mostly detected in wheat flour ( 20% ) , followed by ordinary rice grains ( 4% ) , glutinous rice grains ( 4% ) and glutinous rice flour ( 2% ) . No aflatoxigenic colonies were isolated from rice flour and corn flour samples . Screening of aflatoxin B1 , aflatoxin B2 , aflatoxin G1 and aflatoxin G2 using reversed-phase HPLC were carried out on 84 samples of ordinary rice grains and 83 samples of wheat flour . Two point four percent ( 2 . 4% ) of ordinary rice grains were positive for aflatoxin G1 and 3 . 6% were positive for aflatoxin G2 . All the positive samples were collected from private homes at concentrations ranging from 3 . 69-77 . 50 micrograms/kg . One point two percent ( 1 . 2% ) of wheat flour samples were positive for aflatoxin B1 at a concentration of 25 . 62 micrograms/kg , 4 . 8% were positive for aflatoxin B2 at concentrations ranging from 11 . 25-252 . 50 micrograms/kg , 3 . 6% were positive for aflatoxin G1 at concentrations ranging from 25 . 00-289 . 38 micrograms/kg and 13 . 25% were positive for aflatoxin G2 at concentrations ranging from 16 . 25-436 . 25 micrograms/kg . Similarly , positive wheat flour samples were mostly collected from private homes .
[ Sen. 7, subscore: 1.00 ]: In a survey of starch-based foods sampled from retail outlets in Malaysia , fungal colonies were mostly detected in wheat flour ( 100% ) , followed by rice flour ( 74% ) , glutinous rice grains ( 72% ) , ordinary rice grains ( 60% ) , glutinous rice flour ( 48% ) and corn flour ( 26% ) . All positive samples of ordinary rice and glutinous rice grains had total fungal counts below 10 ( 3 ) cfu/g sample , while among the positive rice flour , glutinous rice flour and corn flour samples , the highest total fungal count was more than 10 ( 3 ) but less than 10 ( 4 ) cfu/g sample respectively . However , in wheat flour samples total fungal count ranged from 10 ( 2 ) cfu/g sample to slightly more than 10 ( 4 ) cfu/g sample . Aflatoxigenic colonies were mostly detected in wheat flour ( 20% ) , followed by ordinary rice grains ( 4% ) , glutinous rice grains ( 4% ) and glutinous rice flour ( 2% ) . No aflatoxigenic colonies were isolated from rice flour and corn flour samples . Screening of aflatoxin B1 , aflatoxin B2 , aflatoxin G1 and aflatoxin G2 using reversed-phase HPLC were carried out on 84 samples of ordinary rice grains and 83 samples of wheat flour . Two point four percent ( 2 . 4% ) of ordinary rice grains were positive for aflatoxin G1 and 3 . 6% were positive for aflatoxin G2 . All the positive samples were collected from private homes at concentrations ranging from 3 . 69-77 . 50 micrograms/kg . One point two percent ( 1 . 2% ) of wheat flour samples were positive for aflatoxin B1 at a concentration of 25 . 62 micrograms/kg , 4 . 8% were positive for aflatoxin B2 at concentrations ranging from 11 . 25-252 . 50 micrograms/kg , 3 . 6% were positive for aflatoxin G1 at concentrations ranging from 25 . 00-289 . 38 micrograms/kg and 13 . 25% were positive for aflatoxin G2 at concentrations ranging from 16 . 25-436 . 25 micrograms/kg . Similarly , positive wheat flour samples were mostly collected from private homes .
[ Sen. 9, subscore: 1.00 ]: In a survey of starch-based foods sampled from retail outlets in Malaysia , fungal colonies were mostly detected in wheat flour ( 100% ) , followed by rice flour ( 74% ) , glutinous rice grains ( 72% ) , ordinary rice grains ( 60% ) , glutinous rice flour ( 48% ) and corn flour ( 26% ) . All positive samples of ordinary rice and glutinous rice grains had total fungal counts below 10 ( 3 ) cfu/g sample , while among the positive rice flour , glutinous rice flour and corn flour samples , the highest total fungal count was more than 10 ( 3 ) but less than 10 ( 4 ) cfu/g sample respectively . However , in wheat flour samples total fungal count ranged from 10 ( 2 ) cfu/g sample to slightly more than 10 ( 4 ) cfu/g sample . Aflatoxigenic colonies were mostly detected in wheat flour ( 20% ) , followed by ordinary rice grains ( 4% ) , glutinous rice grains ( 4% ) and glutinous rice flour ( 2% ) . No aflatoxigenic colonies were isolated from rice flour and corn flour samples . Screening of aflatoxin B1 , aflatoxin B2 , aflatoxin G1 and aflatoxin G2 using reversed-phase HPLC were carried out on 84 samples of ordinary rice grains and 83 samples of wheat flour . Two point four percent ( 2 . 4% ) of ordinary rice grains were positive for aflatoxin G1 and 3 . 6% were positive for aflatoxin G2 . All the positive samples were collected from private homes at concentrations ranging from 3 . 69-77 . 50 micrograms/kg . One point two percent ( 1 . 2% ) of wheat flour samples were positive for aflatoxin B1 at a concentration of 25 . 62 micrograms/kg , 4 . 8% were positive for aflatoxin B2 at concentrations ranging from 11 . 25-252 . 50 micrograms/kg , 3 . 6% were positive for aflatoxin G1 at concentrations ranging from 25 . 00-289 . 38 micrograms/kg and 13 . 25% were positive for aflatoxin G2 at concentrations ranging from 16 . 25-436 . 25 micrograms/kg . Similarly , positive wheat flour samples were mostly collected from private homes .
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Score: 2.00 |
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| Title: Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships .
| | Author: Cabauatan PQ Melcher U Ishikawa K Omura T Hibino H Koganezawa H Azzam O | | Journal: J Gen . Virol . Citation: V : 80 ( Pt 8 ) ( ) P : 2229-37 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10466823 Accession (PMID): 10466823 | | Abstract: The DNA of three biological variants , G1 , Ic and G2 , which originated from the same greenhouse isolate of rice tungro bacilliform virus ( RTBV ) at the International Rice Research Institute ( IRRI ) , was cloned and sequenced .
Comparison of the sequences revealed small differences in genome sizes .
The variants were between 95 and 99% identical at the nucleotide and amino acid levels .
Alignment of the three genome sequences with those of three published RTBV sequences ( Phi-1 , Phi-2 and Phi-3 ) revealed numerous nucleotide substitutions and some insertions and deletions .
The published RTBV sequences originated from the same greenhouse isolate at IRRI 20 , 11 and 9 years ago .
All open reading frames ( ORFs ) and known functional domains were conserved across the six variants .
The cysteine-rich region of ORF3 showed the greatest variation .
When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia ( Serdang ) , similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome .
The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony , distance and maximum-likelihood methods .
The isolates clustered in three groups : Serdang alone ; Ic and G1 ; and Phi-1 , Phi-2 , Phi-3 and G2 .
The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination , as well as substitutions and insertions or deletions , has played a role in the evolution of RTBV variants .
The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The DNA of three biological variants , G1 , Ic and G2 , which originated from the same greenhouse isolate of rice tungro bacilliform virus ( RTBV ) at the International Rice Research Institute ( IRRI ) , was cloned and sequenced . Comparison of the sequences revealed small differences in genome sizes . The variants were between 95 and 99% identical at the nucleotide and amino acid levels . Alignment of the three genome sequences with those of three published RTBV sequences ( Phi-1 , Phi-2 and Phi-3 ) revealed numerous nucleotide substitutions and some insertions and deletions . The published RTBV sequences originated from the same greenhouse isolate at IRRI 20 , 11 and 9 years ago . All open reading frames ( ORFs ) and known functional domains were conserved across the six variants . The cysteine-rich region of ORF3 showed the greatest variation . When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia ( Serdang ) , similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome . The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony , distance and maximum-likelihood methods . The isolates clustered in three groups : Serdang alone ; Ic and G1 ; and Phi-1 , Phi-2 , Phi-3 and G2 .
[ Sen. 10, subscore: 1.00 ]: The DNA of three biological variants , G1 , Ic and G2 , which originated from the same greenhouse isolate of rice tungro bacilliform virus ( RTBV ) at the International Rice Research Institute ( IRRI ) , was cloned and sequenced . Comparison of the sequences revealed small differences in genome sizes . The variants were between 95 and 99% identical at the nucleotide and amino acid levels . Alignment of the three genome sequences with those of three published RTBV sequences ( Phi-1 , Phi-2 and Phi-3 ) revealed numerous nucleotide substitutions and some insertions and deletions . The published RTBV sequences originated from the same greenhouse isolate at IRRI 20 , 11 and 9 years ago . All open reading frames ( ORFs ) and known functional domains were conserved across the six variants . The cysteine-rich region of ORF3 showed the greatest variation . When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia ( Serdang ) , similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome . The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony , distance and maximum-likelihood methods . The isolates clustered in three groups : Serdang alone ; Ic and G1 ; and Phi-1 , Phi-2 , Phi-3 and G2 . The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination , as well as substitutions and insertions or deletions , has played a role in the evolution of RTBV variants . The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses .
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Score: 1.00 |
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| Title: Characterization of chimeric enzymes constructed between two distinct alpha-amylase cDNAs from cultured rice cells .
| | Author: Abe R Yoshida K Aoyagi M Kasahara S Ichishima E Nakajima T | | Journal: Biosci . Biotechnol . Biochem . Citation: V : 63 ( 8 ) P : 1329-35 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10500994 Accession (PMID): 10500994 | | Abstract: Cultured cells of rice ( Oryza sativa cv Sasanishiki ) produce two alpha-amylase isozymes , AMY-I and AMY-III .
Using a bacterial expression system , eight chimeric genes constructed with various combination of AMY-I and AMY-III cDNA fragments were expressed , and each recombinant chimeric protein was characterized .
Four of the eight recombinant enzymes having region c ( one of the four regions having unconserved base sequences between AMY-I and AMY-III cDNAs ) of AMY-I showed the same enzyme characteristics as that of native AMY-I , which had high temperature optimum at 50 degrees C The other four chimeric proteins carrying region c of AMY-III showed the AMY-III type characteristics , which were a low temperature optimum at 25 degrees C and susceptibility to a higher maltooligosaccharide ( G17 ) substrate .
The unconserved region c is involved in the decision of the characteristic of AMY-I or AMY-III . | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Cultured cells of rice ( Oryza sativa cv Sasanishiki ) produce two alpha-amylase isozymes , AMY-I and AMY-III . Using a bacterial expression system , eight chimeric genes constructed with various combination of AMY-I and AMY-III cDNA fragments were expressed , and each recombinant chimeric protein was characterized . Four of the eight recombinant enzymes having region c ( one of the four regions having unconserved base sequences between AMY-I and AMY-III cDNAs ) of AMY-I showed the same enzyme characteristics as that of native AMY-I , which had high temperature optimum at 50 degrees C The other four chimeric proteins carrying region c of AMY-III showed the AMY-III type characteristics , which were a low temperature optimum at 25 degrees C and susceptibility to a higher maltooligosaccharide ( G17 ) substrate . The unconserved region c is involved in the decision of the characteristic of AMY-I or AMY-III .
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Score: 1.00 |
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| Title: Molecular characterization of mitotic cyclins in rice plants .
| | Author: Umeda M Iwamoto N Umeda-Hara C Yamaguchi M Hashimoto J Uchimiya H | | Journal: Mol . Gen . Genet . Citation: V : 262 ( 2 ) P : 230-8 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10517318 Accession (PMID): 10517318 | | Abstract: Cyclins are known to activate cyclin-dependent protein kinases , which are essential for cell cycle progression in eukaryotes .
We isolated full-length cDNAs encoding rice mitotic cyclins named CycA1 ; os ; 1 and CycB2 ; os ; 1 , which are related to A and B-type cyclins , respectively , from animals .
To characterize the function of these mitotic cyclins , as well as that of another B-type cyclin , CycB2 ; os ; 2 , each cDNA was introduced into yeast cells .
When cDNAs encoding CycA1 ; os ; 1 , CycB2 ; os ; or CycB2 ; os ; 2 were overexpressed in the yeast mutant DLI , which is deficient in G1 cyclins , the mutant phenotype was rescued , indicating that these mitotic cyclins are functional in yeast cells .
When the cDNA encoding CycB2 ; os ; 1 was expressed in the wild-type yeast strain , the cells lost the ability to grow , whereas the expression of either cycA1 ; os : 1 or cycB2 ; os ; 2 did not inhibit growth .
In situ hybridization of these mitotic cyclin genes with rice root apices and counterstaining of chromosomes with a DNA-specific dye revealed that cycA1 ; os ; 1 is expressed from the G2 phase to the early M phase , while transcripts of cycB2 : os ; 1 and cycB2 ; os ; 2 accumulated until the end of mitosis .
Our results indicate that these B2-type cyclins may be involved in the control of mitosis , in combination with a G2/M-phase CDK . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Cyclins are known to activate cyclin-dependent protein kinases , which are essential for cell cycle progression in eukaryotes . We isolated full-length cDNAs encoding rice mitotic cyclins named CycA1 ; os ; 1 and CycB2 ; os ; 1 , which are related to A and B-type cyclins , respectively , from animals . To characterize the function of these mitotic cyclins , as well as that of another B-type cyclin , CycB2 ; os ; 2 , each cDNA was introduced into yeast cells . When cDNAs encoding CycA1 ; os ; 1 , CycB2 ; os ; or CycB2 ; os ; 2 were overexpressed in the yeast mutant DLI , which is deficient in G1 cyclins , the mutant phenotype was rescued , indicating that these mitotic cyclins are functional in yeast cells . When the cDNA encoding CycB2 ; os ; 1 was expressed in the wild-type yeast strain , the cells lost the ability to grow , whereas the expression of either cycA1 ; os : 1 or cycB2 ; os ; 2 did not inhibit growth . In situ hybridization of these mitotic cyclin genes with rice root apices and counterstaining of chromosomes with a DNA-specific dye revealed that cycA1 ; os ; 1 is expressed from the G2 phase to the early M phase , while transcripts of cycB2 : os ; 1 and cycB2 ; os ; 2 accumulated until the end of mitosis . Our results indicate that these B2-type cyclins may be involved in the control of mitosis , in combination with a G2/M-phase CDK .
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