| 279 matches found in 161 documents. Search time: 0.342 seconds. |
|---|
|
Score: 7.00 |
|---|
| Title: Molecular characterization of the largest and smallest genome segments , S1 and S12 , of Rice gall dwarf virus .
| | Author: Zhang HM Yang J Xin X Chen JP Adams MJ | | Journal: Virus Genes Citation: V : 35 P : 815-23 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17674177 Accession (PMID): 17674177 | | Abstract: The nucleotide sequences of segments S1 and S12 of a Chinese isolate of Rice gall dwarf virus ( RGDV ) were determined .
This provides the first complete sequences of these segments .
The complete sequence of S1 , the largest genome segment of RGDV , was 4 , 505 nucleotides in length and was predicted to encode a large protein of 1 , 458 amino acids with a calculated molecular mass of nearly 166 . 2 kDa .
The protein was related to that encoded by S1 of Rice dwarf virus ( RDV ; 50% identity and 67% similarity ) and ( to a lesser extent ) to some large proteins of other reoviruses .
It appears to be an RNA-dependent RNA polymerase ( RdRp ) and is probably present in particles as a minor core protein .
S12 , the smallest genome segment of RGDV , was 853 nucleotides in length , encoding a single major protein of 206 amino acids with a calculated molecular mass of nearly 23 . 6 kDa .
This protein , though a little larger than those of RDV S11 and Wound tumor virus ( WTV ) S12 in size , showed some similarity to them , especially in the conserved N-terminal region and may have RNA-binding properties .
Despite having a common host plant , RDV and RGDV were not more closely related to one another than either of them was to WTV .
Phylogenetic analysis of the RdRp showed that members of the genus Phytoreovirus were more closely related to those of the genus Rotavirus than to any other genus within the family Reoviridae .
| Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: The nucleotide sequences of segments S1 and S12 of a Chinese isolate of Rice gall dwarf virus ( RGDV ) were determined .
[ Sen. 7, subscore: 2.00 ]: This protein , though a little larger than those of RDV S11 and Wound tumor virus ( WTV ) S12 in size , showed some similarity to them , especially in the conserved N-terminal region and may have RNA-binding properties .
[ Sen. 3, subscore: 1.00 ]: The complete sequence of S1 , the largest genome segment of RGDV , was 4 , 505 nucleotides in length and was predicted to encode a large protein of 1 , 458 amino acids with a calculated molecular mass of nearly 166 . 2 kDa .
[ Sen. 4, subscore: 1.00 ]: The protein was related to that encoded by S1 of Rice dwarf virus ( RDV ; 50% identity and 67% similarity ) and ( to a lesser extent ) to some large proteins of other reoviruses .
[ Sen. 6, subscore: 1.00 ]: S12 , the smallest genome segment of RGDV , was 853 nucleotides in length , encoding a single major protein of 206 amino acids with a calculated molecular mass of nearly 23 . 6 kDa .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Isolation and 16S rRNA sequence analysis of the beneficial bacteria from the rhizosphere of rice .
| | Author: Mehnaz S Mirza MS Haurat J Bally R Normand P Bano A Malik KA .
| | Journal: Can .
J Microbiol .
Citation: V : 47 ( 2 ) P : 110-7 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11261489 Accession (PMID): 11261489 | | Abstract: The present study deals with the isolation of plant growth promoting rhizobacteria ( PGPR ) from rice ( variety NIAB IRRI-9 ) and the beneficial effects of these inoculants on two Basmati rice varieties .
Nitrogen-fixing activity ( acetylene-reduction activity ) was detected in the roots and submerged shoots of field-grown rice variety NIAB IRRI-9 .
Estimation of the population size of diazotrophic bacteria by ARA-based MPN ( acetylene reduction assay-based most probable number ) in roots and shoots indicated about 10 ( 5 ) -10 ( 6 ) counts/g dry weight at panicle initiation and grain filling stages .
Four bacterial isolates from rice roots and shoots were obtained in pure culture which produced phytohormone indoleacetic acid ( IAA ) in the growth medium .
Among these , three isolates S1 , S4 , and R3 reduced acetylene to ethylene in nitrogen-free semi-solid medium .
Morphological and physiological characteristics of the isolates indicated that three nitrogen-fixing isolates S1 , S4 , and R3 belonged to the genus Enterobacter , while the non-fixing isolate R8 belonged to the genus Aeromonas .
16S rRNA sequence of one isolate from root ( R8 ) and one isolate from shoot ( S1 ) was obtained which confirmed identification of the isolates as Aeromonas veronii and Enterobacter cloacae , respectively .
The 1517-nucleotide-long sequence of the isolate R8 showed 99% similarity with Aeromonas veronii ( accession No AF099023 ) while partial 16S rRNA sequence ( two stretches of total 1271 nucleotide length ) of S1 showed 97% similarity with the sequence of Enterobacter cloacae ( accession No AJ251469 ) .
The seedlings of two rice varieties Basmati 385 and Super Basmati were inoculated with the four bacterial isolates from rice and one Azospirillum brasilense strain Wb3 , which was isolated from wheat .
In the rice variety Basmati 385 , maximum increase in root area and plant biomass was obtained in plants inoculated with Enterobacter S1 and Azospirillum Wb3 , whereas in the rice variety Super Basmati , inoculation with Enterobacter R3 resulted in maximum increase of root area and plant biomass .
Nitrogen fixation was quantified by using 15N isotopic dilution method .
Maximum fixation was observed in Basmati 385 with the inoculants Azospirillum Wb3 and Enterobacter S1 where nearly 46% and 41% of the nitrogen was derived from atmosphere ( %Ndfa ) , respectively .
In general , higher nitrogen fixation was observed in variety Basmati 385 than in Super Basmati , and different bacterial strains were found more effective as inoculants for the rice varieties Basmati 385 and Super Basmati . | Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Among these , three isolates S1 , S4 , and R3 reduced acetylene to ethylene in nitrogen-free semi-solid medium .
[ Sen. 6, subscore: 1.00 ]: Morphological and physiological characteristics of the isolates indicated that three nitrogen-fixing isolates S1 , S4 , and R3 belonged to the genus Enterobacter , while the non-fixing isolate R8 belonged to the genus Aeromonas .
[ Sen. 7, subscore: 1.00 ]: 16S rRNA sequence of one isolate from root ( R8 ) and one isolate from shoot ( S1 ) was obtained which confirmed identification of the isolates as Aeromonas veronii and Enterobacter cloacae , respectively .
[ Sen. 8, subscore: 1.00 ]: The 1517-nucleotide-long sequence of the isolate R8 showed 99% similarity with Aeromonas veronii ( accession No AF099023 ) while partial 16S rRNA sequence ( two stretches of total 1271 nucleotide length ) of S1 showed 97% similarity with the sequence of Enterobacter cloacae ( accession No AJ251469 ) .
[ Sen. 10, subscore: 1.00 ]: In the rice variety Basmati 385 , maximum increase in root area and plant biomass was obtained in plants inoculated with Enterobacter S1 and Azospirillum Wb3 , whereas in the rice variety Super Basmati , inoculation with Enterobacter R3 resulted in maximum increase of root area and plant biomass .
[ Sen. 12, subscore: 1.00 ]: Maximum fixation was observed in Basmati 385 with the inoculants Azospirillum Wb3 and Enterobacter S1 where nearly 46% and 41% of the nitrogen was derived from atmosphere ( %Ndfa ) , respectively .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Molecular analysis of Fiji disease Fijivirus genome segments 1 and 3 .
| | Author: McQualter RB Smith GR Dale JL Harding RM .
| | Journal: Virus Genes Citation: V : 26 ( 3 ) P : 283-9 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12876456 Accession (PMID): 12876456 | | Abstract: Fiji disease fijivirus ( FDV ) genomic segments 1 ( S1 ) and 3 ( S3 ) were completely sequenced .
FDV S1 comprised 4 , 532 nt and was predicted to encode a 170 . 6 kDa protein .
FDV S3 comprised 3 , 623 nt and was predicted to encode a 135 . 5 kDa protein .
The terminal sequences of S1 and S3 were 5 AAGUUUUU . . . . . . CAGCUAGCGUC 3 and 5 AAGUUUUU . . . . . . CAGCAGAUGUC 3 , respectively , and located immediately adjacent to these sequences were 12 bp imperfect inverted repeats .
The predicted translation product of FDV S1 showed highest similarity to Rice black-streaked dwarf virus ( RBSDV ) S1 and is thought to encode the viral RNA-dependent RNA polymerase ( RdRp ) .
The predicted translation product of FDV S3 was found to be most similar to RBSDV S4 which is thought to encode the B-spike protein .
The FDV sequence contained an ATP/GTP binding motif and a leucine zipper motif , but these motifs were not found in the RBSDV sequence .
Phylogenetic analysis based on the amino acid sequences of the RdRp of FDV S1 and other reoviruses revealed that the fijiviruses form a cluster close to the oryzaviruses .
The RdRp sequences were grouped into genera that were consistent with the current reovirus classification scheme that is based on physico-chemical and biological properties .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: The predicted translation product of FDV S1 showed highest similarity to Rice black-streaked dwarf virus ( RBSDV ) S1 and is thought to encode the viral RNA-dependent RNA polymerase ( RdRp ) .
[ Sen. 1, subscore: 1.00 ]: Fiji disease fijivirus ( FDV ) genomic segments 1 ( S1 ) and 3 ( S3 ) were completely sequenced .
[ Sen. 2, subscore: 1.00 ]: FDV S1 comprised 4 , 532 nt and was predicted to encode a 170 . 6 kDa protein .
[ Sen. 4, subscore: 1.00 ]: The terminal sequences of S1 and S3 were 5 AAGUUUUU . . . . . . CAGCUAGCGUC 3 and 5 AAGUUUUU . . . . . . CAGCAGAUGUC 3 , respectively , and located immediately adjacent to these sequences were 12 bp imperfect inverted repeats .
[ Sen. 8, subscore: 1.00 ]: Phylogenetic analysis based on the amino acid sequences of the RdRp of FDV S1 and other reoviruses revealed that the fijiviruses form a cluster close to the oryzaviruses .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Circadian regulation of rice ( Oryza sativa L ) CONSTANS-like gene transcripts .
| | Author: Shin BS Lee JH Lee JH Jeong HJ Yun CH Kim JK .
| | Journal: Mol .
Cells Citation: V : 17 ( 1 ) P : 10-6 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15055520 Accession (PMID): 15055520 | | Abstract: We identified three rice cDNA clones showing amino acid similarity to the Arabidopsis CONSTANS-like proteins from a database search ( S12569 , S3574 , and C60910 ) , to examine if their transcript abundances were under circadian control .
Unlike the other two proteins , the protein encoded by the S12569 cDNA contains only one CONSTANS-like zinc finger B box , and a CCT region .
We found that the transcript levels of these rice CONSTANS-like ( COL ) genes were under circadian control .
The oscillation phase of the S12569 gene transcript was more or less opposite to those of OsGI ( rice GIGANTEA homolog ) and Hd1 ( rice COSTANS homolog ) , whereas the phases of the other two gene transcripts were similar to that of the Hd1 transcript .
S12569 mRNA started to increase about 3 h after the onset of the dark period , with a peak about 3 h after its end .
The S3574 and C60910 genes were expressed to similar extents during the vegetative and reproductive phases , like OsGI .
Higher levels of S12569 transcripts , however , like those of Hd1 , were detected in the earlier stages of panicle development .
Unlike Hd1 transcripts , S12569 , S3574 , and C60910 transcripts were present at similar levels in the aerial parts of plants and in their roots during the vegetative phase .
In conclusion , the rice COL genes showed distinctive expression patterns from the CO and COL genes , as well as Hd1 , a rice CO homolog . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: We identified three rice cDNA clones showing amino acid similarity to the Arabidopsis CONSTANS-like proteins from a database search ( S12569 , S3574 , and C60910 ) , to examine if their transcript abundances were under circadian control .
[ Sen. 2, subscore: 1.00 ]: Unlike the other two proteins , the protein encoded by the S12569 cDNA contains only one CONSTANS-like zinc finger B box , and a CCT region .
[ Sen. 4, subscore: 1.00 ]: The oscillation phase of the S12569 gene transcript was more or less opposite to those of OsGI ( rice GIGANTEA homolog ) and Hd1 ( rice COSTANS homolog ) , whereas the phases of the other two gene transcripts were similar to that of the Hd1 transcript .
[ Sen. 5, subscore: 1.00 ]: S12569 mRNA started to increase about 3 h after the onset of the dark period , with a peak about 3 h after its end .
[ Sen. 7, subscore: 1.00 ]: Higher levels of S12569 transcripts , however , like those of Hd1 , were detected in the earlier stages of panicle development .
[ Sen. 8, subscore: 1.00 ]: Unlike Hd1 transcripts , S12569 , S3574 , and C60910 transcripts were present at similar levels in the aerial parts of plants and in their roots during the vegetative phase .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Molecular analysis of six segments of Tobacco leaf enation virus , a novel phytoreovirus from tobacco | | Author: Picton A Potgieter C Rey ME .
| | Journal: Citation: V : ( ) P : Year: 2007 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17356907 Accession (PMID): 17356907 | | Abstract: Tobacco leaf enation virus ( TLEV ) is a putative member of the genus Phytoreovirus within the family Reoviridae .
Previous western blot analysis of structural viral proteins ( apparent molecular weights of 93 kDa ; 58 kDa ; 48 kDa ; 39 kDa and 36 kDa ) associated with TLEV , isolated from infected tobacco in South Africa , suggested that these proteins may correspond to structural Wound tumor virus ( WTV ) proteins .
To further establish the nature of this novel virus disease phenotype in tobacco , molecular characterization of six dsRNA components was undertaken .
Full-length cDNA clones were obtained by an optimized modified single-primer amplification sequence-independent dsRNA cloning method .
Results of this study revealed the conserved terminal sequence : 5GG ( U/C ) . . . UGAU 3 of segments S6-S12 , while adjacent to these conserved terminal sequences are imperfect inverted repeats ( 7-15 bp in length ) , both features being common to reoviruses .
The complete nucleotide sequences of segments S5 ( 2 , 610 bp ) , S7 ( 1 , 740 bp ) , S8 ( 1 , 439 bp ) , S10 ( 1 , 252 bp ) , S11 ( 1 , 187 bp ) and S12 ( 836 bp ) were determined .
Comparison of full-length nucleotide sequences with corresponding segments of other phytoreoviruses , Rice gall dwarf virus ( RGDV ) , Rice dwarf virus ( RDV ) and WTV has shown nucleotide and predicted amino acid identities within the range of 30-60% .
TLEV consistently shows a higher identity to WTV than to other phytoreovirus species where sequence data is available .
Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of S5 ( 90 . 6 kDa ) ; S7 ( 58 . 1 kDa ) ; S8 ( 47 . 7 kDa ) ; S10 ( 39 . 8 kDa ) ; S11 ( 35 kDa ) and S12 ( 19 . 5 kDa ) .
The relatively low nucleotide and amino acid identity to other members of the genus demonstrates that TLEV is a novel phytoreovirus , distinct from the only other reported dicotyledenous-infecting WTV and is the first phytoreovirus reported to emerge in Africa .
| Matching Sentences:
[ Sen. 6, subscore: 3.00 ]: The complete nucleotide sequences of segments S5 ( 2 , 610 bp ) , S7 ( 1 , 740 bp ) , S8 ( 1 , 439 bp ) , S10 ( 1 , 252 bp ) , S11 ( 1 , 187 bp ) and S12 ( 836 bp ) were determined .
[ Sen. 9, subscore: 3.00 ]: Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of S5 ( 90 . 6 kDa ) ; S7 ( 58 . 1 kDa ) ; S8 ( 47 . 7 kDa ) ; S10 ( 39 . 8 kDa ) ; S11 ( 35 kDa ) and S12 ( 19 . 5 kDa ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
