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| Title: P instability factor : an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases .
| | Author: Zhang X Feschotte C Zhang Q Jiang N Eggleston WB Wessler SR .
| | Journal: Proc . Natl . Acad . Sci . USA Citation: V : 98 ( 22 ) P : 12572-7 Year: 2001 | | Literature: oryza Field: abstract Doc ID: pub11675493 Accession (PMID): 11675493 | | Abstract: Miniature inverted-repeat transposable elements ( MITEs ) are widespread and abundant in both plant and animal genomes .
Despite the discovery and characterization of many MITE families , their origin and transposition mechanism are still poorly understood , largely because MITEs are nonautonomous elements with no coding capacity .
The starting point for this study was P instability factor ( PIF ) , an active DNA transposable element family from maize that was first identified following multiple mutagenic insertions into exactly the same site in intron 2 of the maize anthocyanin regulatory gene R In this study we report the isolation of a maize Tourist-like MITE family called miniature PIF ( mPIF ) that shares several features with PIF elements , including identical terminal inverted repeats , similar subterminal sequences , and an unusual but striking preference for an extended 9-bp target site .
These shared features indicate that mPIF and PIF elements were amplified by the same or a closely related transposase .
This transposase was identified through the isolation of several PIF elements and the identification of one element ( called PIFa ) that cosegregated with PIF activity .
PIFa encodes a putative protein with homologs in Arabidopsis , rice , sorghum , nematodes , and a fungus .
Our data suggest that PIFa and these PIF-like elements belong to a new eukaryotic DNA transposon superfamily that is distantly related to the bacterial IS5 group and are responsible for the origin and spread of Tourist-like MITEs .
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[ Sen. 3, subscore: 1.00 ]: Miniature inverted-repeat transposable elements ( MITEs ) are widespread and abundant in both plant and animal genomes . Despite the discovery and characterization of many MITE families , their origin and transposition mechanism are still poorly understood , largely because MITEs are nonautonomous elements with no coding capacity . The starting point for this study was P instability factor ( PIF ) , an active DNA transposable element family from maize that was first identified following multiple mutagenic insertions into exactly the same site in intron 2 of the maize anthocyanin regulatory gene R In this study we report the isolation of a maize Tourist-like MITE family called miniature PIF ( mPIF ) that shares several features with PIF elements , including identical terminal inverted repeats , similar subterminal sequences , and an unusual but striking preference for an extended 9-bp target site . These shared features indicate that mPIF and PIF elements were amplified by the same or a closely related transposase . This transposase was identified through the isolation of several PIF elements and the identification of one element ( called PIFa ) that cosegregated with PIF activity . PIFa encodes a putative protein with homologs in Arabidopsis , rice , sorghum , nematodes , and a fungus . Our data suggest that PIFa and these PIF-like elements belong to a new eukaryotic DNA transposon superfamily that is distantly related to the bacterial IS5 group and are responsible for the origin and spread of Tourist-like MITEs .
[ Sen. 4, subscore: 1.00 ]: Miniature inverted-repeat transposable elements ( MITEs ) are widespread and abundant in both plant and animal genomes . Despite the discovery and characterization of many MITE families , their origin and transposition mechanism are still poorly understood , largely because MITEs are nonautonomous elements with no coding capacity . The starting point for this study was P instability factor ( PIF ) , an active DNA transposable element family from maize that was first identified following multiple mutagenic insertions into exactly the same site in intron 2 of the maize anthocyanin regulatory gene R In this study we report the isolation of a maize Tourist-like MITE family called miniature PIF ( mPIF ) that shares several features with PIF elements , including identical terminal inverted repeats , similar subterminal sequences , and an unusual but striking preference for an extended 9-bp target site . These shared features indicate that mPIF and PIF elements were amplified by the same or a closely related transposase . This transposase was identified through the isolation of several PIF elements and the identification of one element ( called PIFa ) that cosegregated with PIF activity . PIFa encodes a putative protein with homologs in Arabidopsis , rice , sorghum , nematodes , and a fungus . Our data suggest that PIFa and these PIF-like elements belong to a new eukaryotic DNA transposon superfamily that is distantly related to the bacterial IS5 group and are responsible for the origin and spread of Tourist-like MITEs .
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Score: 4.00 |
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| Title: An active DNA transposon family in rice .
| | Author: Jiang N Bao Z Zhang X Hirochika H Eddy SR McCouch SR Wessler SR .
| | Journal: Nature Citation: V : 421 ( 6919 ) P : 163-7 Year: 2003 | | Literature: oryza Field: abstract Doc ID: pub12520302 Accession (PMID): 12520302 | | Abstract: The publication of draft sequences for the two subspecies of Oryza sativa ( rice ) , japonica ( cv .
Nipponbare ) and indica ( cv .
93-11 ) , provides a unique opportunity to study the dynamics of transposable elements in this important crop plant .
Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element ( MITE ) from any organism .
A sequence classified as a Tourist-like MITE of 430 base pairs , called miniature Ping ( mPing ) , was present in about 70 copies in Nipponbare and in about 14 copies in 93-11 .
These mPing elements , which are all nearly identical , transpose actively in an indica cell-culture line .
Database searches identified a family of related transposase-encoding elements ( called Pong ) , which also transpose actively in the same cells .
Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome .
Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation . | Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: The publication of draft sequences for the two subspecies of Oryza sativa ( rice ) , japonica ( cv . Nipponbare ) and indica ( cv . 93-11 ) , provides a unique opportunity to study the dynamics of transposable elements in this important crop plant . Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element ( MITE ) from any organism . A sequence classified as a Tourist-like MITE of 430 base pairs , called miniature Ping ( mPing ) , was present in about 70 copies in Nipponbare and in about 14 copies in 93-11 . These mPing elements , which are all nearly identical , transpose actively in an indica cell-culture line . Database searches identified a family of related transposase-encoding elements ( called Pong ) , which also transpose actively in the same cells . Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome . Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation .
[ Sen. 6, subscore: 1.00 ]: The publication of draft sequences for the two subspecies of Oryza sativa ( rice ) , japonica ( cv . Nipponbare ) and indica ( cv . 93-11 ) , provides a unique opportunity to study the dynamics of transposable elements in this important crop plant . Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element ( MITE ) from any organism . A sequence classified as a Tourist-like MITE of 430 base pairs , called miniature Ping ( mPing ) , was present in about 70 copies in Nipponbare and in about 14 copies in 93-11 . These mPing elements , which are all nearly identical , transpose actively in an indica cell-culture line . Database searches identified a family of related transposase-encoding elements ( called Pong ) , which also transpose actively in the same cells . Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome . Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation .
[ Sen. 8, subscore: 1.00 ]: The publication of draft sequences for the two subspecies of Oryza sativa ( rice ) , japonica ( cv . Nipponbare ) and indica ( cv . 93-11 ) , provides a unique opportunity to study the dynamics of transposable elements in this important crop plant . Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element ( MITE ) from any organism . A sequence classified as a Tourist-like MITE of 430 base pairs , called miniature Ping ( mPing ) , was present in about 70 copies in Nipponbare and in about 14 copies in 93-11 . These mPing elements , which are all nearly identical , transpose actively in an indica cell-culture line . Database searches identified a family of related transposase-encoding elements ( called Pong ) , which also transpose actively in the same cells . Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome . Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation .
[ Sen. 9, subscore: 1.00 ]: The publication of draft sequences for the two subspecies of Oryza sativa ( rice ) , japonica ( cv . Nipponbare ) and indica ( cv . 93-11 ) , provides a unique opportunity to study the dynamics of transposable elements in this important crop plant . Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element ( MITE ) from any organism . A sequence classified as a Tourist-like MITE of 430 base pairs , called miniature Ping ( mPing ) , was present in about 70 copies in Nipponbare and in about 14 copies in 93-11 . These mPing elements , which are all nearly identical , transpose actively in an indica cell-culture line . Database searches identified a family of related transposase-encoding elements ( called Pong ) , which also transpose actively in the same cells . Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome . Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation .
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Score: 3.00 |
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| Title: The plant MITE mPing is mobilized in anther culture .
| | Author: Kikuchi K Terauchi K Wada M Hirano HY .
| | Journal: Nature Citation: V : 421 ( 6919 ) P : 167-70 Year: 2003 | | Literature: oryza Field: abstract Doc ID: pub12520303 Accession (PMID): 12520303 | | Abstract: Transposable elements constitute a large portion of eukaryotic genomes and contribute to their evolution and diversification .
Miniature inverted-repeat transposable elements ( MITEs ) constitute one of the main groups of transposable elements and are distributed ubiquitously in the genomes of plants and animals such as maize , rice , Arabidopsis , human , insect and nematode .
Because active MITEs have not been identified , the transposition mechanism of MITEs and their accumulation in eukaryotic genomes remain poorly understood .
Here we describe a new class of MITE , called miniature Ping ( mPing ) , in the genome of Oryza sativa ( rice ) . mPing elements are activated in cells derived from anther culture , where they are excised efficiently from original sites and reinserted into new loci .
An mPing-associated Ping element , which has a putative PIF family transposase , is implicated in the recent proliferation of this MITE family in a subspecies of rice . | Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: Transposable elements constitute a large portion of eukaryotic genomes and contribute to their evolution and diversification . Miniature inverted-repeat transposable elements ( MITEs ) constitute one of the main groups of transposable elements and are distributed ubiquitously in the genomes of plants and animals such as maize , rice , Arabidopsis , human , insect and nematode . Because active MITEs have not been identified , the transposition mechanism of MITEs and their accumulation in eukaryotic genomes remain poorly understood . Here we describe a new class of MITE , called miniature Ping ( mPing ) , in the genome of Oryza sativa ( rice ) . mPing elements are activated in cells derived from anther culture , where they are excised efficiently from original sites and reinserted into new loci . An mPing-associated Ping element , which has a putative PIF family transposase , is implicated in the recent proliferation of this MITE family in a subspecies of rice .
[ Sen. 5, subscore: 1.00 ]: Transposable elements constitute a large portion of eukaryotic genomes and contribute to their evolution and diversification . Miniature inverted-repeat transposable elements ( MITEs ) constitute one of the main groups of transposable elements and are distributed ubiquitously in the genomes of plants and animals such as maize , rice , Arabidopsis , human , insect and nematode . Because active MITEs have not been identified , the transposition mechanism of MITEs and their accumulation in eukaryotic genomes remain poorly understood . Here we describe a new class of MITE , called miniature Ping ( mPing ) , in the genome of Oryza sativa ( rice ) . mPing elements are activated in cells derived from anther culture , where they are excised efficiently from original sites and reinserted into new loci . An mPing-associated Ping element , which has a putative PIF family transposase , is implicated in the recent proliferation of this MITE family in a subspecies of rice .
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Score: 6.00 |
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| Title: Mobilization of a transposon in the rice genome .
| | Author: Nakazaki T Okumoto Y Horibata A Yamahira S Teraishi M Nishida H Inoue H Tanisaka T | | Journal: Nature Citation: V : 421 ( 6919 ) P : 170-2 Year: 2003 | | Literature: oryza Field: abstract Doc ID: pub12520304 Accession (PMID): 12520304 | | Abstract: Rice ( Oryza sativa L ) is an important crop worldwide and , with the availability of the draft sequence , a useful model for analysing the genome structure of grasses .
To practice efficient rice breeding through genetic engineering techniques , it is important to identify the economically important genes in this crop .
The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes .
Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain .
The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele .
Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements .
Excision of mPing from slg plants results in reversion to a wild-type phenotype .
The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes . | Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: Rice ( Oryza sativa L ) is an important crop worldwide and , with the availability of the draft sequence , a useful model for analysing the genome structure of grasses . To practice efficient rice breeding through genetic engineering techniques , it is important to identify the economically important genes in this crop . The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes . Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain . The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele . Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements . Excision of mPing from slg plants results in reversion to a wild-type phenotype . The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes .
[ Sen. 4, subscore: 1.00 ]: Rice ( Oryza sativa L ) is an important crop worldwide and , with the availability of the draft sequence , a useful model for analysing the genome structure of grasses . To practice efficient rice breeding through genetic engineering techniques , it is important to identify the economically important genes in this crop . The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes . Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain . The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele . Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements . Excision of mPing from slg plants results in reversion to a wild-type phenotype . The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes .
[ Sen. 5, subscore: 1.00 ]: Rice ( Oryza sativa L ) is an important crop worldwide and , with the availability of the draft sequence , a useful model for analysing the genome structure of grasses . To practice efficient rice breeding through genetic engineering techniques , it is important to identify the economically important genes in this crop . The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes . Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain . The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele . Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements . Excision of mPing from slg plants results in reversion to a wild-type phenotype . The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes .
[ Sen. 7, subscore: 1.00 ]: Rice ( Oryza sativa L ) is an important crop worldwide and , with the availability of the draft sequence , a useful model for analysing the genome structure of grasses . To practice efficient rice breeding through genetic engineering techniques , it is important to identify the economically important genes in this crop . The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes . Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain . The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele . Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements . Excision of mPing from slg plants results in reversion to a wild-type phenotype . The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes .
[ Sen. 8, subscore: 1.00 ]: Rice ( Oryza sativa L ) is an important crop worldwide and , with the availability of the draft sequence , a useful model for analysing the genome structure of grasses . To practice efficient rice breeding through genetic engineering techniques , it is important to identify the economically important genes in this crop . The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes . Here we identify an active rice transposon named miniature Ping ( mPing ) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain . The mPing transposon is inserted in the slender glume ( slg ) mutant allele but not in the wild-type allele . Search of the O sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing , indicating that mPing constitutes a family of transposon elements . Excision of mPing from slg plants results in reversion to a wild-type phenotype . The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes .
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Score: 15.00 |
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| Title: Purification and characterization of a high molecular mass serine carboxypeptidase from Monascus pilosus .
| | Author: Liu F Tachibana S Taira T Ishihara M Kato F Yasuda M | | Journal: J Ind . Microbiol . Biotechnol . Citation: V : 31 ( 12 ) P : 572-80 Year: 2004 | | Literature: oryza Field: abstract Doc ID: pub15592905 Accession (PMID): 15592905 | | Abstract: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 .
MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa .
This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase .
The two purified enzymes were both acidic glycoproteins .
MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively .
The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 .
MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 .
Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases .
Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes .
The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 2, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 5, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 6, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 7, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 8, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 10, subscore: 2.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
[ Sen. 3, subscore: 1.00 ]: Two serine carboxypeptidases , MpiCP-1 and MpiCP-2 , were purified to homogeneity from Monascus pilosus IFO 4480 . MpiCP-1 is a homodimer with a native molecular mass of 125 kDa composed of two identical subunits of 61 kDa , while MpiCP-2 is a high mass homooligomer with a native molecular mass of 2 , 263 kDa composed of about 38 identical subunits of 59 kDa . This is unique among carboxypeptidases and distinguishes MpiCP-2 as the largest known carboxypeptidase . The two purified enzymes were both acidic glycoproteins . MpiCP-1 has an isoelectric point of 3 . 7 and a carbohydrate content of 11% , while for MpiCP-2 these values were 4 . 0 and 33% , respectively . The optimum pH and temperature were around 4 . 0 and 50 degrees C for MpiCP-1 , and 3 . 5 and 50 degrees C for MpiCP-2 . MpiCP-1 was stable over a broad range of pH between 2 . 0 and 8 . 0 at 37 degrees C for 1 h , and up to 55 degrees C for 15 min at pH 6 . 0 , but MpiCP-2 was stable in a narrow range of pH between 5 . 5 and 6 . 5 , and up to 50 degrees C for 15 min at pH 6 . 0 . Phenylmethylsulfonylfluoride strongly inhibited MpiCP-1 and completely inhibited MpiCP-2 , suggesting that they are both serine carboxypeptidases . Of the substrates tested , benzyloxycarbonyl-L : -tyrosyl-L : -glutamic acid ( Z-Tyr-Glu ) was the best for both enzymes . The Km , Vmax , Kcat and Kcat/Km values of MpiCP-1 for Z-Tyr-Glu at pH 4 . 0 and 37 degrees C were 1 . 33 mM , 1 . 49 mM min ( -1 ) , 723 s ( -1 ) and 545 mM ( -1 ) s ( -1 ) , and those of MpiCP-2 at pH 3 . 5 and 37 degrees C were 1 . 55 mM , 1 . 54 mM min ( -1 ) , 2 , 039 s ( -1 ) and 1 , 318 mM ( -1 ) s ( -1 ) , respectively .
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Score: 2.00 |
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| Title: Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice ( Zizania latifolia Griseb . ) .
| | Author: Shan X Liu Z Dong Z Wang Y Chen Y Lin X Long L Han F Dong Y Liu B | | Journal: Mol . Biol . Evol Citation: V : 22 ( 4 ) P : 976-90 Year: 2005 | | Literature: oryza Field: abstract Doc ID: pub15647520 Accession (PMID): 15647520 | | Abstract: Hybridization between different species plays an important role in plant genome evolution , as well as is a widely used approach for crop improvement .
McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated .
However , direct experimental evidence showing a causal relationship between plant wide hybridization and transposon mobilization has not yet been reported .
The miniature-Ping ( mPing ) is a recently isolated active miniature inverted-repeat transposable element transposon from rice , which is mobilized by it issue culture and gamma-ray irradiation .
We show herein that mPing , together with its putative transposase-encoding partner , Pong , is mobilized in three homologous recombinant inbred lines ( RILs ) , derived from hybridization between rice ( cultivar Matsumae ) and wild rice ( Zizania latifolia Griseb . ) , harboring introgressed genomic DNA from wild rice .
In contrast , both elements remain immobile in two lines sharing the same parentage to the RILs but possessing no introgressed DNA .
Thus , we have presented direct evidence that is consistent with McClintocks insight by demonstrating a causal link between wide hybridization and transposon mobilization in rice .
In addition , we report an atypical behavior of mPing/Pong mobilization in these lines , ie , the exclusive absence of footprints after excision . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Hybridization between different species plays an important role in plant genome evolution , as well as is a widely used approach for crop improvement . McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated . However , direct experimental evidence showing a causal relationship between plant wide hybridization and transposon mobilization has not yet been reported . The miniature-Ping ( mPing ) is a recently isolated active miniature inverted-repeat transposable element transposon from rice , which is mobilized by it issue culture and gamma-ray irradiation . We show herein that mPing , together with its putative transposase-encoding partner , Pong , is mobilized in three homologous recombinant inbred lines ( RILs ) , derived from hybridization between rice ( cultivar Matsumae ) and wild rice ( Zizania latifolia Griseb . ) , harboring introgressed genomic DNA from wild rice . In contrast , both elements remain immobile in two lines sharing the same parentage to the RILs but possessing no introgressed DNA . Thus , we have presented direct evidence that is consistent with McClintocks insight by demonstrating a causal link between wide hybridization and transposon mobilization in rice . In addition , we report an atypical behavior of mPing/Pong mobilization in these lines , ie , the exclusive absence of footprints after excision .
[ Sen. 5, subscore: 1.00 ]: Hybridization between different species plays an important role in plant genome evolution , as well as is a widely used approach for crop improvement . McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated . However , direct experimental evidence showing a causal relationship between plant wide hybridization and transposon mobilization has not yet been reported . The miniature-Ping ( mPing ) is a recently isolated active miniature inverted-repeat transposable element transposon from rice , which is mobilized by it issue culture and gamma-ray irradiation . We show herein that mPing , together with its putative transposase-encoding partner , Pong , is mobilized in three homologous recombinant inbred lines ( RILs ) , derived from hybridization between rice ( cultivar Matsumae ) and wild rice ( Zizania latifolia Griseb . ) , harboring introgressed genomic DNA from wild rice . In contrast , both elements remain immobile in two lines sharing the same parentage to the RILs but possessing no introgressed DNA . Thus , we have presented direct evidence that is consistent with McClintocks insight by demonstrating a causal link between wide hybridization and transposon mobilization in rice . In addition , we report an atypical behavior of mPing/Pong mobilization in these lines , ie , the exclusive absence of footprints after excision .
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Score: 1.00 |
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| Title: Species-specific analysis of protein sequence motifs using mutual information .
| | Author: Hummel J Keshvari N Weckwerth W Selbig J | | Journal: BMC Bioinformatics Citation: V : 6 ( ) P : 164 Year: | | Literature: oryza Field: abstract Doc ID: pub15987530 Accession (PMID): 15987530 | | Abstract: BACKGROUND : Protein sequence motifs are by definition short fragments of conserved amino acids , often associated with a specific function .
Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences .
Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions .
Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and , in particular , evolutionary features of the underlying sequences .
RESULTS : We describe the tool PROfile analysis based on Mutual Information ( PROMI ) that enables comparative analysis of user-classified protein sequences .
PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side .
On the client-side platform-independence is achieved by generally applied internet delivery standards .
As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool .
CONCLUSION : The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences .
It is available at http : //promi . mpimp-golm . mpg . de where additional documentation can be found . | Matching Sentences:
[ Sen. 10, subscore: 1.00 ]: BACKGROUND : Protein sequence motifs are by definition short fragments of conserved amino acids , often associated with a specific function . Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences . Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions . Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and , in particular , evolutionary features of the underlying sequences . RESULTS : We describe the tool PROfile analysis based on Mutual Information ( PROMI ) that enables comparative analysis of user-classified protein sequences . PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side . On the client-side platform-independence is achieved by generally applied internet delivery standards . As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool . CONCLUSION : The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences . It is available at http : //promi . mpimp-golm . mpg . de where additional documentation can be found .
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Score: 2.00 |
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| Title: Pathogen-induced production of the antifungal AFP protein from Aspergillus giganteus confers resistance to the blast fungus Magnaporthe grisea in transgenic rice .
| | Author: Moreno AB Peas G Rufat M Bravo JM Estop M Messeguer J San Segundo B | | Journal: Mol .
Plant Microbe Interact .
Citation: V : 18 ( 9 ) P : 960-72 Year: 2005 | | Literature: oryza Field: abstract Doc ID: pub16167766 Accession (PMID): 16167766 | | Abstract: Rice blast , caused by Magnaporthe grisea , is the most important fungal disease of cultivated rice worldwide .
We have developed a strategy for creating disease resistance to M grisea whereby pathogen-induced expression of the afp ( antifungal protein ) gene from Aspergillus giganteus occurs in transgenic rice plants .
Here , we evaluated the activity of the promoters from three maize pathogenesis-related ( PR ) genes , ZmPR4 , mpi , and PRms , in transgenic rice .
Chimeric gene fusions were prepared between the maize promoters and the beta-glucuronidase reporter gene ( gus A ) .
Histochemical assays of GUS activity in transgenic rice revealed that the ZmPR4 promoter is strongly induced in response to fungal infection , treatment with fungal elicitors , and mechanical wounding .
The ZmPR4 promoter is not active in the seed endosperm .
The mpi promoter also proved responsiveness to fungal infection and wounding but not to treatment with elicitors .
In contrast , no activity of the PRms promoter in leaves of transgenic rice was observed .
Transgenic plants expressing the afp gene under the control of the ZmPR4 promoter were generated .
Transformants showed resistance to M grisea at various levels .
Our results suggest that pathogen-inducible expression of the afp gene in rice plants may be a practical way for protection against the blast fungus .
Most agricultural crop species suffer from a vast array of fungal diseases that cause severe yield losses all over the world .
Rice blast , caused by the fungus Magnaporthe grisea ( Herbert ) Barr ( anamorph Pyricularia grisea ) , is the most devastating disease of cultivated rice ( Oryza sativa L ) , due to its | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Rice blast , caused by Magnaporthe grisea , is the most important fungal disease of cultivated rice worldwide . We have developed a strategy for creating disease resistance to M grisea whereby pathogen-induced expression of the afp ( antifungal protein ) gene from Aspergillus giganteus occurs in transgenic rice plants . Here , we evaluated the activity of the promoters from three maize pathogenesis-related ( PR ) genes , ZmPR4 , mpi , and PRms , in transgenic rice . Chimeric gene fusions were prepared between the maize promoters and the beta-glucuronidase reporter gene ( gus A ) . Histochemical assays of GUS activity in transgenic rice revealed that the ZmPR4 promoter is strongly induced in response to fungal infection , treatment with fungal elicitors , and mechanical wounding . The ZmPR4 promoter is not active in the seed endosperm . The mpi promoter also proved responsiveness to fungal infection and wounding but not to treatment with elicitors . In contrast , no activity of the PRms promoter in leaves of transgenic rice was observed . Transgenic plants expressing the afp gene under the control of the ZmPR4 promoter were generated . Transformants showed resistance to M grisea at various levels . Our results suggest that pathogen-inducible expression of the afp gene in rice plants may be a practical way for protection against the blast fungus . Most agricultural crop species suffer from a vast array of fungal diseases that cause severe yield losses all over the world .
[ Sen. 7, subscore: 1.00 ]: Rice blast , caused by Magnaporthe grisea , is the most important fungal disease of cultivated rice worldwide . We have developed a strategy for creating disease resistance to M grisea whereby pathogen-induced expression of the afp ( antifungal protein ) gene from Aspergillus giganteus occurs in transgenic rice plants . Here , we evaluated the activity of the promoters from three maize pathogenesis-related ( PR ) genes , ZmPR4 , mpi , and PRms , in transgenic rice . Chimeric gene fusions were prepared between the maize promoters and the beta-glucuronidase reporter gene ( gus A ) . Histochemical assays of GUS activity in transgenic rice revealed that the ZmPR4 promoter is strongly induced in response to fungal infection , treatment with fungal elicitors , and mechanical wounding . The ZmPR4 promoter is not active in the seed endosperm . The mpi promoter also proved responsiveness to fungal infection and wounding but not to treatment with elicitors . In contrast , no activity of the PRms promoter in leaves of transgenic rice was observed . Transgenic plants expressing the afp gene under the control of the ZmPR4 promoter were generated . Transformants showed resistance to M grisea at various levels . Our results suggest that pathogen-inducible expression of the afp gene in rice plants may be a practical way for protection against the blast fungus . Most agricultural crop species suffer from a vast array of fungal diseases that cause severe yield losses all over the world . Rice blast , caused by the fungus Magnaporthe grisea ( Herbert ) Barr ( anamorph Pyricularia grisea ) , is the most devastating disease of cultivated rice ( Oryza sativa L ) , due to its
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Score: 1.00 |
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| Title: Alterations in DNA methylation and genome structure in two rice mutant lines induced by high pressure .
| | Author: Shen S Wang Z Shan X Wang H Li L Lin X Long L Weng K Liu B Zou G | | Journal: Sci .
China , C , Life Sci .
Citation: V : 49 ( 2 ) P : 97-104 Year: 2006 | | Literature: oryza Field: abstract Doc ID: pub16704112 Accession (PMID): 16704112 | | Abstract: By using high-pressure treatment , two mutant lines were obtained from a genetically stable japonica rice cultivar Bijing38 .
Genomic DNA of the mutant lines , together with the original line ( Bijing38 ) , was either undigested or digested by Hpa IIMsp I , and then subjected to molecular analysis using two markers , ISSR and RAPD .
Results indicated that changes in the PCR amplification profiles of both markers are apparent in the two mutant lines compared with the original rice cultivar , suggesting that there had been both sequence changes and DNA methylation modifications in the mutant lines .
Southern blot analysis using diverse sequences , including two cellular genes ( S2 and S3 ) , a set of retrotransposons ( Osr7 , Osr36 , Tos19 and more ) , and a MITE transposon family ( mPing and Pong ) , confirmed the results , and indicated that changes in DNA methylation pattern , genomic structure , and possible activation of some transposons indeed occurred in the mutant lines .
Moreover , these changes are stably maintained through selfed generations and in different organs .
Thus , our results indicate that it is possible to obtain stable mutants in rice by high pressure treatments , and the molecular basis of the mutants may include both genetic and epigenetic changes .
Therefore , high hydrostatic pressure seems a promising approach for plant mutagenesis . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: By using high-pressure treatment , two mutant lines were obtained from a genetically stable japonica rice cultivar Bijing38 . Genomic DNA of the mutant lines , together with the original line ( Bijing38 ) , was either undigested or digested by Hpa IIMsp I , and then subjected to molecular analysis using two markers , ISSR and RAPD . Results indicated that changes in the PCR amplification profiles of both markers are apparent in the two mutant lines compared with the original rice cultivar , suggesting that there had been both sequence changes and DNA methylation modifications in the mutant lines . Southern blot analysis using diverse sequences , including two cellular genes ( S2 and S3 ) , a set of retrotransposons ( Osr7 , Osr36 , Tos19 and more ) , and a MITE transposon family ( mPing and Pong ) , confirmed the results , and indicated that changes in DNA methylation pattern , genomic structure , and possible activation of some transposons indeed occurred in the mutant lines . Moreover , these changes are stably maintained through selfed generations and in different organs . Thus , our results indicate that it is possible to obtain stable mutants in rice by high pressure treatments , and the molecular basis of the mutants may include both genetic and epigenetic changes . Therefore , high hydrostatic pressure seems a promising approach for plant mutagenesis .
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Score: 13.00 |
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| Title: In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization .
| | Author: Lin X Long L Shan X Zhang S Shen S Liu B | | Journal: J Exp . Bot . Citation: V : 57 ( 10 ) P : 2313-23 Year: | | Literature: oryza Field: abstract Doc ID: pub16818484 Accession (PMID): 16818484 | | Abstract: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation .
It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes .
Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong .
Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars .
Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants .
In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay .
Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision .
Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing .
No evidence for further mPing activity was detected in the P2 plants tested .
In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile .
Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare .
Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant . | Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare .
[ Sen. 8, subscore: 2.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
[ Sen. 1, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile .
[ Sen. 3, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
[ Sen. 4, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
[ Sen. 6, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
[ Sen. 7, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
[ Sen. 9, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
[ Sen. 10, subscore: 1.00 ]: The miniature Ping ( mPing ) is a recently discovered endogenous miniature inverted repeat transposable element ( MITE ) in rice , which can be mobilized by it issue culture or irradiation . It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
[ Sen. 11, subscore: 1.00 ]: It is reported here that mPing , together with one of its putative transposase-encoding partners , Pong , was efficiently mobilized in somatic cells of intact rice plants of two distinct cultivars derived from germinating seeds subjected to high hydrostatic pressure , whereas the other autonomous element of mPing , Ping , remained static in the plants studied . mPing excision was detected in several plants of both cultivars in the treated generation ( P0 ) , which were selected based on their novel phenotypes . Southern blot analysis and transposon-display assay on selfed progenies ( P1 generation ) of two selected P0 plants , one from each of the cultivars , revealed polymorphic banding patterns consistent with mobilization of mPing and Pong . Various mPing excisions and de novo insertions , as detected by element-bracketing , locus-specific PCR assays , occurred in the different P1 plants of both cultivars . Pong excision at one locus for each cultivar was also detected by using a Pong internal primer together with locus-specific flanking primers in the P1 plants . In contrast to the pressurized plants , immobility of both mPing and Pong in control plants , and the absence of within-cultivar heterozygosity at the analysed loci were verified by Southern blotting and/or locus-assay . Sequencing at 18 mPing empty donor sites isolated from the pressurized plants indicated properties characteristic of the element excision . Sequence-based mapping of 10 identified mPing de novo insertions from P1 progenies of pressurized plants indicated that all were in unique or low-copy regions , conforming with the targeting propensity of mPing . No evidence for further mPing activity was detected in the P2 plants tested . In spite of the high activity of mPing and Pong in the pressurized plants , amplified fragment length polymorphism ( AFLP ) analysis denoted their general genomic stability , and several potentially active retrotransposons also remained largely immobile . Further investigation showed that the same hydrostatic pressure treatments also caused mobilization of mPing in the standard laboratory cultivar for japonica rice , Nipponbare . Thus , a simple and robust approach for in planta MITE-mobilization in rice has been established by using high hydrostatic pressure treatment , which may be useful as an alternative for gene-tagging in this important crop plant .
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Score: 1.00 |
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| Title: The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE : consequences for the transposition mechanism of MITEs .
| | Author: Loot C Santiago N Sanz A Casacuberta JM .
| | Journal: Nucleic Acids Res .
Citation: V : 34 ( 18 ) P : 5238-46 Year: | | Literature: oryza Field: abstract Doc ID: pub17003053 Accession (PMID): 17003053 | | Abstract: MITEs ( miniature inverted-repeated transposable elements ) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements .
Although an active MITE , the mPing element , has recently been characterized in rice , the transposition mechanism of MITEs remains unknown .
It has been proposed that transposases of related transposons could mobilize MITEs in trans .
Moreover , it has also been proposed that the presence of conserved terminal inverted-repeated ( TIR ) sequences could be the only requirement of MITEs for mobilization , allowing divergent or unrelated elements to be mobilized by a particular transposase .
We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon , a pogo-related element , to specifically bind Emigrant elements .
This suggests that Lemi1 could mobilize Emigrant elements and makes the Lemi1/Emigrant couple an ideal system to study the transposition mechanism of MITEs .
Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs .
The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases .
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[ Sen. 2, subscore: 1.00 ]: MITEs ( miniature inverted-repeated transposable elements ) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements . Although an active MITE , the mPing element , has recently been characterized in rice , the transposition mechanism of MITEs remains unknown . It has been proposed that transposases of related transposons could mobilize MITEs in trans . Moreover , it has also been proposed that the presence of conserved terminal inverted-repeated ( TIR ) sequences could be the only requirement of MITEs for mobilization , allowing divergent or unrelated elements to be mobilized by a particular transposase . We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon , a pogo-related element , to specifically bind Emigrant elements . This suggests that Lemi1 could mobilize Emigrant elements and makes the Lemi1/Emigrant couple an ideal system to study the transposition mechanism of MITEs . Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs . The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases .
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Score: 4.00 |
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| Title: Dramatic amplification of a rice transposable element during recent domestication .
| | Author: Naito K Cho E Yang G Campbell MA Yano K Okumoto Y Tanisaka T Wessler SR .
| | Journal: Proc . Natl . Acad . Sci . USA Citation: V : 103 ( 47 ) P : 17620-5 Year: 2006 | | Literature: oryza Field: abstract Doc ID: pub17101970 Accession (PMID): 17101970 | | Abstract: Despite the prevalence of transposable elements in the genomes of higher eukaryotes , what is virtually unknown is how they amplify to very high copy numbers without killing their host Here , we report the discovery of rice strains where a miniature inverted-repeat transposable element ( mPing ) has amplified from approximately 50 to approximately 1 , 000 copies in four rice strains .
We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented .
Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors : ( i ) the rapid selection against detrimental insertions , ( ii ) the neutral or minimal effect of the remaining insertions on gene transcription , and ( iii ) the continued mobility of mPingelements in strains that already have > 1 , 000 copies .
The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice .
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[ Sen. 3, subscore: 2.00 ]: Despite the prevalence of transposable elements in the genomes of higher eukaryotes , what is virtually unknown is how they amplify to very high copy numbers without killing their host Here , we report the discovery of rice strains where a miniature inverted-repeat transposable element ( mPing ) has amplified from approximately 50 to approximately 1 , 000 copies in four rice strains . We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented . Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors : ( i ) the rapid selection against detrimental insertions , ( ii ) the neutral or minimal effect of the remaining insertions on gene transcription , and ( iii ) the continued mobility of mPingelements in strains that already have > 1 , 000 copies . The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice .
[ Sen. 1, subscore: 1.00 ]: Despite the prevalence of transposable elements in the genomes of higher eukaryotes , what is virtually unknown is how they amplify to very high copy numbers without killing their host Here , we report the discovery of rice strains where a miniature inverted-repeat transposable element ( mPing ) has amplified from approximately 50 to approximately 1 , 000 copies in four rice strains . We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented . Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors : ( i ) the rapid selection against detrimental insertions , ( ii ) the neutral or minimal effect of the remaining insertions on gene transcription , and ( iii ) the continued mobility of mPingelements in strains that already have > 1 , 000 copies . The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice .
[ Sen. 4, subscore: 1.00 ]: Despite the prevalence of transposable elements in the genomes of higher eukaryotes , what is virtually unknown is how they amplify to very high copy numbers without killing their host Here , we report the discovery of rice strains where a miniature inverted-repeat transposable element ( mPing ) has amplified from approximately 50 to approximately 1 , 000 copies in four rice strains . We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented . Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors : ( i ) the rapid selection against detrimental insertions , ( ii ) the neutral or minimal effect of the remaining insertions on gene transcription , and ( iii ) the continued mobility of mPingelements in strains that already have > 1 , 000 copies . The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice .
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Score: 2.00 |
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| Title: Bt rice harbouring cry genes controlled by a constitutive or wound-inducible promoter : protection and transgene expression under Mediterranean field conditions .
| | Author: Breitler JC Vassal JM Del Mar Catala M Meynard D MarfEV MelEE Royer M Murillo I San Segundo B Guiderdoni E Messeguer J | | Journal: Plant Biotechnol .
J Citation: V : 2 ( 5 ) P : 417-30 Year: 2004 | | Literature: oryza Field: abstract Doc ID: pub17168888 Accession (PMID): 17168888 | | Abstract: Seven homozygous transgenic lines of two European commercial cultivars of rice ( Ariete ( A ) and Senia ( S ) ) , harbouring the cry1B or cry1Aa Bacillus thuringiensis ( Bt ) delta-endotoxin genes , were field evaluated for protection from striped stem borer ( SSB ) ( Chilo suppressalis ) damage during the 2001 and 2002 summer crop seasons in the Delta de lEbre region , Spain .
The plant codon-optimized toxin gene was placed under the control of the promoter of either the constitutive ubi1 gene or the wound-inducible mpi gene from maize .
Stable , high-level , insecticidal protein accumulation was observed throughout root , leaf and seed it issues of field-grown plants harbouring the cry1B ( lines A64 . 1 , A33 . 1 , A3 . 4 and S98 . 9 ) or cry1Aa ( lines S05 . 1 and A19 . 14 ) genes under the control of the ubi1 promoter .
Conversely , no toxin was detected in unwounded vegetative it issues of the A9 . 1 line harbouring the cry1B gene controlled by the mpi promoter , indicating that natural environmental stresses did not trigger the activity of the wound-inducible promoter .
However , the toxin accumulated at 0 . 2% total soluble proteins in A9 . 1 sheath it issue exhibiting brown lesions resulting from SSB damage .
The agronomical traits and performance of the transgenic lines were generally comparable with parental controls , except in the two lines accumulating Cry1Aa , which exhibited a high frequency of plants non-true to type .
Natural infestation was assisted with manual infestations of L2/L3 SSB larvae in border control plants surrounding the experimental plots , which served as a reservoir for the second-cycle SSB population .
The observation of damage ( brown lesions and dead hearts ) during the crop season and dissection of plants at harvest stage revealed a range of protection amongst the transgenic lines , which was highly consistent with the level of toxin accumulation and with previous experience in greenhouse assays .
Lines A3 . 4 and S05 . 1 were found to exhibit stable and full protection against SSB attacks , mediated by the accumulation of Cry1B and Cry1Aa toxin , respectively , which was comparable with that afforded by the spraying of chemical insecticides on control plants .
The wound-induced A9 . 1 line exhibited a satisfactory level of protection , with a notably low level of penetration of SSB larvae in the stems , but higher external symptoms than constitutive lines , probably due to the time lag to benefit from the protective effect of Cry1B .
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[ Sen. 2, subscore: 1.00 ]: Seven homozygous transgenic lines of two European commercial cultivars of rice ( Ariete ( A ) and Senia ( S ) ) , harbouring the cry1B or cry1Aa Bacillus thuringiensis ( Bt ) delta-endotoxin genes , were field evaluated for protection from striped stem borer ( SSB ) ( Chilo suppressalis ) damage during the 2001 and 2002 summer crop seasons in the Delta de lEbre region , Spain . The plant codon-optimized toxin gene was placed under the control of the promoter of either the constitutive ubi1 gene or the wound-inducible mpi gene from maize . Stable , high-level , insecticidal protein accumulation was observed throughout root , leaf and seed it issues of field-grown plants harbouring the cry1B ( lines A64 . 1 , A33 . 1 , A3 . 4 and S98 . 9 ) or cry1Aa ( lines S05 . 1 and A19 . 14 ) genes under the control of the ubi1 promoter . Conversely , no toxin was detected in unwounded vegetative it issues of the A9 . 1 line harbouring the cry1B gene controlled by the mpi promoter , indicating that natural environmental stresses did not trigger the activity of the wound-inducible promoter . However , the toxin accumulated at 0 . 2% total soluble proteins in A9 . 1 sheath it issue exhibiting brown lesions resulting from SSB damage . The agronomical traits and performance of the transgenic lines were generally comparable with parental controls , except in the two lines accumulating Cry1Aa , which exhibited a high frequency of plants non-true to type . Natural infestation was assisted with manual infestations of L2/L3 SSB larvae in border control plants surrounding the experimental plots , which served as a reservoir for the second-cycle SSB population . The observation of damage ( brown lesions and dead hearts ) during the crop season and dissection of plants at harvest stage revealed a range of protection amongst the transgenic lines , which was highly consistent with the level of toxin accumulation and with previous experience in greenhouse assays . Lines A3 . 4 and S05 . 1 were found to exhibit stable and full protection against SSB attacks , mediated by the accumulation of Cry1B and Cry1Aa toxin , respectively , which was comparable with that afforded by the spraying of chemical insecticides on control plants . The wound-induced A9 . 1 line exhibited a satisfactory level of protection , with a notably low level of penetration of SSB larvae in the stems , but higher external symptoms than constitutive lines , probably due to the time lag to benefit from the protective effect of Cry1B .
[ Sen. 4, subscore: 1.00 ]: Seven homozygous transgenic lines of two European commercial cultivars of rice ( Ariete ( A ) and Senia ( S ) ) , harbouring the cry1B or cry1Aa Bacillus thuringiensis ( Bt ) delta-endotoxin genes , were field evaluated for protection from striped stem borer ( SSB ) ( Chilo suppressalis ) damage during the 2001 and 2002 summer crop seasons in the Delta de lEbre region , Spain . The plant codon-optimized toxin gene was placed under the control of the promoter of either the constitutive ubi1 gene or the wound-inducible mpi gene from maize . Stable , high-level , insecticidal protein accumulation was observed throughout root , leaf and seed it issues of field-grown plants harbouring the cry1B ( lines A64 . 1 , A33 . 1 , A3 . 4 and S98 . 9 ) or cry1Aa ( lines S05 . 1 and A19 . 14 ) genes under the control of the ubi1 promoter . Conversely , no toxin was detected in unwounded vegetative it issues of the A9 . 1 line harbouring the cry1B gene controlled by the mpi promoter , indicating that natural environmental stresses did not trigger the activity of the wound-inducible promoter . However , the toxin accumulated at 0 . 2% total soluble proteins in A9 . 1 sheath it issue exhibiting brown lesions resulting from SSB damage . The agronomical traits and performance of the transgenic lines were generally comparable with parental controls , except in the two lines accumulating Cry1Aa , which exhibited a high frequency of plants non-true to type . Natural infestation was assisted with manual infestations of L2/L3 SSB larvae in border control plants surrounding the experimental plots , which served as a reservoir for the second-cycle SSB population . The observation of damage ( brown lesions and dead hearts ) during the crop season and dissection of plants at harvest stage revealed a range of protection amongst the transgenic lines , which was highly consistent with the level of toxin accumulation and with previous experience in greenhouse assays . Lines A3 . 4 and S05 . 1 were found to exhibit stable and full protection against SSB attacks , mediated by the accumulation of Cry1B and Cry1Aa toxin , respectively , which was comparable with that afforded by the spraying of chemical insecticides on control plants . The wound-induced A9 . 1 line exhibited a satisfactory level of protection , with a notably low level of penetration of SSB larvae in the stems , but higher external symptoms than constitutive lines , probably due to the time lag to benefit from the protective effect of Cry1B .
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Score: 13.00 |
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| Title: Expression of the maize proteinase inhibitor ( mpi ) gene in rice plants enhances resistance against the striped stem borer ( Chilo suppressalis ) : effects on larval growth and insect gut proteinases .
| | Author: Vila L Quilis J Meynard D Breitler JC MarfEV Murillo I Vassal JM Messeguer J Guiderdoni E San Segundo B | | Journal: Plant Biotechnol .
J Citation: V : 3 ( 2 ) P : 187-202 Year: 2005 | | Literature: oryza Field: abstract Doc ID: pub17173619 Accession (PMID): 17173619 | | Abstract: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties .
Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants .
No effect on plant phenotype was observed in mpi-expressing lines .
The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed .
Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice .
In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system .
An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed .
Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth .
The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
| Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 4, subscore: 2.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 8, subscore: 2.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 1, subscore: 1.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 3, subscore: 1.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 5, subscore: 1.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 6, subscore: 1.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 7, subscore: 1.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
[ Sen. 9, subscore: 1.00 ]: The maize proteinase inhibitor ( mpi ) gene was introduced into two elite japonica rice varieties . Both constitutive expression of the mpi gene driven by the maize ubiquitin 1 promoter and wound-inducible expression of the mpi gene driven by its own promoter resulted in the accumulation of MPI protein in the transgenic plants . No effect on plant phenotype was observed in mpi-expressing lines . The stability of transgene expression through successive generations of mpi rice lines ( up to the T ( 4 ) generation ) and the production of functional MPI protein were confirmed . Expression of the mpi gene in rice enhanced resistance to the striped stem borer ( Chilo suppressalis ) , one of the most important pests of rice . In addition , transgenic mpi plants were evaluated in terms of their effects on the growth of C suppressalis larvae and the insect digestive proteolytic system . An important dose-dependent reduction of larval weight of C suppressalis larvae fed on mpi rice , compared with larvae fed on untransformed rice plants , was observed . Analysis of the digestive proteolytic activity from the gut of C suppressalis demonstrated that larvae adapted to mpi transgene expression by increasing the complement of digestive proteolytic activity : the serine and cysteine endoproteinases as well as the exopeptidases leucine aminopeptidase and carboxypeptidases A and B However , the induction of such proteolytic activity did not prevent the deleterious effects of MPI on larval growth . The introduction of the mpi gene into rice plants can thus be considered as a promising strategy to protect rice plants against striped stem borer .
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Score: 1.00 |
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| Title: A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize .
| | Author: Barret P Brinkman M Beckert M | | Journal: Genome Citation: V : 49 ( 11 ) P : 1399-407 Year: 2006 | | Literature: oryza Field: abstract Doc ID: pub17426755 Accession (PMID): 17426755 | | Abstract: Miniature inverted-repeat transposable elements ( MITEs ) are nonautonomous elements that are abundant in plant genomes .
The rice MITE mPing was shown to be mobilized by anther culture , and the associated transposon Pong was shown to transpose actively in an Oryza sativa indica rice cell-culture line .
We have identified 3 sequences in maize named ZmTPAPong-like 1 , 2 , and 3 that displayed homology with the transposase of Pong .
Here , we show that these sequences are differentially expressed during the in vitro androgenetic process in maize .
We also demonstrate that the ZmTPAPong-like 1 and 3 sequences reveal somaclonal variations among plants regenerated from the calli of a doubled haploid line .
These data suggest that the ZmTPAPong-like sequences could form part of a Zea mays element related to the rice Pong element .
The possible activation of this newly discovered element under stress conditions is discussed .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Miniature inverted-repeat transposable elements ( MITEs ) are nonautonomous elements that are abundant in plant genomes . The rice MITE mPing was shown to be mobilized by anther culture , and the associated transposon Pong was shown to transpose actively in an Oryza sativa indica rice cell-culture line . We have identified 3 sequences in maize named ZmTPAPong-like 1 , 2 , and 3 that displayed homology with the transposase of Pong . Here , we show that these sequences are differentially expressed during the in vitro androgenetic process in maize . We also demonstrate that the ZmTPAPong-like 1 and 3 sequences reveal somaclonal variations among plants regenerated from the calli of a doubled haploid line . These data suggest that the ZmTPAPong-like sequences could form part of a Zea mays element related to the rice Pong element . The possible activation of this newly discovered element under stress conditions is discussed .
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Score: 5.00 |
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| Title: Transposon display for active DNA transposons in rice .
| | Author: Takagi K Ishikawa N Maekawa M Tsugane K Iida S | | Journal: Genes Genet Syst Citation: V : 82 P : 109-22 Year: 2007 | | Literature: oryza Field: abstract Doc ID: pub17507777 Accession (PMID): 17507777 | | Abstract: Transposon display ( TD ) is a powerful technique to identify the integration site of transposons in gene tagging as a functional genomic tool for elucidating gene function .
Although active endogenous DNA transposons have been used extensively for gene tagging in maize , only two active endogenous DNA transposons in rice have been identified , the 0 . 43-kb element mPing of the MITE family and the 0 . 6-kb nDart element of the hAT family .
The nDart transposition was shown to be induced by crossing with a line containing its autonomous element aDart and stabilized by segregating aDart under natural growth conditions , while mPing-related elements were shown to transpose in cultured cells , plants regenerated from an anther culture , and gamma-ray-irradiated plants .
No somaclonal variation should occur in nDart-promoted gene tagging because no it issue culture was involved in nDart activation .
As an initial step to develop an effective tagging system using nDart in rice , we tried to visualize GC-rich nDart-related elements comprising 18 nDart-related sequences of 0 . 6-kb and 63 nDart-related elements longer than 2 kb in Nipponbare by TD .
Comparing the observed bands in TD with the anticipated virtual bands of the nDart-related elements based upon the available rice genome sequence , we have improved our TD protocol by optimizing the PCR amplification conditions and are able to visualize approximately 87% of the anticipated bands produced from the nDart-related elements .
To compare the visualization efficiency of these nDart-related elements with that of 50 mPing elements and a unique Ping sequence in Nipponbare , we also tried to visualize the mPing-related elements ; all mPing-related elements are easily visualized .
Based on these results , we discuss the parameters affecting the visualization efficiencies of these rice DNA transposons .
We also discuss the utilization of nDart elements in gene tagging for functional genomics in rice .
| Matching Sentences:
[ Sen. 7, subscore: 3.00 ]: Transposon display ( TD ) is a powerful technique to identify the integration site of transposons in gene tagging as a functional genomic tool for elucidating gene function . Although active endogenous DNA transposons have been used extensively for gene tagging in maize , only two active endogenous DNA transposons in rice have been identified , the 0 . 43-kb element mPing of the MITE family and the 0 . 6-kb nDart element of the hAT family . The nDart transposition was shown to be induced by crossing with a line containing its autonomous element aDart and stabilized by segregating aDart under natural growth conditions , while mPing-related elements were shown to transpose in cultured cells , plants regenerated from an anther culture , and gamma-ray-irradiated plants . No somaclonal variation should occur in nDart-promoted gene tagging because no it issue culture was involved in nDart activation . As an initial step to develop an effective tagging system using nDart in rice , we tried to visualize GC-rich nDart-related elements comprising 18 nDart-related sequences of 0 . 6-kb and 63 nDart-related elements longer than 2 kb in Nipponbare by TD . Comparing the observed bands in TD with the anticipated virtual bands of the nDart-related elements based upon the available rice genome sequence , we have improved our TD protocol by optimizing the PCR amplification conditions and are able to visualize approximately 87% of the anticipated bands produced from the nDart-related elements . To compare the visualization efficiency of these nDart-related elements with that of 50 mPing elements and a unique Ping sequence in Nipponbare , we also tried to visualize the mPing-related elements ; all mPing-related elements are easily visualized . Based on these results , we discuss the parameters affecting the visualization efficiencies of these rice DNA transposons . We also discuss the utilization of nDart elements in gene tagging for functional genomics in rice .
[ Sen. 2, subscore: 1.00 ]: Transposon display ( TD ) is a powerful technique to identify the integration site of transposons in gene tagging as a functional genomic tool for elucidating gene function . Although active endogenous DNA transposons have been used extensively for gene tagging in maize , only two active endogenous DNA transposons in rice have been identified , the 0 . 43-kb element mPing of the MITE family and the 0 . 6-kb nDart element of the hAT family . The nDart transposition was shown to be induced by crossing with a line containing its autonomous element aDart and stabilized by segregating aDart under natural growth conditions , while mPing-related elements were shown to transpose in cultured cells , plants regenerated from an anther culture , and gamma-ray-irradiated plants . No somaclonal variation should occur in nDart-promoted gene tagging because no it issue culture was involved in nDart activation . As an initial step to develop an effective tagging system using nDart in rice , we tried to visualize GC-rich nDart-related elements comprising 18 nDart-related sequences of 0 . 6-kb and 63 nDart-related elements longer than 2 kb in Nipponbare by TD . Comparing the observed bands in TD with the anticipated virtual bands of the nDart-related elements based upon the available rice genome sequence , we have improved our TD protocol by optimizing the PCR amplification conditions and are able to visualize approximately 87% of the anticipated bands produced from the nDart-related elements . To compare the visualization efficiency of these nDart-related elements with that of 50 mPing elements and a unique Ping sequence in Nipponbare , we also tried to visualize the mPing-related elements ; all mPing-related elements are easily visualized . Based on these results , we discuss the parameters affecting the visualization efficiencies of these rice DNA transposons . We also discuss the utilization of nDart elements in gene tagging for functional genomics in rice .
[ Sen. 3, subscore: 1.00 ]: Transposon display ( TD ) is a powerful technique to identify the integration site of transposons in gene tagging as a functional genomic tool for elucidating gene function . Although active endogenous DNA transposons have been used extensively for gene tagging in maize , only two active endogenous DNA transposons in rice have been identified , the 0 . 43-kb element mPing of the MITE family and the 0 . 6-kb nDart element of the hAT family . The nDart transposition was shown to be induced by crossing with a line containing its autonomous element aDart and stabilized by segregating aDart under natural growth conditions , while mPing-related elements were shown to transpose in cultured cells , plants regenerated from an anther culture , and gamma-ray-irradiated plants . No somaclonal variation should occur in nDart-promoted gene tagging because no it issue culture was involved in nDart activation . As an initial step to develop an effective tagging system using nDart in rice , we tried to visualize GC-rich nDart-related elements comprising 18 nDart-related sequences of 0 . 6-kb and 63 nDart-related elements longer than 2 kb in Nipponbare by TD . Comparing the observed bands in TD with the anticipated virtual bands of the nDart-related elements based upon the available rice genome sequence , we have improved our TD protocol by optimizing the PCR amplification conditions and are able to visualize approximately 87% of the anticipated bands produced from the nDart-related elements . To compare the visualization efficiency of these nDart-related elements with that of 50 mPing elements and a unique Ping sequence in Nipponbare , we also tried to visualize the mPing-related elements ; all mPing-related elements are easily visualized . Based on these results , we discuss the parameters affecting the visualization efficiencies of these rice DNA transposons . We also discuss the utilization of nDart elements in gene tagging for functional genomics in rice .
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Score: 6.00 |
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| Title: Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana .
| | Author: Yang G Zhang F Hancock CN Wessler SR | | Journal: Proc Natl Acad Sci U S A Citation: V : 104 P : 10962-7 Year: 2007 | | Literature: oryza Field: abstract Doc ID: pub17578919 Accession (PMID): 17578919 | | Abstract: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence .
The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication .
However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome .
Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript .
In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition .
Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes .
As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence . The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication . However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome . Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript . In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition . Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes . As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
[ Sen. 2, subscore: 1.00 ]: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence . The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication . However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome . Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript . In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition . Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes . As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
[ Sen. 3, subscore: 1.00 ]: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence . The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication . However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome . Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript . In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition . Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes . As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
[ Sen. 4, subscore: 1.00 ]: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence . The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication . However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome . Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript . In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition . Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes . As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
[ Sen. 5, subscore: 1.00 ]: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence . The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication . However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome . Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript . In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition . Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes . As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
[ Sen. 6, subscore: 1.00 ]: An active miniature inverted repeat transposable element ( MITE ) , mPing , was discovered by computer-assisted analysis of rice genome sequence . The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1 , 000 copies during recent domestication . However , determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome . Here , we report that mPing is active in Arabidopsis thaliana , where its transposition is catalyzed by three sources of transposase from rice : the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript . In addition to transposase , the product of a second element-encoded ORF of unknown function is also required for mPing transposition . Excision of mPing in A thaliana is usually precise , and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes . As such , this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes .
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Score: 2.00 |
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| Title: Somaclonal variation at the nucleotide sequence level in rice ( Oryza sativa L ) as revealed by RAPD and ISSR markers , and by pairwise sequence analysis .
| | Author: Ngezahayo F Dong Y Liu B | | Journal: J Appl Genet Citation: V : 48 P : 329-36 Year: 2007 | | Literature: oryza Field: abstract Doc ID: pub17998589 Accession (PMID): 17998589 | | Abstract: The nature of somaclonal variation at the nucleotide sequence level was studied in rice cv .
Nipponbare .
First , we investigated genomic variations by using 2 molecular marker systems : RAPD ( random amplified polymorphic DNA ) and ISSR ( inter-simple sequence repeat ) .
This was followed by sequencing of selected bands that represented genomic variations , and pairwise sequence analysis taking advantage of the whole genome sequence of rice .
In addition , transpositional activity of the active MITE , mPing , was analysed by locus-specific PCR amplifications .
The 2-year-old calli and their regenerated plants , analysed with 24 RAPD and 20 ISSR primers , showed moderate levels of genomic variation ( 20 . 83% and 17 . 04% , respectively ) .
To test whether DNA methylation plays a role in somaclonal variation , the calli were treated with 5-azacytidine , a chemical agent that reduces cytosine methylation by blocking the activity of DNA methyltransferase .
Though dwarfism occurred in regenerants from treated calli ( a hallmark of the drug treatment ) , there was only a slight increase in the frequency of somaclonal variation detected in the treated calli and their regenerated plants relative to untreated controls .
The transposon mPing also remained immobile in both treated and untreated calli .
Nevertheless , dendrograms constructed according to the Jaccard coefficient calculated by UPGMA of the ISSR bands revealed that the 5-azacytidine-treated and untreated somaclones were grouped into 2 distinct clusters , suggesting a possible indirect effect of the treatment on the genomic changes , depending on the marker used .
Sequence analysis indicated a low level of variation ( 0 . 31% ) , with single-base-pair substitutions predominating .
| Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: The nature of somaclonal variation at the nucleotide sequence level was studied in rice cv . Nipponbare . First , we investigated genomic variations by using 2 molecular marker systems : RAPD ( random amplified polymorphic DNA ) and ISSR ( inter-simple sequence repeat ) . This was followed by sequencing of selected bands that represented genomic variations , and pairwise sequence analysis taking advantage of the whole genome sequence of rice . In addition , transpositional activity of the active MITE , mPing , was analysed by locus-specific PCR amplifications . The 2-year-old calli and their regenerated plants , analysed with 24 RAPD and 20 ISSR primers , showed moderate levels of genomic variation ( 20 . 83% and 17 . 04% , respectively ) . To test whether DNA methylation plays a role in somaclonal variation , the calli were treated with 5-azacytidine , a chemical agent that reduces cytosine methylation by blocking the activity of DNA methyltransferase . Though dwarfism occurred in regenerants from treated calli ( a hallmark of the drug treatment ) , there was only a slight increase in the frequency of somaclonal variation detected in the treated calli and their regenerated plants relative to untreated controls . The transposon mPing also remained immobile in both treated and untreated calli . Nevertheless , dendrograms constructed according to the Jaccard coefficient calculated by UPGMA of the ISSR bands revealed that the 5-azacytidine-treated and untreated somaclones were grouped into 2 distinct clusters , suggesting a possible indirect effect of the treatment on the genomic changes , depending on the marker used . Sequence analysis indicated a low level of variation ( 0 . 31% ) , with single-base-pair substitutions predominating .
[ Sen. 9, subscore: 1.00 ]: The nature of somaclonal variation at the nucleotide sequence level was studied in rice cv . Nipponbare . First , we investigated genomic variations by using 2 molecular marker systems : RAPD ( random amplified polymorphic DNA ) and ISSR ( inter-simple sequence repeat ) . This was followed by sequencing of selected bands that represented genomic variations , and pairwise sequence analysis taking advantage of the whole genome sequence of rice . In addition , transpositional activity of the active MITE , mPing , was analysed by locus-specific PCR amplifications . The 2-year-old calli and their regenerated plants , analysed with 24 RAPD and 20 ISSR primers , showed moderate levels of genomic variation ( 20 . 83% and 17 . 04% , respectively ) . To test whether DNA methylation plays a role in somaclonal variation , the calli were treated with 5-azacytidine , a chemical agent that reduces cytosine methylation by blocking the activity of DNA methyltransferase . Though dwarfism occurred in regenerants from treated calli ( a hallmark of the drug treatment ) , there was only a slight increase in the frequency of somaclonal variation detected in the treated calli and their regenerated plants relative to untreated controls . The transposon mPing also remained immobile in both treated and untreated calli . Nevertheless , dendrograms constructed according to the Jaccard coefficient calculated by UPGMA of the ISSR bands revealed that the 5-azacytidine-treated and untreated somaclones were grouped into 2 distinct clusters , suggesting a possible indirect effect of the treatment on the genomic changes , depending on the marker used . Sequence analysis indicated a low level of variation ( 0 . 31% ) , with single-base-pair substitutions predominating .
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Score: 1.00 |
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| Title: A transposon , ping , is integrated into intron 4 of the DROOPING LEAF gene of rice , weakly reducing its expression and causing a mild drooping leaf phenotype .
| | Author: Ohmori Y Abiko M Horibata A Hirano HY | | Journal: Plant Cell Physiol Citation: V : 49 P : 1176-84 Year: 2008 | | Literature: oryza Field: abstract Doc ID: pub18593744 Accession (PMID): 18593744 | | Abstract: The YABBY gene DROOPING LEAF ( DL ) regulates midrib formation in the leaves and carpel specification in the flowers of rice ( Oryza sativa L ) .
We found a new dl allele ( dl-5 ) that caused a mild phenotype in the descendants of a mutable line , IM294 .
In plants homozygous for this allele , midrib structures were formed but their sizes were reduced .
Molecular analysis revealed that a transposon , Ping , was inserted in the fourth intron of DL .
Together with mPing and Pong , Ping is a member of a transposon family that was first identified as a group of active transposable elements in rice .
Our finding of the Ping insertion in the DL gene is a first indication that Ping is active in planta , and that it can be transposed and integrated in a new locus .
Ping seems to be still active because it was excised from intron 4 of DL at a relatively high frequency in rice calli .
Real-time PCR analysis and in situ hybridization indicated that DL transcript levels were reduced in dl-5 without alterations in the spatial expression pattern of the DL gene .
The reduction of DL expression may be due to inefficient splicing of the large intron caused by Ping insertion .
By comparing the expression levels of DL and leaf phenotypes in the dl mutants with different severities , we confirmed our previous hypothesis that DL promotes cell proliferation in the central region of leaf primordia , and that this cell proliferation is critical for midrib formation in the mature leaves .
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[ Sen. 5, subscore: 1.00 ]: The YABBY gene DROOPING LEAF ( DL ) regulates midrib formation in the leaves and carpel specification in the flowers of rice ( Oryza sativa L ) . We found a new dl allele ( dl-5 ) that caused a mild phenotype in the descendants of a mutable line , IM294 . In plants homozygous for this allele , midrib structures were formed but their sizes were reduced . Molecular analysis revealed that a transposon , Ping , was inserted in the fourth intron of DL . Together with mPing and Pong , Ping is a member of a transposon family that was first identified as a group of active transposable elements in rice . Our finding of the Ping insertion in the DL gene is a first indication that Ping is active in planta , and that it can be transposed and integrated in a new locus . Ping seems to be still active because it was excised from intron 4 of DL at a relatively high frequency in rice calli . Real-time PCR analysis and in situ hybridization indicated that DL transcript levels were reduced in dl-5 without alterations in the spatial expression pattern of the DL gene . The reduction of DL expression may be due to inefficient splicing of the large intron caused by Ping insertion . By comparing the expression levels of DL and leaf phenotypes in the dl mutants with different severities , we confirmed our previous hypothesis that DL promotes cell proliferation in the central region of leaf primordia , and that this cell proliferation is critical for midrib formation in the mature leaves .
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Score: 3.00 |
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| Title: The prediction of protein-protein interaction networks in rice blast fungus .
| | Author: He F Zhang Y Chen H Zhang Z Peng YL | | Journal: BMC Genomics Citation: V : 9 P : 519 Year: 2008 | | Literature: oryza Field: abstract Doc ID: pub18976500 Accession (PMID): 18976500 | | Abstract: BACKGROUND : Protein-protein interaction ( PPI ) maps are useful tools for investigating the cellular functions of genes .
Thus far , large-scale PPI mapping projects have not been implemented for the rice blast fungus Magnaporthe grisea , which is responsible for the most severe rice disease .
Inspired by recent advances in PPI prediction , we constructed a PPI map of this important fungus .
RESULTS : Using a well-recognized interolog approach , we have predicted 11 , 674 interactions among 3 , 017 M grisea proteins .
Although the scale of the constructed map covers approximately only one-fourth of the M griseas proteome , it is the first PPI map for this crucial organism and will therefore provide new insights into the functional genomics of the rice blast fungus .
Focusing on the network topology of proteins encoded by known pathogenicity genes , we have found that pathogenicity proteins tend to interact with higher numbers of proteins .
The pathogenicity proteins and their interacting partners in the entire network were then used to construct a subnet called a pathogenicity network .
These data may provide further clues for the study of these pathogenicity proteins .
Finally , it has been established that secreted proteins in M grisea interact with fewer proteins .
These secreted proteins and their interacting partners were also compiled into a network of secreted proteins , which may be helpful in constructing an interactome between the rice blast fungus and rice .
CONCLUSION : We predicted the PPIs of M grisea and compiled them into a database server called MPID .
It is hoped that MPID will provide new hints as to the functional genomics of this fungus .
MPID is available at http : //bioinformatics . cau . edu . cn/zzd_lab/MPID . html .
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[ Sen. 11, subscore: 1.00 ]: Thus far , large-scale PPI mapping projects have not been implemented for the rice blast fungus Magnaporthe grisea , which is responsible for the most severe rice disease . Inspired by recent advances in PPI prediction , we constructed a PPI map of this important fungus . RESULTS : Using a well-recognized interolog approach , we have predicted 11 , 674 interactions among 3 , 017 M grisea proteins . Although the scale of the constructed map covers approximately only one-fourth of the M griseas proteome , it is the first PPI map for this crucial organism and will therefore provide new insights into the functional genomics of the rice blast fungus . Focusing on the network topology of proteins encoded by known pathogenicity genes , we have found that pathogenicity proteins tend to interact with higher numbers of proteins . The pathogenicity proteins and their interacting partners in the entire network were then used to construct a subnet called a pathogenicity network . These data may provide further clues for the study of these pathogenicity proteins . Finally , it has been established that secreted proteins in M grisea interact with fewer proteins . These secreted proteins and their interacting partners were also compiled into a network of secreted proteins , which may be helpful in constructing an interactome between the rice blast fungus and rice . CONCLUSION : We predicted the PPIs of M grisea and compiled them into a database server called MPID . It is hoped that MPID will provide new hints as to the functional genomics of this fungus . MPID is available at http : //bioinformatics . cau . edu . cn/zzd_lab/MPID . html .
[ Sen. 12, subscore: 1.00 ]: Inspired by recent advances in PPI prediction , we constructed a PPI map of this important fungus . RESULTS : Using a well-recognized interolog approach , we have predicted 11 , 674 interactions among 3 , 017 M grisea proteins . Although the scale of the constructed map covers approximately only one-fourth of the M griseas proteome , it is the first PPI map for this crucial organism and will therefore provide new insights into the functional genomics of the rice blast fungus . Focusing on the network topology of proteins encoded by known pathogenicity genes , we have found that pathogenicity proteins tend to interact with higher numbers of proteins . The pathogenicity proteins and their interacting partners in the entire network were then used to construct a subnet called a pathogenicity network . These data may provide further clues for the study of these pathogenicity proteins . Finally , it has been established that secreted proteins in M grisea interact with fewer proteins . These secreted proteins and their interacting partners were also compiled into a network of secreted proteins , which may be helpful in constructing an interactome between the rice blast fungus and rice . CONCLUSION : We predicted the PPIs of M grisea and compiled them into a database server called MPID . It is hoped that MPID will provide new hints as to the functional genomics of this fungus . MPID is available at http : //bioinformatics . cau . edu . cn/zzd_lab/MPID . html .
[ Sen. 13, subscore: 1.00 ]: RESULTS : Using a well-recognized interolog approach , we have predicted 11 , 674 interactions among 3 , 017 M grisea proteins . Although the scale of the constructed map covers approximately only one-fourth of the M griseas proteome , it is the first PPI map for this crucial organism and will therefore provide new insights into the functional genomics of the rice blast fungus . Focusing on the network topology of proteins encoded by known pathogenicity genes , we have found that pathogenicity proteins tend to interact with higher numbers of proteins . The pathogenicity proteins and their interacting partners in the entire network were then used to construct a subnet called a pathogenicity network . These data may provide further clues for the study of these pathogenicity proteins . Finally , it has been established that secreted proteins in M grisea interact with fewer proteins . These secreted proteins and their interacting partners were also compiled into a network of secreted proteins , which may be helpful in constructing an interactome between the rice blast fungus and rice . CONCLUSION : We predicted the PPIs of M grisea and compiled them into a database server called MPID . It is hoped that MPID will provide new hints as to the functional genomics of this fungus . MPID is available at http : //bioinformatics . cau . edu . cn/zzd_lab/MPID . html .
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