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Score: 15.00 |
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| Title: Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach .
| | Author: Pessoa-Filho M Rangel PH Ferreira ME | | Journal: BMC Plant Biol Citation: V : 10 P : 127 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20576152 Accession (PMID): 20576152 | | Abstract: BACKGROUND : Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations .
The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes , representative of the genetic variability contained within the gene pool of a specific crop .
The eventual large size of a core collection perpetuates the problem it was originally proposed to solve .
The present study suggests that , in addition to the classic core collection concept , thematic core collections should be also developed for a specific crop , composed of a limited number of accessions , with a manageable size .
RESULTS : The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection , with , approximately , 15% of its size .
The method was compared with other methodologies based on the M strategy , and also with a core collection generated by random sampling .
Higher proportions of retained alleles ( in a core collection of equal size ) or similar proportions of retained alleles ( in a core collection of smaller size ) were detected in the two methods based on the M strategy compared to the proposed methodology .
Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity .
No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds" , for the tested sampling methods .
Effects on linkage disequilibrium between unlinked microsatellite loci , due to sampling , are discussed .
CONCLUSIONS : Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest , and then by pairwise genetic distances , estimated by DNA polymorphism analysis at molecular marker loci .
The resulting thematic core collection potentially reflects the maximum allele richness with the smallest sample size from a larger thematic collection .
As an example , we used the development of a thematic core collection for drought tolerance in rice .
It is expected that such thematic collections increase the use of germplasm by breeding programs and facilitate the study of the traits under consideration .
The definition of a core collection to study drought resistance is a valuable contribution towards the understanding of the genetic control and the physiological mechanisms involved in water use efficiency in plants .
| Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: The present study suggests that , in addition to the classic core collection concept , thematic core collections should be also developed for a specific crop , composed of a limited number of accessions , with a manageable size .
[ Sen. 5, subscore: 2.00 ]: RESULTS : The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection , with , approximately , 15% of its size .
[ Sen. 7, subscore: 2.00 ]: Higher proportions of retained alleles ( in a core collection of equal size ) or similar proportions of retained alleles ( in a core collection of smaller size ) were detected in the two methods based on the M strategy compared to the proposed methodology .
[ Sen. 12, subscore: 2.00 ]: The resulting thematic core collection potentially reflects the maximum allele richness with the smallest sample size from a larger thematic collection .
[ Sen. 2, subscore: 1.00 ]: The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes , representative of the genetic variability contained within the gene pool of a specific crop .
[ Sen. 3, subscore: 1.00 ]: The eventual large size of a core collection perpetuates the problem it was originally proposed to solve .
[ Sen. 6, subscore: 1.00 ]: The method was compared with other methodologies based on the M strategy , and also with a core collection generated by random sampling .
[ Sen. 11, subscore: 1.00 ]: CONCLUSIONS : Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest , and then by pairwise genetic distances , estimated by DNA polymorphism analysis at molecular marker loci .
[ Sen. 13, subscore: 1.00 ]: As an example , we used the development of a thematic core collection for drought tolerance in rice .
[ Sen. 14, subscore: 1.00 ]: It is expected that such thematic collections increase the use of germplasm by breeding programs and facilitate the study of the traits under consideration .
[ Sen. 15, subscore: 1.00 ]: The definition of a core collection to study drought resistance is a valuable contribution towards the understanding of the genetic control and the physiological mechanisms involved in water use efficiency in plants .
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Score: 14.00 |
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| Title: Soluble sugar availability of aerobically germinated barley , oat and rice coleoptiles in anoxia .
| | Author: Kato-Noguchi H Yasuda Y Sasaki R | | Journal: J Plant Physiol Citation: V : 167 P : 1571-6 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20727618 Accession (PMID): 20727618 | | Abstract: Physiological and metabolic responses to anoxia were compared for aerobically germinated seedlings of barley ( Hordeum vulgare ) , oat ( Avena sativa ) and rice ( Oryza sativa ) .
Coleoptile growth of barley , oat and rice seedlings was suppressed by a 24 h-anoxic stress , but the growth of the rice coleoptiles was much greater than that of the barley and oat coleoptiles .
ATP concentration in the anoxic rice coleoptiles was greater than that in the anoxic barley and oat coleoptiles .
Concentrations of ethanol and activity of alcohol dehydrogenase ( ADH ) in the anoxic rice coleoptiles were also greater than those of the anoxic barley and oat coleoptiles , suggesting that ethanolic fermentation may be more active in the rice coleoptiles than in the barley and oat coleoptiles , where glycolysis and ethanolic fermentation are the main source of ATP production .
Soluble sugar concentration in the anoxic rice coleoptiles was greater than that of the anoxic barley and oat coleoptiles .
However , alpha-amylase , which catabolizes reserve starch to soluble sugars , was active in anoxic barley , oat and rice endosperms , and soluble sugar concentration in the anoxic barley , oat and rice endosperms was not significantly different .
Therefore , anoxia stress may inhibit soluble sugar transport from the endosperms to the coleoptiles in barley and oat more than in rice .
Since the availability of soluble sugar is essential for operation of glycolysis and fermentation in plant cells , ability for sugar transport from the endosperms to the coleoptiles may be one means to distinguish the coleoptile growth of these plant species in anoxia and anoxia tolerance of these plants .
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[ Sen. 4, subscore: 4.00 ]: Concentrations of ethanol and activity of alcohol dehydrogenase ( ADH ) in the anoxic rice coleoptiles were also greater than those of the anoxic barley and oat coleoptiles , suggesting that ethanolic fermentation may be more active in the rice coleoptiles than in the barley and oat coleoptiles , where glycolysis and ethanolic fermentation are the main source of ATP production .
[ Sen. 2, subscore: 3.00 ]: Coleoptile growth of barley , oat and rice seedlings was suppressed by a 24 h-anoxic stress , but the growth of the rice coleoptiles was much greater than that of the barley and oat coleoptiles .
[ Sen. 3, subscore: 2.00 ]: ATP concentration in the anoxic rice coleoptiles was greater than that in the anoxic barley and oat coleoptiles .
[ Sen. 5, subscore: 2.00 ]: Soluble sugar concentration in the anoxic rice coleoptiles was greater than that of the anoxic barley and oat coleoptiles .
[ Sen. 8, subscore: 2.00 ]: Since the availability of soluble sugar is essential for operation of glycolysis and fermentation in plant cells , ability for sugar transport from the endosperms to the coleoptiles may be one means to distinguish the coleoptile growth of these plant species in anoxia and anoxia tolerance of these plants .
[ Sen. 7, subscore: 1.00 ]: Therefore , anoxia stress may inhibit soluble sugar transport from the endosperms to the coleoptiles in barley and oat more than in rice .
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Score: 13.00 |
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| Title: Characterization of potentially chemopreventive phenols in extracts of brown rice that inhibit the growth of human breast and colon cancer cells .
| | Author: Hudson EA Dinh PA Kokubun T Simmonds MS Gescher A | | Journal: Cancer Epidemiol .
Biomarkers Prev .
Citation: V : 9 ( 11 ) P : 1163-70 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11097223 Accession (PMID): 11097223 | | Abstract: Rice is a staple diet in Asia , where the incidence of breast and colon cancer is markedly below that in the Western world .
We investigated potential colon and breast tumor-suppressive properties of rice , testing the hypothesis that rice contains phenols that interfere with the proliferation or colony-forming ability of breast or colon cells .
Brown rice , its white milled counterpart , and bran from brown rice were boiled and extracted with ethyl acetate .
The extracts were analyzed by high pressure liquid chromatography-mass spectrometry .
Eight phenols , protocatechuic acid , p-coumaric acid , caffeic acid , ferulic acid , sinapic acid , vanillic acid , methoxycinnamic acid , and tricin , were identified in the extracts of bran and intact brown rice .
These extracts were separated into nine fractions by column chromatography .
The effect of bran extract and its fractions at 100 microg/ml on cell viability and colony-forming ability of human-derived breast and colon cell lines was assessed .
Bran extract decreased numbers of viable MDA MB 468 and HBL 100 breast cells and colon-derived SW 480 and human colonic epithelial cells as judged by the 3- ( 4 , 5-dimethylthiazol-2-yl ) -5- ( 3-carboxymethoxyphenyl ) -2- ( 4 -sulfophenyl ) -2H-tetrazolium assay .
It also reduced colony formation of SW 480 colon and MDA MB 468 breast cells .
Of the eight phenols identified in the brown rice bran , when applied at 50 microM , caffeic acid decreased numbers of all cell types except HBL 100 .
Tricin , ferulic acid , and methoxycinnamic acid interfered with cell viability in one or more cell lines .
Tricin ( 50 microM ) and the other phenols ( 200 microM ) inhibited colony formation of SW 480 cells .
Clonogenicity of MDA MB 468 cells was inhibited by caffeic acid , ferulic acid , and tricin ( 50 microM ) .
Tricin was the most potent anticlonogenic of the compounds with IC50s of 16 microM in the SW 480 colon cells and 0 . 6 microM in the MDA MB 468 breast cells .
The results suggest that : ( a ) brown rice and bran contain compounds with putative cancer chemopreventive properties ; ( b ) certain phenols contained in brown rice bran , eg , tricin , may be associated with this activity ; and ( c ) these phenols are present at much lower levels in white than in brown rice .
Thus , the consumption of rice bran or brown rice instead of milled white rice may be advantageous with respect to cancer prevention . | Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: We investigated potential colon and breast tumor-suppressive properties of rice , testing the hypothesis that rice contains phenols that interfere with the proliferation or colony-forming ability of breast or colon cells .
[ Sen. 7, subscore: 2.00 ]: The effect of bran extract and its fractions at 100 microg/ml on cell viability and colony-forming ability of human-derived breast and colon cell lines was assessed .
[ Sen. 8, subscore: 2.00 ]: Bran extract decreased numbers of viable MDA MB 468 and HBL 100 breast cells and colon-derived SW 480 and human colonic epithelial cells as judged by the 3- ( 4 , 5-dimethylthiazol-2-yl ) -5- ( 3-carboxymethoxyphenyl ) -2- ( 4 -sulfophenyl ) -2H-tetrazolium assay .
[ Sen. 9, subscore: 2.00 ]: It also reduced colony formation of SW 480 colon and MDA MB 468 breast cells .
[ Sen. 1, subscore: 1.00 ]: Rice is a staple diet in Asia , where the incidence of breast and colon cancer is markedly below that in the Western world .
[ Sen. 6, subscore: 1.00 ]: These extracts were separated into nine fractions by column chromatography .
[ Sen. 12, subscore: 1.00 ]: Tricin ( 50 microM ) and the other phenols ( 200 microM ) inhibited colony formation of SW 480 cells .
[ Sen. 14, subscore: 1.00 ]: Tricin was the most potent anticlonogenic of the compounds with IC50s of 16 microM in the SW 480 colon cells and 0 . 6 microM in the MDA MB 468 breast cells .
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Score: 13.00 |
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| Title: Collision energy transfer in collision of NH ( 4 ) ( + ) ( NH ( 3 ) ) ( n-1 ) ( n=3-9 ) with ND ( 3 ) .
| | Author: Orii T Okada Y Takeuchi K Ichihashi M Kondow T | | Journal: Citation: V : 121 ( 19 ) P : 9406-16 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15538860 Accession (PMID): 15538860 | | Abstract: An incorporation of ND ( 3 ) into protonated ammonia cluster ions NH ( 4 ) ( + ) ( NH ( 3 ) ) ( n-1 ) ( n=3-9 ) , together with a dissociation of the cluster ions , was observed in the collision of the cluster with ND ( 3 ) at collision energies ranging from 0 . 04 to 1 . 4 eV in the center-of-mass frame .
The branching fractions of the cluster ion species produced in the reactions were obtained as a function of the collision energy .
The branching fractions of the incorporation products were successfully explained in terms of the Rice-Ramsperger-Kassel ( RRK ) theory at collision energies lower than the binding energy of the cluster ion .
In addition , the internal energy distributions of the parent cluster ions were determined , and found to be in good agreement with those predicted using the evaporative ensemble model .
In incorporations at collision energies lower than the binding energy of the cluster ion , all of the collision energy was transferred to the internal energy of the cluster ions ; subsequently , an evaporation of ammonia molecules occurred in an equilibrium process after a complete energy redistribution in the clusters .
In contrast , at collision energies higher than the binding energy of the cluster ion , a release of an ammonia molecule from the incorporation products occurred in a nonequilibrium process .
The transition from the complex mode to the direct mode in the incorporation was observed at collision energies approximately equal to the binding energy .
On the other hand , the collision energy dependence of the cross sections for the dissociation and for a nonreactive collision were estimated by a RRK simulation in which the collision energy transfer was interpreted by using the classical hard-sphere collision model .
A relationship between reactivity and reaction modes in the collision of NH ( 4 ) ( + ) ( NH ( 3 ) ) ( 4 ) with ND ( 3 ) is discussed via a comparison of the experimental results with the RRK simulation .
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[ Sen. 8, subscore: 4.00 ]: On the other hand , the collision energy dependence of the cross sections for the dissociation and for a nonreactive collision were estimated by a RRK simulation in which the collision energy transfer was interpreted by using the classical hard-sphere collision model .
[ Sen. 1, subscore: 2.00 ]: An incorporation of ND ( 3 ) into protonated ammonia cluster ions NH ( 4 ) ( + ) ( NH ( 3 ) ) ( n-1 ) ( n=3-9 ) , together with a dissociation of the cluster ions , was observed in the collision of the cluster with ND ( 3 ) at collision energies ranging from 0 . 04 to 1 . 4 eV in the center-of-mass frame .
[ Sen. 5, subscore: 2.00 ]: In incorporations at collision energies lower than the binding energy of the cluster ion , all of the collision energy was transferred to the internal energy of the cluster ions ; subsequently , an evaporation of ammonia molecules occurred in an equilibrium process after a complete energy redistribution in the clusters .
[ Sen. 2, subscore: 1.00 ]: The branching fractions of the cluster ion species produced in the reactions were obtained as a function of the collision energy .
[ Sen. 3, subscore: 1.00 ]: The branching fractions of the incorporation products were successfully explained in terms of the Rice-Ramsperger-Kassel ( RRK ) theory at collision energies lower than the binding energy of the cluster ion .
[ Sen. 6, subscore: 1.00 ]: In contrast , at collision energies higher than the binding energy of the cluster ion , a release of an ammonia molecule from the incorporation products occurred in a nonequilibrium process .
[ Sen. 7, subscore: 1.00 ]: The transition from the complex mode to the direct mode in the incorporation was observed at collision energies approximately equal to the binding energy .
[ Sen. 9, subscore: 1.00 ]: A relationship between reactivity and reaction modes in the collision of NH ( 4 ) ( + ) ( NH ( 3 ) ) ( 4 ) with ND ( 3 ) is discussed via a comparison of the experimental results with the RRK simulation .
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Score: 13.00 |
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| Title: Fatty Acids of Rice Coleoptiles in Air and Anoxia .
| | Author: Brown DJ Beevers H | | Journal: Citation: V : 84 ( 2 ) P : 555-559 Year: 1987 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16665478 Accession (PMID): 16665478 | | Abstract: The metabolism of lipids , like that of other components , was adversely and strongly affected when rice ( Oryza sativa L ) coleoptiles were grown anaerobically .
In aerobic coleoptiles , the amounts of total fatty acid , phospholipid , and total lipid per coleoptile increased by 2 . 5 to 3-fold between days three and seven , whereas under anoxia , the increases were all less than 60% .
The total amount of lipid at day seven in anoxia was less than 30% of that in air .
In air , the total fatty acid content at day three was 25 nanomoles per coleoptile and this increased to over 71 nanomoles per coleoptile at day seven .
All acids except 18 : 0 showed substantial increases .
In anoxia , the corresponding values for total fatty acids were 24 nanomoles and 27 nanomoles .
The small increases were confined to the saturated fatty acids ; no significant increase occurred in unsaturated fatty acids .
A minor fatty acid constituent ( 16 : 1 ) increased from 0 . 09 to 1 . 99 nanomoles per coleoptile between days three and seven in air .
This component was never observed in any fatty acid preparation from anaerobic coleoptiles .
The major phospholipids under all conditions were phosphatidylcholine , phosphatidylethanolamine , phosphatidylinositol , and phosphatidic acid .
A small amount of unidentified phosphoester , not present on thin layer chromatography plates from aerobic coleoptiles , was seen in extracts of anaerobic coleoptiles .
The fatty acyl substituents of each of the phospholipids were analyzed at days three and seven in coleoptiles grown aerobically and in anoxia .
Each phospholipid had its own distinctive fatty acid composition which remained fairly constant under all treatments ; 16 : 0 and 18 : 2 were the most abundant fatty acids in every phospholipid class .
In air , the percentages of total fatty acids that were in the phospholipids were 86% on day three and 87% on day seven .
In anoxia , the values at the corresponding ages were 47 and 57% .
Since no net synthesis of unsaturated fatty acids occurred in anaerobic conditions , the small increase in total unsaturated acids in the phospholipids between days three and seven must have occurred at the expense of fatty acids preexisting in the neutral lipid .
No unusual pathways of biosynthesis or unusual precursors are required to explain the presence of unsaturated fatty acids in the rice coleoptile .
The present study and results of experiments where coleoptiles were fed [ ( 14 ) C ] acetate ( BB Vartapetian et al 1978 Plant Sci Lett 13 : 321-328 ) clearly show that unsaturated fatty acid synthesis in rice coleoptiles requires O ( 2 ) , as it does in other plants . | Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: In aerobic coleoptiles , the amounts of total fatty acid , phospholipid , and total lipid per coleoptile increased by 2 . 5 to 3-fold between days three and seven , whereas under anoxia , the increases were all less than 60% .
[ Sen. 4, subscore: 2.00 ]: In air , the total fatty acid content at day three was 25 nanomoles per coleoptile and this increased to over 71 nanomoles per coleoptile at day seven .
[ Sen. 11, subscore: 2.00 ]: A small amount of unidentified phosphoester , not present on thin layer chromatography plates from aerobic coleoptiles , was seen in extracts of anaerobic coleoptiles .
[ Sen. 18, subscore: 2.00 ]: The present study and results of experiments where coleoptiles were fed [ ( 14 ) C ] acetate ( BB Vartapetian et al 1978 Plant Sci Lett 13 : 321-328 ) clearly show that unsaturated fatty acid synthesis in rice coleoptiles requires O ( 2 ) , as it does in other plants .
[ Sen. 1, subscore: 1.00 ]: The metabolism of lipids , like that of other components , was adversely and strongly affected when rice ( Oryza sativa L ) coleoptiles were grown anaerobically .
[ Sen. 8, subscore: 1.00 ]: A minor fatty acid constituent ( 16 : 1 ) increased from 0 . 09 to 1 . 99 nanomoles per coleoptile between days three and seven in air .
[ Sen. 9, subscore: 1.00 ]: This component was never observed in any fatty acid preparation from anaerobic coleoptiles .
[ Sen. 12, subscore: 1.00 ]: The fatty acyl substituents of each of the phospholipids were analyzed at days three and seven in coleoptiles grown aerobically and in anoxia .
[ Sen. 17, subscore: 1.00 ]: No unusual pathways of biosynthesis or unusual precursors are required to explain the presence of unsaturated fatty acids in the rice coleoptile .
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