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| Title: Gene Ontology annotation of the rice blast fungus , Magnaporthe oryzae .
| | Author: Meng S Brown DE Ebbole DJ Torto-Alalibo T Oh YY Deng J Mitchell TK Dean RA | | Journal: BMC Microbiol Citation: V : 9 Suppl 1 P : S8 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19278556 Accession (PMID): 19278556 | | Abstract: BACKGROUND : Magnaporthe oryzae , the causal agent of blast disease of rice , is the most destructive disease of rice worldwide .
The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http : //www . broad . mit . edu/annotation/genome/magnaporthe_grisea/MultiDownloads . html . However , a comprehensive manual curation remains to be performed .
Gene Ontology ( GO ) annotation is a valuable means of assigning functional information using standardized vocabulary .
We report an overview of the GO annotation for Version 5 of M oryzae genome assembly .
METHODS : A similarity-based ( ie , computational ) GO annotation with manual review was conducted , which was then integrated with a literature-based GO annotation with computational assistance .
For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M oryzae and GO proteins from multiple organisms with published associations to GO terms .
Significant alignment pairs were manually reviewed .
Functional assignments were further cross-validated with manually reviewed data , conserved domains , or data determined by wet lab experiments .
Additionally , biological appropriateness of the functional assignments was manually checked .
RESULTS : In total , 6 , 286 proteins received GO term assignment via the homology-based annotation , including 2 , 870 hypothetical proteins .
Literature-based experimental evidence , such as microarray , MPSS , T-DNA insertion mutation , or gene knockout mutation , resulted in 2 , 810 proteins being annotated with GO terms .
Of these , 1 , 673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology ( PAMGO ) .
In addition , 67 experiment-determined secreted proteins were annotated with PAMGO terms .
Integration of the two data sets resulted in 7 , 412 proteins ( 57% ) being annotated with 1 , 957 distinct and specific GO terms .
Unannotated proteins were assigned to the 3 root terms .
The Version 5 GO annotation is publically queryable via the GO site http : //amigo . geneontology . org/cgi-bin/amigo/go . cgi .
Additionally , the genome of M oryzae is constantly being refined and updated as new information is incorporated .
For the latest GO annotation of Version 6 genome , please visit our website http : //scotland . fgl . ncsu . edu/smeng/GoAnnotationMagnaporthegrisea . html .
The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System .
CONCLUSION : Our analysis provides comprehensive and robust GO annotations of the M oryzae genome assemblies that will be solid foundations for further functional interrogation of M oryzae .
| Matching Sentences:
[ Sen. 6, subscore: 3.00 ]: For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M oryzae and GO proteins from multiple organisms with published associations to GO terms .
[ Sen. 5, subscore: 2.00 ]: METHODS : A similarity-based ( ie , computational ) GO annotation with manual review was conducted , which was then integrated with a literature-based GO annotation with computational assistance .
[ Sen. 16, subscore: 2.00 ]: The Version 5 GO annotation is publically queryable via the GO site http : //amigo . geneontology . org/cgi-bin/amigo/go . cgi .
[ Sen. 3, subscore: 1.00 ]: Gene Ontology ( GO ) annotation is a valuable means of assigning functional information using standardized vocabulary .
[ Sen. 4, subscore: 1.00 ]: We report an overview of the GO annotation for Version 5 of M oryzae genome assembly .
[ Sen. 10, subscore: 1.00 ]: RESULTS : In total , 6 , 286 proteins received GO term assignment via the homology-based annotation , including 2 , 870 hypothetical proteins .
[ Sen. 11, subscore: 1.00 ]: Literature-based experimental evidence , such as microarray , MPSS , T-DNA insertion mutation , or gene knockout mutation , resulted in 2 , 810 proteins being annotated with GO terms .
[ Sen. 14, subscore: 1.00 ]: Integration of the two data sets resulted in 7 , 412 proteins ( 57% ) being annotated with 1 , 957 distinct and specific GO terms .
[ Sen. 18, subscore: 1.00 ]: For the latest GO annotation of Version 6 genome , please visit our website http : //scotland . fgl . ncsu . edu/smeng/GoAnnotationMagnaporthegrisea . html .
[ Sen. 19, subscore: 1.00 ]: The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System .
[ Sen. 20, subscore: 1.00 ]: CONCLUSION : Our analysis provides comprehensive and robust GO annotations of the M oryzae genome assemblies that will be solid foundations for further functional interrogation of M oryzae .
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Score: 13.00 |
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| Title: Selenium and iodine in soil , rice and drinking water in relation to endemic goitre in Sri Lanka .
| | Author: Fordyce FM Johnson CC Navaratna UR Appleton JD Dissanayake CB .
| | Journal: Sci .
Total Environ .
Citation: V : 263 ( 1-3 ) P : 127-41 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11194147 Accession (PMID): 11194147 | | Abstract: Endemic goitre has been reported in the climatic wet zone of south-west Sri Lanka for the past 50 years , but rarely occurs in the northern dry zone .
Despite government-sponsored iodised salt programmes , endemic goitre is still prevalent .
In recent years , it has been suggested that Se deficiency may be an important factor in the onset of goitre and other iodine deficiency disorders ( IDD ) .
Prior to the present study , environmental concentrations of Se in Sri Lanka and the possible relationships between Se deficiency and endemic goitre had not been investigated .
During the present study , chemical differences in the environment ( measured in soil , rice and drinking water ) and the Se-status of the human population ( demonstrated by hair samples from women ) were determined for 15 villages .
The villages were characterised by low ( < 10% ) , moderate ( 10-25% ) and high ( > 25% ) goitre incidence ( NIDD , MIDD and HIDD , respectively ) .
Results show that concentrations of soil total Se and iodine are highest in the HIDD villages , however , the soil clay and organic matter content appear to inhibit the bioavailability of these elements .
Concentrations of iodine in rice are low ( < or = 58 ng/g ) and rice does not provide a significant source of iodine in the Sri Lankan diet .
High concentrations of iodine ( up to 84 microg/l ) in drinking water in the dry zone may , in part , explain why goitre is uncommon in this area .
This study has shown for the first time that significant proportions of the Sri Lankan female population may be Se deficient ( 24 , 24 and 40% in the NIDD , MIDD and HIDD villages , respectively ) .
Although Se deficiency is not restricted to areas where goitre is prevalent , a combination of iodine and Se deficiency could be involved in the pathogenesis of goitre in Sri Lanka .
The distribution of red rice cultivation in Sri Lanka is coincident with the HIDD villages .
Varieties of red rice grown in other countries contain anthocyanins and procyanidins , compounds which in other foodstuffs are known goitrogens .
The potential goitrogenic properties of red rice in Sri Lanka are presently unknown and require further investigation .
It is likely that the incidence of goitre in Sri Lanka is multi-factorial , involving trace element deficiencies and other factors such as poor nutrition and goitrogens in foodstuffs . | Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: Despite government-sponsored iodised salt programmes , endemic goitre is still prevalent .
[ Sen. 11, subscore: 2.00 ]: Although Se deficiency is not restricted to areas where goitre is prevalent , a combination of iodine and Se deficiency could be involved in the pathogenesis of goitre in Sri Lanka .
[ Sen. 15, subscore: 2.00 ]: It is likely that the incidence of goitre in Sri Lanka is multi-factorial , involving trace element deficiencies and other factors such as poor nutrition and goitrogens in foodstuffs .
[ Sen. 1, subscore: 1.00 ]: Endemic goitre has been reported in the climatic wet zone of south-west Sri Lanka for the past 50 years , but rarely occurs in the northern dry zone .
[ Sen. 3, subscore: 1.00 ]: In recent years , it has been suggested that Se deficiency may be an important factor in the onset of goitre and other iodine deficiency disorders ( IDD ) .
[ Sen. 4, subscore: 1.00 ]: Prior to the present study , environmental concentrations of Se in Sri Lanka and the possible relationships between Se deficiency and endemic goitre had not been investigated .
[ Sen. 6, subscore: 1.00 ]: The villages were characterised by low ( < 10% ) , moderate ( 10-25% ) and high ( > 25% ) goitre incidence ( NIDD , MIDD and HIDD , respectively ) .
[ Sen. 9, subscore: 1.00 ]: High concentrations of iodine ( up to 84 microg/l ) in drinking water in the dry zone may , in part , explain why goitre is uncommon in this area .
[ Sen. 13, subscore: 1.00 ]: Varieties of red rice grown in other countries contain anthocyanins and procyanidins , compounds which in other foodstuffs are known goitrogens .
[ Sen. 14, subscore: 1.00 ]: The potential goitrogenic properties of red rice in Sri Lanka are presently unknown and require further investigation .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 11.00 |
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| Title: Human factor H interacts selectively with Neisseria gonorrhoeae and results in species-specific complement evasion .
| | Author: Ngampasutadol J Ram S Gulati S Agarwal S Li C Visintin A Monks B Madico G Rice PA | | Journal: J Immunol Citation: V : 180 P : 3426-35 Year: 2008 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub18292569 Accession (PMID): 18292569 | | Abstract: Complement forms a key arm of innate immune defenses against gonococcal infection .
Sialylation of gonococcal lipo-oligosaccharide , or expression of porin 1A ( Por1A ) protein , enables Neisseria gonorrhoeae to bind the alternative pathway complement inhibitor , factor H ( fH ) , and evade killing by human complement .
Using recombinant fH fragment-murine Fc fusion proteins , we localized two N gonorrhoeae Por1A-binding regions in fH : one in complement control protein domain 6 , the other in complement control proteins 18-20 .
The latter is similar to that reported previously for sialylated Por1B gonococci .
Upon incubation with human serum , Por1A and sialylated Por1B strains bound full-length human fH ( HufH ) and fH-related protein 1 .
In addition , Por1A strains bound fH-like protein 1 weakly .
Only HufH , but not fH from other primates , bound directly to gonococci .
Consistent with direct HufH binding , unsialylated Por1A gonococci resisted killing only by human complement , but not complement from other primates , rodents or lagomorphs ; adding HufH to these heterologous sera restored serum resistance .
Lipo-oligosaccharide sialylation of N gonorrhoeae resulted in classical pathway regulation as evidenced by decreased C4 binding in human , chimpanzee , and rhesus serum but was accompanied by serum resistance only in human and chimpanzee serum .
Direct-binding specificity of HufH only to gonococci that prevents serum killing is restricted to humans and may in part explain species-specific restriction of natural gonococcal infection .
Our findings may help to improve animal models for gonorrhea while also having implications in the choice of complement sources to evaluate neisserial vaccine candidates .
| Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: Sialylation of gonococcal lipo-oligosaccharide , or expression of porin 1A ( Por1A ) protein , enables Neisseria gonorrhoeae to bind the alternative pathway complement inhibitor , factor H ( fH ) , and evade killing by human complement .
[ Sen. 10, subscore: 2.00 ]: Direct-binding specificity of HufH only to gonococci that prevents serum killing is restricted to humans and may in part explain species-specific restriction of natural gonococcal infection .
[ Sen. 1, subscore: 1.00 ]: Complement forms a key arm of innate immune defenses against gonococcal infection .
[ Sen. 3, subscore: 1.00 ]: Using recombinant fH fragment-murine Fc fusion proteins , we localized two N gonorrhoeae Por1A-binding regions in fH : one in complement control protein domain 6 , the other in complement control proteins 18-20 .
[ Sen. 4, subscore: 1.00 ]: The latter is similar to that reported previously for sialylated Por1B gonococci .
[ Sen. 7, subscore: 1.00 ]: Only HufH , but not fH from other primates , bound directly to gonococci .
[ Sen. 8, subscore: 1.00 ]: Consistent with direct HufH binding , unsialylated Por1A gonococci resisted killing only by human complement , but not complement from other primates , rodents or lagomorphs ; adding HufH to these heterologous sera restored serum resistance .
[ Sen. 9, subscore: 1.00 ]: Lipo-oligosaccharide sialylation of N gonorrhoeae resulted in classical pathway regulation as evidenced by decreased C4 binding in human , chimpanzee , and rhesus serum but was accompanied by serum resistance only in human and chimpanzee serum .
[ Sen. 11, subscore: 1.00 ]: Our findings may help to improve animal models for gonorrhea while also having implications in the choice of complement sources to evaluate neisserial vaccine candidates .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 11.00 |
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| Title: Expression of the gonococcal global regulatory protein Fur and genes encompassing the Fur and iron regulon during in vitro and in vivo infection in women .
| | Author: Agarwal S Sebastian S Szmigielski B Rice PA Genco CA | | Journal: J Bacteriol Citation: V : 190 P : 3129-39 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18310343 Accession (PMID): 18310343 | | Abstract: The ferric uptake regulatory protein , Fur , functions as a global regulatory protein of gene transcription in the mucosal pathogen Neisseria gonorrhoeae .
We have shown previously that several N gonorrhoeae Fur-repressed genes are expressed in vivo during mucosal gonococcal infection in men , which suggests that this organism infects in an iron-limited environment and that Fur is expressed under these conditions .
In this study we have demonstrated expression of the gonococcal fur gene in vitro , in human cervical epithelial cells , and in specimens from female subjects with uncomplicated gonococcal infection .
In vitro studies confirmed that the expression of the gonococcal fur gene was repressed during growth under iron-replete growth conditions but that a basal level of the protein was maintained .
Using GFP transcriptional fusions constructed from specific Fur binding sequences within the fur promoter/operator region , we determined that this operator region was functional during N gonorrhoeae infection of cervical epithelial cells .
Furthermore , reverse transcription-PCR analysis , as well as microarray analysis , using a custom Neisseria Fur and iron regulon microarray revealed that several Fur and iron-regulated genes were expressed during N gonorrhoeae infection of cervical epithelial cells .
Microarray analysis of specimens obtained from female subjects with uncomplicated gonococcal infection corroborated our in vitro findings and point toward a key role of gonococcal Fur and iron-regulated genes in gonococcal disease .
| Matching Sentences:
[ Sen. 7, subscore: 3.00 ]: Microarray analysis of specimens obtained from female subjects with uncomplicated gonococcal infection corroborated our in vitro findings and point toward a key role of gonococcal Fur and iron-regulated genes in gonococcal disease .
[ Sen. 2, subscore: 2.00 ]: We have shown previously that several N gonorrhoeae Fur-repressed genes are expressed in vivo during mucosal gonococcal infection in men , which suggests that this organism infects in an iron-limited environment and that Fur is expressed under these conditions .
[ Sen. 3, subscore: 2.00 ]: In this study we have demonstrated expression of the gonococcal fur gene in vitro , in human cervical epithelial cells , and in specimens from female subjects with uncomplicated gonococcal infection .
[ Sen. 1, subscore: 1.00 ]: The ferric uptake regulatory protein , Fur , functions as a global regulatory protein of gene transcription in the mucosal pathogen Neisseria gonorrhoeae .
[ Sen. 4, subscore: 1.00 ]: In vitro studies confirmed that the expression of the gonococcal fur gene was repressed during growth under iron-replete growth conditions but that a basal level of the protein was maintained .
[ Sen. 5, subscore: 1.00 ]: Using GFP transcriptional fusions constructed from specific Fur binding sequences within the fur promoter/operator region , we determined that this operator region was functional during N gonorrhoeae infection of cervical epithelial cells .
[ Sen. 6, subscore: 1.00 ]: Furthermore , reverse transcription-PCR analysis , as well as microarray analysis , using a custom Neisseria Fur and iron regulon microarray revealed that several Fur and iron-regulated genes were expressed during N gonorrhoeae infection of cervical epithelial cells .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 10.00 |
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| Title: Golden Rice is an effective source of vitamin A | | Author: Tang G Qin J Dolnikowski GG Russell RM Grusak MA | | Journal: Am J Clin Nutr Citation: V : 89 P : 1776-83 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19369372 Accession (PMID): 19369372 | | Abstract: BACKGROUND : Genetically engineered "Golden Rice" contains up to 35 microg beta-carotene per gram of rice .
It is important to determine the vitamin A equivalency of Golden Rice beta-carotene to project the potential effect of this biofortified grain in rice-consuming populations that commonly exhibit low vitamin A status .
OBJECTIVE : The objective was to determine the vitamin A value of intrinsically labeled dietary Golden Rice in humans .
DESIGN : Golden Rice plants were grown hydroponically with heavy water ( deuterium oxide ) to generate deuterium-labeled [ 2H ] beta-carotene in the rice grains .
Golden Rice servings of 65-98 g ( 130-200 g cooked rice ) containing 0 . 99-1 . 53 mg beta-carotene were fed to 5 healthy adult volunteers ( 3 women and 2 men ) with 10 g butter .
A reference dose of [ 13C10 ] retinyl acetate ( 0 . 4-1 . 0 mg ) in oil was given to each volunteer 1 wk before ingestion of the Golden Rice dose .
Blood samples were collected over 36 d .
RESULTS : Our results showed that the mean ( +/-SD ) area under the curve for the total serum response to [ 2H ] retinol was 39 . 9 +/- 20 . 7 microg x d after the Golden Rice dose .
Compared with that of the [ 13C10 ] retinyl acetate reference dose ( 84 . 7 +/- 34 . 6 microg x d ) , Golden Rice beta-carotene provided 0 . 24-0 . 94 mg retinol .
Thus , the conversion factor of Golden Rice beta-carotene to retinol is 3 . 8 +/- 1 . 7 to 1 with a range of 1 . 9-6 . 4 to 1 by weight , or 2 . 0 +/- 0 . 9 to 1 with a range of 1 . 0-3 . 4 to 1 by moles .
CONCLUSION : Beta-carotene derived from Golden Rice is effectively converted to vitamin A in humans .
This trial was registered at clinicaltrials . gov as NCT00680355 .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: It is important to determine the vitamin A equivalency of Golden Rice beta-carotene to project the potential effect of this biofortified grain in rice-consuming populations that commonly exhibit low vitamin A status .
[ Sen. 3, subscore: 1.00 ]: OBJECTIVE : The objective was to determine the vitamin A value of intrinsically labeled dietary Golden Rice in humans .
[ Sen. 4, subscore: 1.00 ]: DESIGN : Golden Rice plants were grown hydroponically with heavy water ( deuterium oxide ) to generate deuterium-labeled [ 2H ] beta-carotene in the rice grains .
[ Sen. 5, subscore: 1.00 ]: Golden Rice servings of 65-98 g ( 130-200 g cooked rice ) containing 0 . 99-1 . 53 mg beta-carotene were fed to 5 healthy adult volunteers ( 3 women and 2 men ) with 10 g butter .
[ Sen. 6, subscore: 1.00 ]: A reference dose of [ 13C10 ] retinyl acetate ( 0 . 4-1 . 0 mg ) in oil was given to each volunteer 1 wk before ingestion of the Golden Rice dose .
[ Sen. 8, subscore: 1.00 ]: RESULTS : Our results showed that the mean ( +/-SD ) area under the curve for the total serum response to [ 2H ] retinol was 39 . 9 +/- 20 . 7 microg x d after the Golden Rice dose .
[ Sen. 9, subscore: 1.00 ]: Compared with that of the [ 13C10 ] retinyl acetate reference dose ( 84 . 7 +/- 34 . 6 microg x d ) , Golden Rice beta-carotene provided 0 . 24-0 . 94 mg retinol .
[ Sen. 10, subscore: 1.00 ]: Thus , the conversion factor of Golden Rice beta-carotene to retinol is 3 . 8 +/- 1 . 7 to 1 with a range of 1 . 9-6 . 4 to 1 by weight , or 2 . 0 +/- 0 . 9 to 1 with a range of 1 . 0-3 . 4 to 1 by moles .
[ Sen. 11, subscore: 1.00 ]: CONCLUSION : Beta-carotene derived from Golden Rice is effectively converted to vitamin A in humans .
[ Sen. 12, subscore: 1.00 ]: This trial was registered at clinicaltrials . gov as NCT00680355 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 10.00 |
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| Title: Properdin is critical for antibody-dependent bactericidal activity against Neisseria gonorrhoeae that recruit C4b-binding protein .
| | Author: Gulati S Agarwal S Vasudhev S Rice PA Ram S | | Journal: J Immunol Citation: V : 188 P : 3416-25 Year: 2012 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub22368277 Accession (PMID): 22368277 | | Abstract: Gonorrhea , a sexually transmitted disease caused by Neisseria gonorrhoeae , is an important cause of morbidity worldwide .
A safe and effective vaccine against gonorrhea is needed because of emerging resistance of gonococci to almost every class of antibiotic .
A gonococcal lipooligosaccharide epitope defined by the mAb 2C7 is being evaluated as a candidate for development of an Ab-based vaccine .
Immune Abs against N gonorrhoeae need to overcome several subversive mechanisms whereby gonococcus evades complement , including binding to C4b-binding protein ( C4BP ; classical pathway inhibitor ) and factor H ( alternative pathway [ AP ] inhibitor ) .
The role of AP recruitment and , in particular , properdin in assisting killing of gonococci by specific Abs is the subject of this study .
We show that only those gonococcal strains that bind C4BP require properdin for killing by 2C7 , whereas strains that do not bind C4BP are efficiently killed by 2C7 even when AP function is blocked .
C3 deposition on bacteria mirrored killing .
Recruitment of the AP by mAb 2C7 , as measured by factor B binding , occurred in a properdin-dependent manner .
These findings were confirmed using isogenic mutant strains that differed in their ability to bind to C4BP .
Immune human serum that contained bactericidal Abs directed against the 2C7 lipooligosaccharide epitope as well as murine antigonococcal antiserum required functional properdin to kill C4BP-binding strains , but not C4BP-nonbinding strains .
Collectively , these data point to an important role for properdin in facilitating immune Ab-mediated complement-dependent killing of gonococcal strains that inhibit the classical pathway by recruiting C4BP .
| Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Gonorrhea , a sexually transmitted disease caused by Neisseria gonorrhoeae , is an important cause of morbidity worldwide .
[ Sen. 2, subscore: 2.00 ]: A safe and effective vaccine against gonorrhea is needed because of emerging resistance of gonococci to almost every class of antibiotic .
[ Sen. 4, subscore: 2.00 ]: Immune Abs against N gonorrhoeae need to overcome several subversive mechanisms whereby gonococcus evades complement , including binding to C4b-binding protein ( C4BP ; classical pathway inhibitor ) and factor H ( alternative pathway [ AP ] inhibitor ) .
[ Sen. 3, subscore: 1.00 ]: A gonococcal lipooligosaccharide epitope defined by the mAb 2C7 is being evaluated as a candidate for development of an Ab-based vaccine .
[ Sen. 5, subscore: 1.00 ]: The role of AP recruitment and , in particular , properdin in assisting killing of gonococci by specific Abs is the subject of this study .
[ Sen. 6, subscore: 1.00 ]: We show that only those gonococcal strains that bind C4BP require properdin for killing by 2C7 , whereas strains that do not bind C4BP are efficiently killed by 2C7 even when AP function is blocked .
[ Sen. 11, subscore: 1.00 ]: Collectively , these data point to an important role for properdin in facilitating immune Ab-mediated complement-dependent killing of gonococcal strains that inhibit the classical pathway by recruiting C4BP .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 9.00 |
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| Title: Bellilinea caldifistulae gen . nov . , sp . nov . and Longilinea arvoryzae gen . nov . , sp . nov . , strictly anaerobic , filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia .
| | Author: Yamada T Imachi H Ohashi A Harada H Hanada S Kamagata Y Sekiguchi Y | | Journal: Int J Syst Evol Microbiol Citation: V : 57 P : 2299-306 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17911301 Accession (PMID): 17911301 | | Abstract: Thermophilic ( strain GOMI-1 ( T ) ) and mesophilic ( strain KOME-1 ( T ) ) strains were isolated from two different cultures of propionate-degrading consortia obtained from thermophilic digester sludge and rice paddy soil , respectively .
The two strains were non-spore-forming , non-motile and Gram-negative .
Both strains were obligately anaerobic micro-organisms , showing multicellular filamentous morphotypes more than 100 mum in length .
The cell width for strain GOMI-1 ( T ) was 0 . 2-0 . 4 mum and that of strain KOME-1 ( T ) was 0 . 4-0 . 6 mum .
Strain GOMI-1 ( T ) could grow at 45-65 degrees C with a pH range of 6 . 0-7 . 5 ( optimum growth at 55 degrees C , pH 7 . 0 ) .
The temperature range for growth of strain KOME-1 ( T ) was 30-40 degrees C and the pH range was pH 5 . 0-8 . 5 ( optimum growth around 37 degrees C , pH 7 . 0 ) .
Yeast extract was required for growth of both strains .
Strain GOMI-1 ( T ) was able to grow with a number of carbohydrates in the presence of yeast extract .
In yeast extract-containing medium , strain KOME-1 ( T ) could utilize proteins and a limited range of sugars for growth .
The G+C contents of the DNA of strains GOMI-1 ( T ) and KOME-1 ( T ) were respectively 54 . 7 and 57 . 6 mol% .
Major fatty acids of strain GOMI-1 ( T ) were C ( 16 : 0 ) , C ( 14 : 0 ) and iso-C ( 15 : 0 ) , whereas those of strain KOME-1 ( T ) were iso-C ( 15 : 0 ) , anteiso-C ( 15 : 0 ) and C ( 14 : 0 ) .
Based on comparative analysis of 16S rRNA gene sequences of strains GOMI-1 ( T ) and KOME-1 ( T ) , the strains were placed in different phylogenetic positions in the class Anaerolineae of the bacterial phylum Chloroflexi .
Their phenotypic and genetic traits strongly supported the conclusion that the strains should be described as two independent taxa in the class Anaerolineae .
Hence , we propose the names Bellilinea caldifistulae gen . nov . , sp . nov . , and Longilinea arvoryzae gen . nov . , sp . nov . , for strains GOMI-1 ( T ) and KOME-1 ( T ) .
The type strains of Bellilinea caldifistulae and Longilinea arvoryzae are respectively GOMI-1 ( T ) ( =JCM 13669 ( T ) =DSM 17877 ( T ) ) and KOME-1 ( T ) ( =JCM 13670 ( T ) =KTCC 5380 ( T ) ) .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Thermophilic ( strain GOMI-1 ( T ) ) and mesophilic ( strain KOME-1 ( T ) ) strains were isolated from two different cultures of propionate-degrading consortia obtained from thermophilic digester sludge and rice paddy soil , respectively .
[ Sen. 4, subscore: 1.00 ]: The cell width for strain GOMI-1 ( T ) was 0 . 2-0 . 4 mum and that of strain KOME-1 ( T ) was 0 . 4-0 . 6 mum .
[ Sen. 5, subscore: 1.00 ]: Strain GOMI-1 ( T ) could grow at 45-65 degrees C with a pH range of 6 . 0-7 . 5 ( optimum growth at 55 degrees C , pH 7 . 0 ) .
[ Sen. 8, subscore: 1.00 ]: Strain GOMI-1 ( T ) was able to grow with a number of carbohydrates in the presence of yeast extract .
[ Sen. 10, subscore: 1.00 ]: The G+C contents of the DNA of strains GOMI-1 ( T ) and KOME-1 ( T ) were respectively 54 . 7 and 57 . 6 mol% .
[ Sen. 11, subscore: 1.00 ]: Major fatty acids of strain GOMI-1 ( T ) were C ( 16 : 0 ) , C ( 14 : 0 ) and iso-C ( 15 : 0 ) , whereas those of strain KOME-1 ( T ) were iso-C ( 15 : 0 ) , anteiso-C ( 15 : 0 ) and C ( 14 : 0 ) .
[ Sen. 12, subscore: 1.00 ]: Based on comparative analysis of 16S rRNA gene sequences of strains GOMI-1 ( T ) and KOME-1 ( T ) , the strains were placed in different phylogenetic positions in the class Anaerolineae of the bacterial phylum Chloroflexi .
[ Sen. 14, subscore: 1.00 ]: Hence , we propose the names Bellilinea caldifistulae gen . nov . , sp . nov . , and Longilinea arvoryzae gen . nov . , sp . nov . , for strains GOMI-1 ( T ) and KOME-1 ( T ) .
[ Sen. 15, subscore: 1.00 ]: The type strains of Bellilinea caldifistulae and Longilinea arvoryzae are respectively GOMI-1 ( T ) ( =JCM 13669 ( T ) =DSM 17877 ( T ) ) and KOME-1 ( T ) ( =JCM 13670 ( T ) =KTCC 5380 ( T ) ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 9.00 |
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| Title: Diazinon resistance in different selected strains of Chilo suppressalis ( Lepidoptera : Crambidae ) in northern Iran .
| | Author: Zibaee A Sendi JJ Ghadamyari M Alinia F Etebari K | | Journal: J Econ Entomol Citation: V : 102 P : 1189-96 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19610437 Accession (PMID): 19610437 | | Abstract: Asiatic rice borer , Chilo suppressalis ( Walker ) ( Lepidoptera : Crambidae ) , is a cosmopolitan and destructive pest in rice fields of the world .
This pest was reported in 1973 in Iran , and it has since spread widely in rice , Oryza sativa L , fields throughout the country .
In this study , we tried to evaluate comparative toxicity of diazinon in five colonies of C suppressalis , collected from Babol ( Ba ) , Amol ( Am ) of Mazandaran Province and Rasht ( Ra ) , Sheikhmahale ( Sh ) , and Gourabzarmikh ( Go ) of Guilan Province , northern Iran .
The LD50 values were compared .
We also evaluated the general esterases , alkaline phosphatase ( ALP ) , glutathione transferase ( GST ) , and acetylcholinesterase ( AChE ) activities from the five populations .
The LD50 values of Ra , Ba , Am , and Sh ( 12 . 64 , 11 . 4 , 7 . 17 , and 3 . 71 microg/mg larva ( -1 ) ) were 13 . 67- , 12 . 33- , 7 . 75- , and 4 . 02-fold higher than Go population ( 0 . 924 microg/mg larva ( -1 ) ) .
Using alpha-naphthyl acetate as substrate , the general esterase activities in Ra , Ba , Am , and Sh colonies were , respectively , 1 . 81- , 1 . 68- , 1 . 75- , and 1 . 35-fold more than those in Go population .
When beta-naphthyl acetate was used as the substrate , activity ratio was measured 1 . 98- , 2 . 58- , 1 . 25- , and 1 . 24-fold compared with the Go population .
Glutathione transferase activities in Ra , Ba , Am , and Sh populations were 1 . 27- , 1 . 68- , 0 . 98- , and 1 . 7-fold more than those in Go , when 1-chloro-2 , 4-dinitrobenzene was used as the substrate .
When 1 , 2-dichloro-4-nitro-benzene was used as the substrate , activity ratio was measured 1 . 14- , 1 . 42- , 0 . 56- , and 0 . 95-fold compared with Go population .
The ALP activity demonstrated a significant difference among these populations and in Ra , Ba , Am , and Sh larvae were 3 . 54- , 4 . 62- , 3 . 84- , and 2 . 18-fold more than Go .
The AChE inhibition or I50 value was 0 . 19 , 0 . 22 , 0 . 31 , 0 . 19 , and 0 . 26 mM in Ra , Ba , Am , Sh and Go populations , respectively .
However , the results showed no significant differences in studied colonies .
These biochemical characterizations of general esterases ALP , GST , and AChE were consistent with diazinon bioassay in the five populations .
It is inferred from increased esterase , alkaline phosphatase and glutathione transferase , activities that might play an important role in the increasing resistance in C suppressalis to diazinon among these five populations .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: In this study , we tried to evaluate comparative toxicity of diazinon in five colonies of C suppressalis , collected from Babol ( Ba ) , Amol ( Am ) of Mazandaran Province and Rasht ( Ra ) , Sheikhmahale ( Sh ) , and Gourabzarmikh ( Go ) of Guilan Province , northern Iran .
[ Sen. 6, subscore: 1.00 ]: The LD50 values of Ra , Ba , Am , and Sh ( 12 . 64 , 11 . 4 , 7 . 17 , and 3 . 71 microg/mg larva ( -1 ) ) were 13 . 67- , 12 . 33- , 7 . 75- , and 4 . 02-fold higher than Go population ( 0 . 924 microg/mg larva ( -1 ) ) .
[ Sen. 7, subscore: 1.00 ]: Using alpha-naphthyl acetate as substrate , the general esterase activities in Ra , Ba , Am , and Sh colonies were , respectively , 1 . 81- , 1 . 68- , 1 . 75- , and 1 . 35-fold more than those in Go population .
[ Sen. 8, subscore: 1.00 ]: When beta-naphthyl acetate was used as the substrate , activity ratio was measured 1 . 98- , 2 . 58- , 1 . 25- , and 1 . 24-fold compared with the Go population .
[ Sen. 9, subscore: 1.00 ]: Glutathione transferase activities in Ra , Ba , Am , and Sh populations were 1 . 27- , 1 . 68- , 0 . 98- , and 1 . 7-fold more than those in Go , when 1-chloro-2 , 4-dinitrobenzene was used as the substrate .
[ Sen. 10, subscore: 1.00 ]: When 1 , 2-dichloro-4-nitro-benzene was used as the substrate , activity ratio was measured 1 . 14- , 1 . 42- , 0 . 56- , and 0 . 95-fold compared with Go population .
[ Sen. 11, subscore: 1.00 ]: The ALP activity demonstrated a significant difference among these populations and in Ra , Ba , Am , and Sh larvae were 3 . 54- , 4 . 62- , 3 . 84- , and 2 . 18-fold more than Go .
[ Sen. 12, subscore: 1.00 ]: The AChE inhibition or I50 value was 0 . 19 , 0 . 22 , 0 . 31 , 0 . 19 , and 0 . 26 mM in Ra , Ba , Am , Sh and Go populations , respectively .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 9.00 |
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| Title: Effects of different sources of dietary non-starch polysaccharides on the growth performance , development of digestive tract and activities of pancreatic enzymes in goslings .
| | Author: Lin PH Shih BL Hsu JC | | Journal: Br Poult Sci Citation: V : 51 P : 270-7 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20461588 Accession (PMID): 20461588 | | Abstract: 1 .
The purpose of this study was to investigate the effects of different sources of dietary non-starch polysaccharides ( NSP ) on growth performance , development of gastrointestinal tract , and activities of pancreatic enzymes in goslings from 0 to 21 d of age .
2 .
A total of 100 one-day-old White Roman female goslings were selected and randomly divided into 5 dietary treatment groups .
Each group had 4 replicate cages ( 100 x 60 x 58 cm ) of 5 goslings .
Goslings in each group were given one of 5 isoenergetic and isonitrogenous semi-purified diets .
Experimental diets were designed to contain 90 g/kg of different sources of dietary NSP from maize ( control ) , barley hull , rice bran , wheat bran , or pectin , respectively , and 97 . 4 g/kg NSP were supplied by soybean meal 3 .
The goslings receiving the pectin diet had significantly higher viscosity in intestinal digesta than the other treatment diets .
However , the daily feed intake , daily weight gain , and feed conversion ratio of goslings in the pectin group were significantly lower than those given the other diets .
4 .
The relative weights of proventriculus , gizzard , liver and pancreas , as well as the relative weights and lengths of various intestinal segments in the goslings that received the pectin diet , were significantly higher than those receiving the other diets .
The specific activities ( SA ) of amylase , lipase , trypsin , and chymotrypsin in the pancreatic it issue of goslings in the pectin group were significantly lower than those in the other groups .
5 .
Goslings given a soluble NSP source ( pectin ) diet tended to exhibit inhibited growth and decreased activity of pancreatic enzymes .
However , compared with maize , the inclusion of insoluble NSP sources from barley hull , rice bran , and wheat bran did not negatively affect growth and also were not significantly different among the treatment diets .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The purpose of this study was to investigate the effects of different sources of dietary non-starch polysaccharides ( NSP ) on growth performance , development of gastrointestinal tract , and activities of pancreatic enzymes in goslings from 0 to 21 d of age .
[ Sen. 4, subscore: 1.00 ]: A total of 100 one-day-old White Roman female goslings were selected and randomly divided into 5 dietary treatment groups .
[ Sen. 5, subscore: 1.00 ]: Each group had 4 replicate cages ( 100 x 60 x 58 cm ) of 5 goslings .
[ Sen. 6, subscore: 1.00 ]: Goslings in each group were given one of 5 isoenergetic and isonitrogenous semi-purified diets .
[ Sen. 8, subscore: 1.00 ]: The goslings receiving the pectin diet had significantly higher viscosity in intestinal digesta than the other treatment diets .
[ Sen. 9, subscore: 1.00 ]: However , the daily feed intake , daily weight gain , and feed conversion ratio of goslings in the pectin group were significantly lower than those given the other diets .
[ Sen. 11, subscore: 1.00 ]: The relative weights of proventriculus , gizzard , liver and pancreas , as well as the relative weights and lengths of various intestinal segments in the goslings that received the pectin diet , were significantly higher than those receiving the other diets .
[ Sen. 12, subscore: 1.00 ]: The specific activities ( SA ) of amylase , lipase , trypsin , and chymotrypsin in the pancreatic it issue of goslings in the pectin group were significantly lower than those in the other groups .
[ Sen. 14, subscore: 1.00 ]: Goslings given a soluble NSP source ( pectin ) diet tended to exhibit inhibited growth and decreased activity of pancreatic enzymes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 9.00 |
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| Title: Tunable nanostructures as photothermal theranostic agents .
| | Author: Young JK Figueroa ER Drezek RA | | Journal: Ann Biomed Eng Citation: V : 40 P : 438-59 Year: 2012 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub22134466 Accession (PMID): 22134466 | | Abstract: The theranostic potential of several nanostructures has been discussed in the context of photothermal therapies and imaging .
In the last several decades , the burden of cancer has grown rapidly , making the need for new theranostic approaches vital Lasers have emerged as promising tools in cancer treatment , especially with the advent of photothermal therapies wherein light absorbing dyes or plasmonic gold nanoparticles are used to generate heat and achieve tumor damage .
Recently , photoabsorbing nanostructures have materialized that can be employed in conjunction with lasers in the near-infrared region in order to enhance both imaging and photothermal effects .
The incorporation of tunable nanostructures has resulted in improved specificity in cancer treatment .
Silica-cored gold nanoshells and gold nanorods currently serve as the chief plasmonic structures for photothermal therapy .
Although gold nanorods and silica-cored gold nanoshells have shown promise as therapeutic agents , over the past few years new nanostructures have emerged that offer comparable and even superior theranostic properties .
In the present review , several theranostic agents and their impact on the development of more effective photothermal therapies for the treatment of cancer are discussed .
These agents include hollow gold nanoshells , gold gold-sulfide nanoparticles , gold nanocages , carbon and titanium nanotubes , photothermal-based nanobubbles , polymeric nanoparticles and copper-based nanocrystals .
| Matching Sentences:
[ Sen. 8, subscore: 4.00 ]: These agents include hollow gold nanoshells , gold gold-sulfide nanoparticles , gold nanocages , carbon and titanium nanotubes , photothermal-based nanobubbles , polymeric nanoparticles and copper-based nanocrystals .
[ Sen. 5, subscore: 2.00 ]: Silica-cored gold nanoshells and gold nanorods currently serve as the chief plasmonic structures for photothermal therapy .
[ Sen. 6, subscore: 2.00 ]: Although gold nanorods and silica-cored gold nanoshells have shown promise as therapeutic agents , over the past few years new nanostructures have emerged that offer comparable and even superior theranostic properties .
[ Sen. 2, subscore: 1.00 ]: In the last several decades , the burden of cancer has grown rapidly , making the need for new theranostic approaches vital Lasers have emerged as promising tools in cancer treatment , especially with the advent of photothermal therapies wherein light absorbing dyes or plasmonic gold nanoparticles are used to generate heat and achieve tumor damage .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 8.00 |
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| Title: Estimation of the nuclear DNA content of gossypium species .
| | Author: Hendrix B Stewart JM .
| | Journal: Ann . Bot . Citation: V : 95 ( 5 ) P : 789-97 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15701660 Accession (PMID): 15701660 | | Abstract: BACKGROUND AND AIMS : Gossypium is an economically important , globally distributed taxon comprising more than 50 species .
DNA content estimates from about half of the species indicate over a 3-fold variation exists .
However , the nine DNA content estimates for G hirsutum reveal over a 2-fold difference for this species alone .
Recent reports have shown that several plant compounds can bias DNA content estimates obtained by commonly used methods .
The purpose of this research was to examine the standardization procedures used for DNA content determinations with flow cytometry as applied to Gossypium , and generate revised DNA content estimates for all available Gossypium species using best-standard practices .
METHODS : Flow cytometry was used to measure fluorescence of isolated Gossypium nuclei stained with propidium iodide .
Fluorescence values were converted to DNA content estimates based on the nuclear fluorescence of standard genotypes of barley , corn and rice .
Various combinations of nuclei preparations relative to the standards were evaluated for their influence on the estimates .
KEY RESULTS : Both external standardization and internal standardization with Oryza sativa IR36 yielded statistically similar DNA content estimates for Gossypium .
Internal standardization with Hordeum vulgare Sultan resulted in a high estimate of DNA content .
Nuclear DNA content estimates were generated for 37 Gossypium species using external standardization .
Estimates of ancestral genome sizes reveal that both increases and decreases in nuclear DNA content have occurred .
Variation in intraspecific and intragenomic DNA content was low , and the allopolyploid AD-genome size was nearly the additive of its progenitor genomes .
CONCLUSIONS : Due to unknown factors , internal standardization with H vulgare Sultan may not be appropriate for DNA content determinations of Gossypium .
The current DNA content estimates support accepted cytogenetic divisions of the genus .
Gossypium is a genus that exhibits genome constancy both through speciation within genomic groups and allopolyploidization . | Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: The purpose of this research was to examine the standardization procedures used for DNA content determinations with flow cytometry as applied to Gossypium , and generate revised DNA content estimates for all available Gossypium species using best-standard practices .
[ Sen. 1, subscore: 1.00 ]: BACKGROUND AND AIMS : Gossypium is an economically important , globally distributed taxon comprising more than 50 species .
[ Sen. 6, subscore: 1.00 ]: METHODS : Flow cytometry was used to measure fluorescence of isolated Gossypium nuclei stained with propidium iodide .
[ Sen. 9, subscore: 1.00 ]: KEY RESULTS : Both external standardization and internal standardization with Oryza sativa IR36 yielded statistically similar DNA content estimates for Gossypium .
[ Sen. 11, subscore: 1.00 ]: Nuclear DNA content estimates were generated for 37 Gossypium species using external standardization .
[ Sen. 14, subscore: 1.00 ]: CONCLUSIONS : Due to unknown factors , internal standardization with H vulgare Sultan may not be appropriate for DNA content determinations of Gossypium .
[ Sen. 16, subscore: 1.00 ]: Gossypium is a genus that exhibits genome constancy both through speciation within genomic groups and allopolyploidization .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 8.00 |
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| Title: Development of multianalyte flow-through and lateral-flow assays using gold particles and horseradish peroxidase as tracers for the rapid determination of carbaryl and endosulfan in agricultural products .
| | Author: Zhang C Zhang Y Wang S | | Journal: J Agric .
Food Chem .
Citation: V : 54 ( 7 ) P : 2502-7 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16569035 Accession (PMID): 16569035 | | Abstract: Membrane-based competitive immunoassays using gold particles and horseradish peroxidase ( HRP ) as tracers in flow-through and lateral-flow formats for multianalysis of carbaryl and endosulfan were developed .
For gold-based immunoassay , membrane strips were coated with goat anti-rabbit IgG ( control line ) and carbaryl hapten-ovalbumin ( OVA ) and endosulfan hapten-OVA ( test lines ) .
The visual detection limits for carbaryl and endosulfan were 100 and 10 microg/L in gold-based assays , respectively .
For immunoassay using HRP as tracer , anti-carbaryl and anti-endosulfan antibodies were separately coated on the membrane as test lines , and the visual detection limits were 10 microg/L for carbaryl and 1 microg/L for endosulfan .
The developed assays used gold particles and HRP as labels , respectively ; 10 times enhancement in the visual detection limit using HRP label was obtained in the study .
Matrix interference was eliminated by appropriate dilution of sample extracts with buffer .
For the validation of the multianalyte assay , the samples were screened by multianalyte gold-based assay and confirmed by HPLC for carbaryl determination and by GC for endosulfan determination .
The results of multianalyte gold-based flow-through assay for the determination of carbaryl and endosulfan were in good agreement with the results of instrumental analysis ( HPLC with ultraviolet detection and GC with electron capture detection ) .
The developed multianalyte immunoassays for which the results were interpreted visually can be used as convenient qualitative tools for on-site rapid screening of carbaryl and endosulfan simultaneously in agricultural products . | Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: For gold-based immunoassay , membrane strips were coated with goat anti-rabbit IgG ( control line ) and carbaryl hapten-ovalbumin ( OVA ) and endosulfan hapten-OVA ( test lines ) .
[ Sen. 8, subscore: 2.00 ]: The results of multianalyte gold-based flow-through assay for the determination of carbaryl and endosulfan were in good agreement with the results of instrumental analysis ( HPLC with ultraviolet detection and GC with electron capture detection ) .
[ Sen. 1, subscore: 1.00 ]: Membrane-based competitive immunoassays using gold particles and horseradish peroxidase ( HRP ) as tracers in flow-through and lateral-flow formats for multianalysis of carbaryl and endosulfan were developed .
[ Sen. 3, subscore: 1.00 ]: The visual detection limits for carbaryl and endosulfan were 100 and 10 microg/L in gold-based assays , respectively .
[ Sen. 5, subscore: 1.00 ]: The developed assays used gold particles and HRP as labels , respectively ; 10 times enhancement in the visual detection limit using HRP label was obtained in the study .
[ Sen. 7, subscore: 1.00 ]: For the validation of the multianalyte assay , the samples were screened by multianalyte gold-based assay and confirmed by HPLC for carbaryl determination and by GC for endosulfan determination .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 8.00 |
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| Title: Novel Triazine JPC-2067-B Inhibits Toxoplasma gondii In Vitro and In Vivo .
| | Author: Mui EJ Schiehser GA Milhous WK Hsu H Roberts CW Kirisits M Muench S Rice D Dubey JP Fowble JW Rathod PK Queener SF Liu SR Jacobus DP McLeod R | | Journal: PLoS Negl Trop Dis Citation: V : 2 P : e190 Year: 2008 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub18320016 Accession (PMID): 18320016 | | Abstract: BACKGROUND AND METHODOLOGY : Toxoplasma gondii causes substantial morbidity , mortality , and costs for healthcare in the developed and developing world .
Current medicines are not well tolerated and cause hypersensitivity reactions .
The dihydrotriazine JPC-2067-B ( 4 , 6-diamino-1 , 2-dihydro-2 , 2-dimethyl-1- ( 3 ( 2-chloro- , 4-trifluoromethoxyphenoxy ) propyloxy ) -1 , 3 , 5-triazine ) , which inhibits dihydrofolate reductase ( DHFR ) , is highly effective against Plasmodium falciparum , Plasmodium vivax , and apicomplexans related to T gondii .
JPC-2067-B is the primary metabolite of the orally active biguanide JPC-2056 1- ( 3- ( 2-chloro-4-trifluoromethoxyphenyloxy ) propyl oxy ) - 5-isopropylbiguanide , which is being advanced to clinical trials for malaria .
Efficacy of the prodrug JPC-2056 and the active metabolite JPC-2067-B against T gondii and T gondii DHFR as well as toxicity toward mammalian cells were tested .
PRINCIPAL FINDINGS AND CONCLUSIONS : Herein , we found that JPC-2067-B is highly effective against T gondii .
We demonstrate that JPC-2067-B inhibits T gondii growth in culture ( IC50 20 nM ) , inhibits the purified enzyme ( IC50 6 . 5 nM ) , is more efficacious than pyrimethamine , and is cidal in vitro .
JPC-2067-B administered parenterally and the orally administered pro-drug ( JPC-2056 ) are also effective against T gondii tachyzoites in vivo .
A molecular model of T gondii DHFR-TS complexed with JPC-2067-B was developed .
We found that the three main parasite clonal types and isolates from South and Central America , the United States , Canada , China , and Sri Lanka have the same amino acid sequences preserving key binding sites for the triazine .
SIGNIFICANCE : JPC-2056/JPC-2067-B have potential to be more effective and possibly less toxic treatments for toxoplasmosis than currently available medicines .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: Efficacy of the prodrug JPC-2056 and the active metabolite JPC-2067-B against T gondii and T gondii DHFR as well as toxicity toward mammalian cells were tested .
[ Sen. 1, subscore: 1.00 ]: BACKGROUND AND METHODOLOGY : Toxoplasma gondii causes substantial morbidity , mortality , and costs for healthcare in the developed and developing world .
[ Sen. 3, subscore: 1.00 ]: The dihydrotriazine JPC-2067-B ( 4 , 6-diamino-1 , 2-dihydro-2 , 2-dimethyl-1- ( 3 ( 2-chloro- , 4-trifluoromethoxyphenoxy ) propyloxy ) -1 , 3 , 5-triazine ) , which inhibits dihydrofolate reductase ( DHFR ) , is highly effective against Plasmodium falciparum , Plasmodium vivax , and apicomplexans related to T gondii .
[ Sen. 6, subscore: 1.00 ]: PRINCIPAL FINDINGS AND CONCLUSIONS : Herein , we found that JPC-2067-B is highly effective against T gondii .
[ Sen. 7, subscore: 1.00 ]: We demonstrate that JPC-2067-B inhibits T gondii growth in culture ( IC50 20 nM ) , inhibits the purified enzyme ( IC50 6 . 5 nM ) , is more efficacious than pyrimethamine , and is cidal in vitro .
[ Sen. 8, subscore: 1.00 ]: JPC-2067-B administered parenterally and the orally administered pro-drug ( JPC-2056 ) are also effective against T gondii tachyzoites in vivo .
[ Sen. 9, subscore: 1.00 ]: A molecular model of T gondii DHFR-TS complexed with JPC-2067-B was developed .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 8.00 |
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| Title: Amelioration of salinity stress by exogenously applied spermidine or spermine in three varieties of indica rice differing in their level of salt tolerance .
| | Author: Roychoudhury A Basu S Sengupta DN | | Journal: J Plant Physiol Citation: V : 168 P : 317-28 Year: 2011 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub20728960 Accession (PMID): 20728960 | | Abstract: We present here the comparative protective potentiality of exogenously applied polyamines ( PAs ) , namely spermidine ( Spd ) and spermine ( Spm ) , in mitigating NaCl toxicity and inducing short-term salinity tolerance in three indica rice varieties , namely M-1-48 ( salt-sensitive ) , Nonabokra ( salt-tolerant ) and Gobindobhog ( highly sensitive ) .
The retardation in root length or shoot length and toxic Na ( + ) accumulation or K ( + ) loss , the considerable increment in malondialdehyde/H ( 2 ) O ( 2 ) accumulation or lipoxygenase activity , all of which were particularly noteworthy in M-1-48 and Gobindobhog during salinity stress , was appreciably reduced by co-treatment with Spd or Spm .
Both the PAs also inhibited the extent of salt-induced protein carbonylation in all the varieties and enhanced protease activity , especially in Gobindobhog .
The prevention of chlorophyll degradation was better with Spd in Nonabokra and Gobindobhog .
While the salt-induced increase in anthocyanin or reducing sugar level was further prompted by Spd or Spm in all the varieties , the proline content was elevated by Spd particularly in Gobindobhog .
During salinity stress , both the PAs were effective in lowering the putrescine accumulation in M-1-48 and Gobindobhog , and strikingly increasing the Spm level in all the varieties , the highest being in Gobindobhog .
In addition , they enhanced the activity of peroxidases and compensated for the decreased catalase activity in all the varieties .
Thus the two PAs could recuperate all the three varieties from salt-induced damages to different degrees .
The salt injuries , encountered in M-1-48 and Gobindobhog , both of which showed greater susceptibility to salinity stress , were more pronouncedly alleviated and counteracted by the PAs , than the salt-tolerant Nonabokra .
The reversal of inhibitory effect of salinity stress was conferred by preventing growth inhibition or various forms of cellular damages , maintaining proper K ( + ) /Na ( + ) balance or triggering the level of osmolytes and activity of antioxidant enzymes .
Our communication offers a referenced evidence for an understanding of the mechanism by which higher PAs relieve the damages particularly in salt-sensitive rice varieties .
| Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: During salinity stress , both the PAs were effective in lowering the putrescine accumulation in M-1-48 and Gobindobhog , and strikingly increasing the Spm level in all the varieties , the highest being in Gobindobhog .
[ Sen. 1, subscore: 1.00 ]: We present here the comparative protective potentiality of exogenously applied polyamines ( PAs ) , namely spermidine ( Spd ) and spermine ( Spm ) , in mitigating NaCl toxicity and inducing short-term salinity tolerance in three indica rice varieties , namely M-1-48 ( salt-sensitive ) , Nonabokra ( salt-tolerant ) and Gobindobhog ( highly sensitive ) .
[ Sen. 2, subscore: 1.00 ]: The retardation in root length or shoot length and toxic Na ( + ) accumulation or K ( + ) loss , the considerable increment in malondialdehyde/H ( 2 ) O ( 2 ) accumulation or lipoxygenase activity , all of which were particularly noteworthy in M-1-48 and Gobindobhog during salinity stress , was appreciably reduced by co-treatment with Spd or Spm .
[ Sen. 3, subscore: 1.00 ]: Both the PAs also inhibited the extent of salt-induced protein carbonylation in all the varieties and enhanced protease activity , especially in Gobindobhog .
[ Sen. 4, subscore: 1.00 ]: The prevention of chlorophyll degradation was better with Spd in Nonabokra and Gobindobhog .
[ Sen. 5, subscore: 1.00 ]: While the salt-induced increase in anthocyanin or reducing sugar level was further prompted by Spd or Spm in all the varieties , the proline content was elevated by Spd particularly in Gobindobhog .
[ Sen. 9, subscore: 1.00 ]: The salt injuries , encountered in M-1-48 and Gobindobhog , both of which showed greater susceptibility to salinity stress , were more pronouncedly alleviated and counteracted by the PAs , than the salt-tolerant Nonabokra .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 8.00 |
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| Title: Pristine graphite oxide .
| | Author: Dimiev A Kosynkin DV Alemany LB Chaguine P Tour JM | | Journal: J Am Chem Soc Citation: V : 134 P : 2815-22 Year: 2012 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub22239610 Accession (PMID): 22239610 | | Abstract: Graphite oxide ( GO ) is a lamellar substance with an ambiguous structure due to material complexity .
Recently published GO-related studies employ only one out of several existing models to interpret the experimental data .
Because the models are different , this leads to confusion in understanding the nature of the observed phenomena .
Lessening the structural ambiguity would lead to further developments in functionalization and use of GO .
Here , we show that the structure and properties of GO depend significantly on the quenching and purification procedures , rather than , as is commonly thought , on the type of graphite used or oxidation protocol .
We introduce a new purification protocol that produces a product that we refer to as pristine GO ( pGO ) in contrast to the commonly known material that we will refer to as conventional GO ( cGO ) .
We explain the differences between pGO and cGO by transformations caused by reaction with water .
We produce ultraviolet-visible spectroscopic , Fourier transform infrared spectroscopic , solid-state nuclear magnetic resonance spectroscopic , thermogravimetric , and scanning electron microscopic analytical evidence for the structure of pGO .
This work provides a new explanation for the acidity of GO solutions and allows us to add critical details to existing GO models .
| Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: We introduce a new purification protocol that produces a product that we refer to as pristine GO ( pGO ) in contrast to the commonly known material that we will refer to as conventional GO ( cGO ) .
[ Sen. 9, subscore: 2.00 ]: This work provides a new explanation for the acidity of GO solutions and allows us to add critical details to existing GO models .
[ Sen. 1, subscore: 1.00 ]: Graphite oxide ( GO ) is a lamellar substance with an ambiguous structure due to material complexity .
[ Sen. 2, subscore: 1.00 ]: Recently published GO-related studies employ only one out of several existing models to interpret the experimental data .
[ Sen. 4, subscore: 1.00 ]: Lessening the structural ambiguity would lead to further developments in functionalization and use of GO .
[ Sen. 5, subscore: 1.00 ]: Here , we show that the structure and properties of GO depend significantly on the quenching and purification procedures , rather than , as is commonly thought , on the type of graphite used or oxidation protocol .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Structure and Function of the Golgi Complex in Rice Cells ( II .
Purification and Characterization of Golgi Membrane-Bound Nucleoside Diphosphatase ) .
| | Author: Mitsui T Honma M Kondo T Hashimoto N Kimura S Igaue I | | Journal: Citation: V : 106 ( 1 ) P : 119-125 Year: 1994 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12232309 Accession (PMID): 12232309 | | Abstract: Inosine diphosphatase bound to Golgi membranes was studied in rice ( Oryza sativa L cv Nipponkai ) cells .
The enzyme was solubilized with Triton X-100 from isolated rice Golgi membranes and was highly purified employing a series of chromatography steps in the presence of 20% glycerol and 0 . 1% Triton X-100 .
The apparent molecular mass of the enzyme was estimated by gel filtration column chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis to be 200 and 55 kD , respectively .
The isoelectric point of the enzyme was determined to be 7 . 5 .
The optimal pH for the enzyme activity was around 7 and the enzyme required Mg2+ for hydrolyzing activity .
IDP , UDP , and GDP were effective substrate for the purified rice Golgi membrane-bound inosine diphosphatase , whereas activity with ADP , CDP , and thymidine 5 [ prime ] -diphosphate was 10 to 20% of IDP .
The Km values for IDP , UDP , and GDP were 0 . 48 , 0 . 50 , and 0 . 67 mM , respectively , and Vmax values were 1 . 85 , 1 . 54 , and 1 . 67 [ mu ] mol min-1 mg-1 , respectively .
These results indicate that the rice Golgi enzyme is a nucleoside diphosphatase that is specific for IDP , UDP , and GDP .
Furthermore , this rice Golgi nucleoside diphosphatase stimulated the activity of glucan synthase I also localized in rice Golgi membranes .
The results strongly support the view that this nucleoside diphosphatase is involved in regulation of [ beta ] -glucan synthesis in the plant Golgi complex | Matching Sentences:
[ Sen. 9, subscore: 2.00 ]: Furthermore , this rice Golgi nucleoside diphosphatase stimulated the activity of glucan synthase I also localized in rice Golgi membranes .
[ Sen. 1, subscore: 1.00 ]: Inosine diphosphatase bound to Golgi membranes was studied in rice ( Oryza sativa L cv Nipponkai ) cells .
[ Sen. 2, subscore: 1.00 ]: The enzyme was solubilized with Triton X-100 from isolated rice Golgi membranes and was highly purified employing a series of chromatography steps in the presence of 20% glycerol and 0 . 1% Triton X-100 .
[ Sen. 6, subscore: 1.00 ]: IDP , UDP , and GDP were effective substrate for the purified rice Golgi membrane-bound inosine diphosphatase , whereas activity with ADP , CDP , and thymidine 5 [ prime ] -diphosphate was 10 to 20% of IDP .
[ Sen. 8, subscore: 1.00 ]: These results indicate that the rice Golgi enzyme is a nucleoside diphosphatase that is specific for IDP , UDP , and GDP .
[ Sen. 10, subscore: 1.00 ]: The results strongly support the view that this nucleoside diphosphatase is involved in regulation of [ beta ] -glucan synthesis in the plant Golgi complex
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Induction of H2O2 in transgenic rice leads to cell death and enhanced resistance to both bacterial and fungal pathogens .
| | Author: Kachroo A He Z Patkar R Zhu Q Zhong J Li D Ronald P Lamb C Chattoo BB .
| | Journal: Transgenic Res .
Citation: V : 12 ( 5 ) P : 577-86 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub14601656 Accession (PMID): 14601656 | | Abstract: Oxidative burst , mediated by hydrogen peroxide ( H2O2 ) , has been recognized as a key component of plant defense response during an incompatible interaction .
To determine if elevated levels of H2O2 lead to cell death , activation of defense genes and enhanced resistance to diverse pathogens , transgenic rice plants expressing a fungal glucose oxidase gene ( GOX ) were generated using both constitutive and inducible expression systems .
Constitutive or wound/pathogen-induced expression of GOX also allowed us to determine the effectiveness of these systems in conferring long lasting resistance to various pathogens .
Both constitutive and wound/pathogen-induced expression of GOX lead to increases in the endogenous levels of H2O2 , which in turn caused cell death .
Elevated levels of H2O2 also activated the expression of several defense genes and these transgenic plants showed enhanced resistance to both bacterial and fungal pathogens .
In comparison to inducible expression , constitutive expression of GOX resulted in 3-10-fold higher levels of the GOX transcript and the corresponding enzymatic activity .
Such increased levels of GOX , which would result in elevated levels of H2O2 , caused improper seed set and decreased seed viability in transgenic plants constitutively expressing GOX .
Our results suggest that pathogen inducible expression of heterologous genes may be a practical and robust way of generating broad spectrum disease resistance . | Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: In comparison to inducible expression , constitutive expression of GOX resulted in 3-10-fold higher levels of the GOX transcript and the corresponding enzymatic activity .
[ Sen. 7, subscore: 2.00 ]: Such increased levels of GOX , which would result in elevated levels of H2O2 , caused improper seed set and decreased seed viability in transgenic plants constitutively expressing GOX .
[ Sen. 2, subscore: 1.00 ]: To determine if elevated levels of H2O2 lead to cell death , activation of defense genes and enhanced resistance to diverse pathogens , transgenic rice plants expressing a fungal glucose oxidase gene ( GOX ) were generated using both constitutive and inducible expression systems .
[ Sen. 3, subscore: 1.00 ]: Constitutive or wound/pathogen-induced expression of GOX also allowed us to determine the effectiveness of these systems in conferring long lasting resistance to various pathogens .
[ Sen. 4, subscore: 1.00 ]: Both constitutive and wound/pathogen-induced expression of GOX lead to increases in the endogenous levels of H2O2 , which in turn caused cell death .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Effects of diets containing gossypol on ovarian histology , function and fertility in prepubertal beef heifers .
| | Author: Gambill MD Humphrey WD .
| | Journal: Theriogenology Citation: V : 40 ( 3 ) P : 585-93 Year: 1993 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16727341 Accession (PMID): 16727341 | | Abstract: Forty-five crossbred beef heifers ( weight = 268 . 3 +/- 5 . 7 kg ) were used to determine the effects of dietary gossypol on ovarian morphology , erythrocyte fragility and fertility .
Heifers were randomly assigned to 1 of 3 isonitrogenous dietary treatments .
The diet consisted of rice mill feed and milo supplemented with soybean meal ( n = 13 ; control ) , cottonseed meal ( n = 16 ; low supplementation ) which supplied 6 . 1 g free gossypol animal ( -1 ) day ( -1 ) , or whole cottonseed ( n = 16 ; high supplementation ) which supplied 13 . 7 g free gossypol animal ( -1 ) day ( -1 ) .
The heifers were group-fed each diet for 64 days and were maintained on similar but separate fescue pastures overseeded with wheat .
After 64 days , 4 heifers from each diet were confined and fed their respective diets .
On Day 10 following estrus , each animal was unilaterally ovariectomized , and the ovary containing the corpus luteum was removed .
The remaining ovary was removed 6 to 12 hours after detection of estrus in the next cycle .
Erythrocyte fragility increased ( P < 0 . 02 ) in heifers receiving gossypol compared with that of the controls .
Cyclicity in the heifers was 81 . 3 , 68 . 8 and 38 . 4% for high , low and control diets , respectively , at the end of the 64-day treatment period .
First service conception rate , as determined by palpation per rectum , was similar among treatments ( 58 . 3 , 33 . 3 , 33 . 3% for high , low and control groups , respectively ) .
Weight gain increased ( P < 0 . 03 ) in control heifers compared with that of heifers receiving gossypol .
Gross ovarian morphology and histology were similar for all heifers .
Although gossypol produced mild toxicosis in heifers , no adverse reproductive effects could be detected from gossypol intake .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: The diet consisted of rice mill feed and milo supplemented with soybean meal ( n = 13 ; control ) , cottonseed meal ( n = 16 ; low supplementation ) which supplied 6 . 1 g free gossypol animal ( -1 ) day ( -1 ) , or whole cottonseed ( n = 16 ; high supplementation ) which supplied 13 . 7 g free gossypol animal ( -1 ) day ( -1 ) .
[ Sen. 13, subscore: 2.00 ]: Although gossypol produced mild toxicosis in heifers , no adverse reproductive effects could be detected from gossypol intake .
[ Sen. 1, subscore: 1.00 ]: Forty-five crossbred beef heifers ( weight = 268 . 3 +/- 5 . 7 kg ) were used to determine the effects of dietary gossypol on ovarian morphology , erythrocyte fragility and fertility .
[ Sen. 8, subscore: 1.00 ]: Erythrocyte fragility increased ( P < 0 . 02 ) in heifers receiving gossypol compared with that of the controls .
[ Sen. 11, subscore: 1.00 ]: Weight gain increased ( P < 0 . 03 ) in control heifers compared with that of heifers receiving gossypol .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: WEGO : a web tool for plotting GO annotations .
| | Author: Ye J Fang L Zheng H Zhang Y Chen J Zhang Z Wang J Li S Li R Bolund L Wang J | | Journal: Nucleic Acids Res .
Citation: V : 34 ( Web Server issue ) P : W293-7 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16845012 Accession (PMID): 16845012 | | Abstract: Unified , structured vocabularies and classifications freely provided by the Gene Ontology ( GO ) Consortium are widely accepted in most of the large scale gene annotation projects .
Consequently , many tools have been created for use with the GO ontologies .
WEGO ( Web Gene Ontology Annotation Plot ) is a simple but useful tool for visualizing , comparing and plotting GO annotation results .
Different from other commercial software for creating chart , WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results .
WEGO has been used widely in many important biological research projects , such as the rice genome project and the silkworm genome project .
It has become one of the daily tools for downstream gene annotation analysis , especially when performing comparative genomics tasks .
WEGO , along with the two other tools , namely External to GO Query and GO Archive Query , are freely available for all users at http : //wego . genomics . org . cn .
There are two available mirror sites at http : //wego2 . genomics . org . cn and http : //wego . genomics . com . cn .
Any suggestions are welcome at wego@genomics . org . cn .
| Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: Different from other commercial software for creating chart , WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results .
[ Sen. 7, subscore: 2.00 ]: WEGO , along with the two other tools , namely External to GO Query and GO Archive Query , are freely available for all users at http : //wego . genomics . org . cn .
[ Sen. 1, subscore: 1.00 ]: Unified , structured vocabularies and classifications freely provided by the Gene Ontology ( GO ) Consortium are widely accepted in most of the large scale gene annotation projects .
[ Sen. 2, subscore: 1.00 ]: Consequently , many tools have been created for use with the GO ontologies .
[ Sen. 3, subscore: 1.00 ]: WEGO ( Web Gene Ontology Annotation Plot ) is a simple but useful tool for visualizing , comparing and plotting GO annotation results .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Differentiation of the two rice subspecies indica and japonica : a Gene Ontology perspective .
| | Author: Johns MA Mao L | | Journal: Citation: V : ( ) P : Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17131138 Accession (PMID): 17131138 | | Abstract: Cultivated rice ( Oryza sativa ) is comprised of two subspecies : japonica and indica .
Polymorphism levels between putative homologues were determined for genes whose japonica homologue had been classified into functional categories using the Gene Ontology ( GO ) system .
Genes were partitioned into below-average and above-average polymorphism groups , and then the set of genes having each GO term was checked for the randomness of its distribution into these polymorphism groups using a series of False Discovery Rate ( FDR ) tests .
The robustness of the conclusions was enhanced by employing different cutoff values and sequence samplings in the FDR tests .
Significant nonrandom polymorphism distributions were found for protein-coding sequences in many GO categories .
In contrast , a random distribution for nearly all GO terms was seen with intron sequences .
These results were extended by measuring the nonsynonymous to synonymous codon usage ratio ( dN/dS ) using a permutation test , which showed that some above-average polymorphism GO categories also had a high proportion of genes with a dN/dS ratio greater than one , suggesting positive selection on these GO categories during indica-japonica differentiation .
An analysis of predominant gene names in the significant GO categories divided them into four functional classes : production of defense-related compounds , cell wall , cell signaling , and transcription factors . | Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: These results were extended by measuring the nonsynonymous to synonymous codon usage ratio ( dN/dS ) using a permutation test , which showed that some above-average polymorphism GO categories also had a high proportion of genes with a dN/dS ratio greater than one , suggesting positive selection on these GO categories during indica-japonica differentiation .
[ Sen. 2, subscore: 1.00 ]: Polymorphism levels between putative homologues were determined for genes whose japonica homologue had been classified into functional categories using the Gene Ontology ( GO ) system .
[ Sen. 3, subscore: 1.00 ]: Genes were partitioned into below-average and above-average polymorphism groups , and then the set of genes having each GO term was checked for the randomness of its distribution into these polymorphism groups using a series of False Discovery Rate ( FDR ) tests .
[ Sen. 5, subscore: 1.00 ]: Significant nonrandom polymorphism distributions were found for protein-coding sequences in many GO categories .
[ Sen. 6, subscore: 1.00 ]: In contrast , a random distribution for nearly all GO terms was seen with intron sequences .
[ Sen. 8, subscore: 1.00 ]: An analysis of predominant gene names in the significant GO categories divided them into four functional classes : production of defense-related compounds , cell wall , cell signaling , and transcription factors .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Mercury emission and distribution : Potential environmental risks at a small-scale gold mining operation , Phichit Province , Thailand .
| | Author: Pataranawat P Parkpian P Polprasert C Delaune RD Jugsujinda A | | Journal: J Environ Sci Health A Tox Hazard Subst Environ Eng Citation: V : 42 P : 1081-93 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17616880 Accession (PMID): 17616880 | | Abstract: Mercury ( Hg ) contamination was assessed in environment near an amalgamation gold recovery operation located at a small scale mining operation ( Phanom Pha ) in Phichit Province , Thailand .
Total mercury ( THg ) concentrations was determined in water , sediment , bivalves in the aquatic environment and as dry deposition or atmospheric fallout on surface soil and leaves of Neem tree ( Azadirachta indica Juss . var . siamensis Valeton ) near the mining operation .
THg in surface soil , Neem flowers ( edible part ) and rice grain in surrounding terrestrial habitat and with distance from the mining area were also evaluated for possible contamination .
Potential environmental risks were evaluated using the hazard quotient equation .
Hg analyses conducted in the aquatic habitat showed that THg in water , sediment and bivalves ( Scabies cripata Gould ) ranged from 0 . 4 to 4 microg L ( -1 ) , 96 to 402 microg kg ( -1 ) dry weight ( dw ) and 15 to 584 microg kg ( -1 ) wet weight ( ww ) , respectively .
High concentrations of THg in water , sediment and bivalves were observed in the receiving stream near the mining operation which was located near the Khao Chet Luk Reservoir .
Whereas the THg concentration in water , sediment and bivalves from monitoring stations outside the gold mining operation ( upstream and downstream ) , were considerably lower with the values of 0 . 4-0 . 8 microg L ( -1 ) , 96-140 microg kg ( -1 ) dw and 88-658 microg kg ( -1 ) dw , respectively .
The elevated concentration of Hg found in the sediment near the mining operation was consistent with Hg accumulation measured in bivalves .
The elevated Hg levels found in living bivalves collected from highly contaminated sites suggested that the sediment bound Hg was bioavailable .
THg in surface soils , brown rice grain ( Jasmine rice 105 ) and Neem flowers of terrestrial habitats were in the range of 16 to 180 microg kg ( -1 ) dw , 190 to 300 microg kg ( -1 ) dw , and 622 to 2150 microg kg ( -1 ) dw , respectively .
Elevated concentrations of mercury were found in Neem flowers with the concentration greater than 600 microg kg ( -1 ) ww , which exceeds the maximum permissible concentration reported for biota it issue ( 500 microg kg ( -1 ) ww ) .
An evaluation of air and soil pollution near the mining operations showed high concentrations of THg in dry deposit from atmospheric fallout ( 139 microg m ( -2 ) d ( -1 ) ) , and in surface soil ( 10 , 564 microg kg ( -1 ) dw ) at station near where open burning of gold ore extracts using the amalgamation process occurred .
High or elevated concentration of THg ( 1172-1301 microg kg ( -1 ) dw ) in leaves of Neem tree was also measured near the mining operations .
A survey of Hg in surface soil showed elevated Hg concentrations near the site which corresponded to the elevated THg concentration in dry deposition .
These results suggested that atmospheric fallout is a major source of Hg to the area surrounding the mining or gold ore extraction .
Results also suggest that Hg emitted into the air ( estimated to be 60-150 g d ( -1 ) ) from the gold mining activities ( over the past 10 years ) contaminated air , the aquatic environment , surface soil and biota in the area surrounding the gold mining operation .
| Matching Sentences:
[ Sen. 16, subscore: 2.00 ]: Results also suggest that Hg emitted into the air ( estimated to be 60-150 g d ( -1 ) ) from the gold mining activities ( over the past 10 years ) contaminated air , the aquatic environment , surface soil and biota in the area surrounding the gold mining operation .
[ Sen. 1, subscore: 1.00 ]: Mercury ( Hg ) contamination was assessed in environment near an amalgamation gold recovery operation located at a small scale mining operation ( Phanom Pha ) in Phichit Province , Thailand .
[ Sen. 5, subscore: 1.00 ]: Hg analyses conducted in the aquatic habitat showed that THg in water , sediment and bivalves ( Scabies cripata Gould ) ranged from 0 . 4 to 4 microg L ( -1 ) , 96 to 402 microg kg ( -1 ) dry weight ( dw ) and 15 to 584 microg kg ( -1 ) wet weight ( ww ) , respectively .
[ Sen. 7, subscore: 1.00 ]: Whereas the THg concentration in water , sediment and bivalves from monitoring stations outside the gold mining operation ( upstream and downstream ) , were considerably lower with the values of 0 . 4-0 . 8 microg L ( -1 ) , 96-140 microg kg ( -1 ) dw and 88-658 microg kg ( -1 ) dw , respectively .
[ Sen. 12, subscore: 1.00 ]: An evaluation of air and soil pollution near the mining operations showed high concentrations of THg in dry deposit from atmospheric fallout ( 139 microg m ( -2 ) d ( -1 ) ) , and in surface soil ( 10 , 564 microg kg ( -1 ) dw ) at station near where open burning of gold ore extracts using the amalgamation process occurred .
[ Sen. 15, subscore: 1.00 ]: These results suggested that atmospheric fallout is a major source of Hg to the area surrounding the mining or gold ore extraction .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Comparative physiological and molecular responses of a common aromatic indica rice cultivar to high salinity with non-aromatic indica rice cultivars .
| | Author: Roychoudhury A Basu S Sarkar SN Sengupta DN | | Journal: Plant Cell Rep Citation: V : 27 P : 1395-410 Year: 2008 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub18509653 Accession (PMID): 18509653 | | Abstract: In an attempt to understand the molecular basis of salt-stress response in the aromatic rice Gobindobhog , a comprehensive analysis encompassing physiological or biochemical assays and gene expression studies under high salt ( 200 mM NaCl ) supply regimes were initiated and compared with a salt-sensitive ( M-1-48 ) and salt-tolerant ( Nonabokra ) rice .
The detrimental effects of salinity stress were the most pronounced in Gobindobhog , as reflected by the maximally increased root to shoot ratio , the highest chlorophyll degeneration , the highest foliar concentration of Na ( + ) ions and peroxide content , with their maximum increment after salt treatment .
The amplification of oxidative damages was further stimulated by the accumulation of putrescine and lipid peroxidation-derived toxic degradation products ( increased malondialdehyde and lipoxygenase activity ) , which were comparable in M-1-48 and Gobindobhog .
Antioxidants like anthocyanin and particularly cysteine and the osmolytes like reducing sugar , proline and polyamines ( spermidine and spermine ) showed the highest level in Nonabokra .
While the inhibition of catalase activity occurred in all the varieties following salt-stress , the maximum induction in guaiacol peroxidase activity , elevated cysteine and proline levels in Gobindobhog probably constituted the detoxification mechanism obligatory for its survival Intensification of the aroma content with salt treatment was markedly noted in Gobindobhog .
A very low abundance of Rab16A/SamDC transcript and the corresponding proteins were observed both in M-1-48 and Gobindobhog , induced only after salt-stress , whereas they were constitutively expressed in Nonabokra .
Thus , our data reflect Gobindobhog as a salt-sensitive cultivar , susceptible to high-stress-induced growth-inhibition , ion imbalances , membrane/oxidative damages with lower expression of stress-tolerant genes .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: While the inhibition of catalase activity occurred in all the varieties following salt-stress , the maximum induction in guaiacol peroxidase activity , elevated cysteine and proline levels in Gobindobhog probably constituted the detoxification mechanism obligatory for its survival Intensification of the aroma content with salt treatment was markedly noted in Gobindobhog .
[ Sen. 1, subscore: 1.00 ]: In an attempt to understand the molecular basis of salt-stress response in the aromatic rice Gobindobhog , a comprehensive analysis encompassing physiological or biochemical assays and gene expression studies under high salt ( 200 mM NaCl ) supply regimes were initiated and compared with a salt-sensitive ( M-1-48 ) and salt-tolerant ( Nonabokra ) rice .
[ Sen. 2, subscore: 1.00 ]: The detrimental effects of salinity stress were the most pronounced in Gobindobhog , as reflected by the maximally increased root to shoot ratio , the highest chlorophyll degeneration , the highest foliar concentration of Na ( + ) ions and peroxide content , with their maximum increment after salt treatment .
[ Sen. 3, subscore: 1.00 ]: The amplification of oxidative damages was further stimulated by the accumulation of putrescine and lipid peroxidation-derived toxic degradation products ( increased malondialdehyde and lipoxygenase activity ) , which were comparable in M-1-48 and Gobindobhog .
[ Sen. 6, subscore: 1.00 ]: A very low abundance of Rab16A/SamDC transcript and the corresponding proteins were observed both in M-1-48 and Gobindobhog , induced only after salt-stress , whereas they were constitutively expressed in Nonabokra .
[ Sen. 7, subscore: 1.00 ]: Thus , our data reflect Gobindobhog as a salt-sensitive cultivar , susceptible to high-stress-induced growth-inhibition , ion imbalances , membrane/oxidative damages with lower expression of stress-tolerant genes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Metal-based nanorods as molecule-specific contrast agents for reflectance imaging in 3D it issues .
| | Author: Javier DJ Nitin N Roblyer DM Richards-Kortum R | | Journal: J Nanophotonics Citation: V : 2 P : 23506 Year: 2008 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub19066632 Accession (PMID): 19066632 | | Abstract: Anisotropic metal-based nanomaterials have been proposed as potential contrast agents due to their strong surface plasmon resonance .
We evaluated the contrast properties of gold , silver , and gold-silver hybrid nanorods for molecular imaging applications in three-dimensional biological samples .
We used diffuse reflectance spectroscopy to predict the contrast properties of different types of nanorods embedded in biological model systems of increasing complexity .
The predicted contrast properties were then validated using wide-field and high-resolution imaging .
Results demonstrated that silver nanorods yield images with higher positive-contrast than gold nanorods ; however , it is more difficult to synthesize silver nanorods which are homogeneous in shape and size .
Gold-silver hybrid nanorods combine the homogeneous synthesis of gold nanorods with the higher scattering properties of silver nanorods .
The spectroscopic and imaging results demonstrated that the image contrast properties that can be achieved with anisotropic nanomaterials depend strongly on the material composition , mode of imaging , presence of targeting molecules , and the biological environment .
We also found that gold , silver , and gold-silver hybrid nanorods are stable and biocompatible sources of positive and absorptive contrast for use in reflectance molecular imaging and are promising for future clinical translation .
| Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: We evaluated the contrast properties of gold , silver , and gold-silver hybrid nanorods for molecular imaging applications in three-dimensional biological samples .
[ Sen. 6, subscore: 2.00 ]: Gold-silver hybrid nanorods combine the homogeneous synthesis of gold nanorods with the higher scattering properties of silver nanorods .
[ Sen. 8, subscore: 2.00 ]: We also found that gold , silver , and gold-silver hybrid nanorods are stable and biocompatible sources of positive and absorptive contrast for use in reflectance molecular imaging and are promising for future clinical translation .
[ Sen. 5, subscore: 1.00 ]: Results demonstrated that silver nanorods yield images with higher positive-contrast than gold nanorods ; however , it is more difficult to synthesize silver nanorods which are homogeneous in shape and size .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Comparison of effect of high intake of magnesium with high intake of phosphorus and potassium on urolithiasis in goats fed with cottonseed meal diet .
| | Author: Wang JY Sun WD Wang XL | | Journal: Res Vet Sci Citation: V : 87 P : 79-84 Year: 2009 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub19091365 Accession (PMID): 19091365 | | Abstract: The effect of high intake of Mg on urolithiasis was compared with high intake of P and K in goats being fed with a cottonseed meal and rice straw diet .
Eighteen wether goats were randomly allocated into group A , B and C evenly and fed with cottonseed meal and rice straw diet for three months .
From day 60 onwards , KH ( 2 ) PO ( 4 ) and K ( 2 ) HPO ( 4 ) were provided via drinking water to goats in group B to increase the intake of P , K , and MgO to goats in group C to increase the intake of Mg .
Blood and urine samples were collected to analyze the concentration of P , K , Mg and Ca , and the activity product ( AP ) of potassium magnesium phosphate ( MKP ) in urine was also calculated .
The composition of calculi and urinary sedimentary crystals were examined by chemical qualitative analysis , X-ray diffraction , X-ray energy dispersive spectrometry and Fourier transform infrared spectroscopy .
The results showed that the incidence of urolithiasis in group C ( 6/6 ) was higher than that in group A ( 1/6 ) and B ( 1/6 ) ( P<0 . 05 ) .
The calculi were mainly composed of magnesium ammonium phosphate ( MAP ) and partly composed of MKP .
MKP presented in crystals of different phases in this experiment .
The high intake of Mg contributed to a significant increase of plasma Mg , but additional P , K did not cause a further increase of plasma P , K Urine P , K , Mg and Ca and AP of MKP in group C decreased significantly after the onset of urolithiasis .
In conclusion , high intake of Mg was more important in inducing struvite calculi compared with high intake of K and P in goats under these feeding conditions .
Cottonseed meal and rice straw with additional Mg is a good dietary model for inducing struvite calculi in castrated goats .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: From day 60 onwards , KH ( 2 ) PO ( 4 ) and K ( 2 ) HPO ( 4 ) were provided via drinking water to goats in group B to increase the intake of P , K , and MgO to goats in group C to increase the intake of Mg .
[ Sen. 11, subscore: 2.00 ]: Cottonseed meal and rice straw with additional Mg is a good dietary model for inducing struvite calculi in castrated goats .
[ Sen. 1, subscore: 1.00 ]: The effect of high intake of Mg on urolithiasis was compared with high intake of P and K in goats being fed with a cottonseed meal and rice straw diet .
[ Sen. 2, subscore: 1.00 ]: Eighteen wether goats were randomly allocated into group A , B and C evenly and fed with cottonseed meal and rice straw diet for three months .
[ Sen. 10, subscore: 1.00 ]: In conclusion , high intake of Mg was more important in inducing struvite calculi compared with high intake of K and P in goats under these feeding conditions .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Gonadal apoptosis during sex reversal of the rice field eel : implications for an evolutionarily conserved role of the molecular chaperone heat shock protein 10 .
| | Author: He Y Shang X Sun J Zhang L Zhao W Tian Y Cheng H Zhou R | | Journal: J Exp Zool B Mol Dev Evol Citation: V : 314 P : 257-66 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20035552 Accession (PMID): 20035552 | | Abstract: Role of apoptosis in gonadal transformation of the rice field eel remains unknown .
Here we report characterization of apoptotic pattern of testis , ovary , and ovotestis of the rice field eel , a vertebrate with natural sex reversal characteristic .
DNA laddering assay showed typical ladder with step around 200 bp in the gonads , especially in testis .
Terminal transferase dUTP nick end labeling on gonads indicated obvious apoptotic signals in the seminiferous tubules .
Western blot analysis revealed that pro-apoptotic genes , Caspase 9 and p53 , were upregulated and anti-apoptotic factor Bcl2 was downregulated in testis compared with both ovary and ovotestis .
These data indicated that sex reversal process is accompanied by gonadal apoptosis with the highest proportion of cell death in the testis .
Furthermore , we identified the Hsp10 by differentially screening of testis , ovary , and ovotestis using microarray technique , which is evolutionarily conserved and differentially expressed during gonadal transformation .
Downregulation of Hsp10 is consistent with high apoptosis during the gonadal transformation .
Flow cytometry assay confirmed that Hsp10 inhibits the apoptosis in male gonadal cells .
Moreover , upregulation and mis-localization at sub-cellular level of the HSP10 together with its partner HSP60 is associated with tumorigenesis in human testis .
These results suggest that downregulation of Hsp10 would be one of the main causes of apoptosis in testis , overexpression of Hsp10 suppresses apoptosis , and potentially results in testis tumorigenesis , which provide clues for understanding the mechanisms of germ cell apoptosis .
Development of Hsp10 as a diagnostic marker or even treatment target will be promising in testis cancer diagnosis and therapy .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Role of apoptosis in gonadal transformation of the rice field eel remains unknown .
[ Sen. 3, subscore: 1.00 ]: DNA laddering assay showed typical ladder with step around 200 bp in the gonads , especially in testis .
[ Sen. 4, subscore: 1.00 ]: Terminal transferase dUTP nick end labeling on gonads indicated obvious apoptotic signals in the seminiferous tubules .
[ Sen. 6, subscore: 1.00 ]: These data indicated that sex reversal process is accompanied by gonadal apoptosis with the highest proportion of cell death in the testis .
[ Sen. 7, subscore: 1.00 ]: Furthermore , we identified the Hsp10 by differentially screening of testis , ovary , and ovotestis using microarray technique , which is evolutionarily conserved and differentially expressed during gonadal transformation .
[ Sen. 8, subscore: 1.00 ]: Downregulation of Hsp10 is consistent with high apoptosis during the gonadal transformation .
[ Sen. 9, subscore: 1.00 ]: Flow cytometry assay confirmed that Hsp10 inhibits the apoptosis in male gonadal cells .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Suppression of glutamate synthase genes significantly affects carbon and nitrogen metabolism in rice ( Oryza sativa L ) .
| | Author: Lu Y Luo F Yang M Li X Lian X | | Journal: Sci China Life Sci Citation: V : 54 P : 651-63 Year: 2011 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21748588 Accession (PMID): 21748588 | | Abstract: Rice ( Oryza sativa ) glutamate synthase ( GOGAT , EC 1 . 4 . 1 . 14 ) enzymes have been proposed to have great potential for improving nitrogen use efficiency , but their functions in vivo and their effects on carbon and nitrogen metabolism have not been systematically explored .
In this research , we analyzed transcriptional profiles of rice GOGAT genes using a genome-wide microarray database , and investigated the effects of suppression of glutamate synthase genes on carbon and nitrogen metabolism using GOGAT co-suppressed rice plants .
Transcriptional profiles showed that rice GOGAT genes were expressed differently in various it issues and organs , which suggested that they have different roles in vivo .
Compared with the wild-type , tiller number , total shoot dry weight , and yield of GOGAT co-suppressed plants were significantly decreased .
Physiological and biochemical studies showed that the contents of nitrate , several kinds of free amino acids , chlorophyll , sugars , sugar phosphates , and pyridine nucleotides were significantly decreased in leaves of GOGAT co-suppressed plants , but the contents of free ammonium , 2-oxoglutarate , and isocitrate in leaves were increased .
We conclude that GOGATs play essential roles in carbon and nitrogen metabolism , and that they are indispensable for efficient nitrogen assimilation in rice .
| Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: In this research , we analyzed transcriptional profiles of rice GOGAT genes using a genome-wide microarray database , and investigated the effects of suppression of glutamate synthase genes on carbon and nitrogen metabolism using GOGAT co-suppressed rice plants .
[ Sen. 1, subscore: 1.00 ]: Rice ( Oryza sativa ) glutamate synthase ( GOGAT , EC 1 . 4 . 1 . 14 ) enzymes have been proposed to have great potential for improving nitrogen use efficiency , but their functions in vivo and their effects on carbon and nitrogen metabolism have not been systematically explored .
[ Sen. 3, subscore: 1.00 ]: Transcriptional profiles showed that rice GOGAT genes were expressed differently in various it issues and organs , which suggested that they have different roles in vivo .
[ Sen. 4, subscore: 1.00 ]: Compared with the wild-type , tiller number , total shoot dry weight , and yield of GOGAT co-suppressed plants were significantly decreased .
[ Sen. 5, subscore: 1.00 ]: Physiological and biochemical studies showed that the contents of nitrate , several kinds of free amino acids , chlorophyll , sugars , sugar phosphates , and pyridine nucleotides were significantly decreased in leaves of GOGAT co-suppressed plants , but the contents of free ammonium , 2-oxoglutarate , and isocitrate in leaves were increased .
[ Sen. 6, subscore: 1.00 ]: We conclude that GOGATs play essential roles in carbon and nitrogen metabolism , and that they are indispensable for efficient nitrogen assimilation in rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: Cellular compartmentation of ammonium assimilation in rice and barley .
| | Author: Tobin AK Yamaya T | | Journal: J Exp . Bot . Citation: V : 52 ( 356 ) P : 591-604 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11373307 Accession (PMID): 11373307 | | Abstract: This review describes immunolocalization studies of the it issue and cellular location of glutamine synthetase ( GS ; EC 6 . 3 . 1 . 2 ) and glutamate synthase ( Fd GOGAT ; EC 1 . 4 . 7 . 1 and NADH-GOGAT ; EC 1 . 4 . 1 . 14 ) proteins in roots and leaves of rice ( Oryza sativa L ) and barley ( Hordeum vulgare L ) .
In rice , cytosolic GS ( GS1 ) protein was distributed homogeneously through all cells of the root .
NADH GOGAT protein was strongly induced and its cellular location altered by ammonium treatment , becoming concentrated within the epidermal and exodermal cells .
Fd GOGAT protein location changed with root development , from a widespread distribution in young cells to becoming concentrated within the central cylinder as cells matured .
Plastid GS protein was barely detectable in rice roots , but was the major isoform in leaves , being present in the mesophyll and parenchyma sheath cells .
GS1 was specific to the vascular bundle , as was NADH GOGAT , whereas Fd GOGAT was primarily found in mesophyll cells .
In barley roots , GS1 protein was found in the cortical and vascular parenchyma and its concentration was highest in N-deficient seedlings .
Plastid GS protein was detected in both cortical and vascular cells , where different plastid forms , containing different concentrations of GS protein , were identified .
In barley leaves , GS2 protein was detected in the mesophyll chloroplasts and GS1 was found in the mesophyll and vascular cells .
N nutrition strongly influenced this distribution , with a marked increase in GS1 concentration in the vascular cells in response to nitrate and ammonium , and an increase in mesophyll GS2 concentration in nitrate-grown seedlings .
Fd GOGAT protein was found in both the mesophyll and vascular plastids .
These localization studies show that the GS/GOGAT cycle is highly compartmentalized at both the subcellular and cellular levels .
Reasons for this compartmentation , and the roles of each isoform , are discussed . | Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: GS1 was specific to the vascular bundle , as was NADH GOGAT , whereas Fd GOGAT was primarily found in mesophyll cells .
[ Sen. 1, subscore: 1.00 ]: This review describes immunolocalization studies of the it issue and cellular location of glutamine synthetase ( GS ; EC 6 . 3 . 1 . 2 ) and glutamate synthase ( Fd GOGAT ; EC 1 . 4 . 7 . 1 and NADH-GOGAT ; EC 1 . 4 . 1 . 14 ) proteins in roots and leaves of rice ( Oryza sativa L ) and barley ( Hordeum vulgare L ) .
[ Sen. 3, subscore: 1.00 ]: NADH GOGAT protein was strongly induced and its cellular location altered by ammonium treatment , becoming concentrated within the epidermal and exodermal cells .
[ Sen. 4, subscore: 1.00 ]: Fd GOGAT protein location changed with root development , from a widespread distribution in young cells to becoming concentrated within the central cylinder as cells matured .
[ Sen. 11, subscore: 1.00 ]: Fd GOGAT protein was found in both the mesophyll and vascular plastids .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: The promoter of the rice gene GOS2 is active in various different monocot it issues and binds rice nuclear factor ASF-1 .
| | Author: de Pater BS van der Mark F Rueb S Katagiri F Chua NH Schilperoort RA Hensgens LA .
| | Journal: Plant J Citation: V : 2 ( 6 ) P : 837-44 Year: 1992 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub1302635 Accession (PMID): 1302635 | | Abstract: A single copy gene has been isolated , termed GOS2 , from rice .
Sequence comparison revealed highly similar genes in mammals and yeast , indicating that GOS2 encodes an evolutionary conserved protein .
GOS2 mRNA was detected in all it issues examined .
When the upstream region was translationally fused to the reporter gene gusA it was found to drive expression in a variety of rice it issues and in cell suspensions of other monocot species following introduction by particle bombardment .
Therefore , the GOS2 promoter is potentially useful for genetic engineering of monocots .
A DNA-binding activity from rice , termed rice ASF-1 , with similar binding specificity as the cloned tobacco transcription factor TGA-1a , was found to bind to a TGACG sequence motif in the GOS2 promoter .
Possible roles for rice ASF-1 in the transcriptional activation of the GOS2 promoter are discussed . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A single copy gene has been isolated , termed GOS2 , from rice .
[ Sen. 2, subscore: 1.00 ]: Sequence comparison revealed highly similar genes in mammals and yeast , indicating that GOS2 encodes an evolutionary conserved protein .
[ Sen. 3, subscore: 1.00 ]: GOS2 mRNA was detected in all it issues examined .
[ Sen. 5, subscore: 1.00 ]: Therefore , the GOS2 promoter is potentially useful for genetic engineering of monocots .
[ Sen. 6, subscore: 1.00 ]: A DNA-binding activity from rice , termed rice ASF-1 , with similar binding specificity as the cloned tobacco transcription factor TGA-1a , was found to bind to a TGACG sequence motif in the GOS2 promoter .
[ Sen. 7, subscore: 1.00 ]: Possible roles for rice ASF-1 in the transcriptional activation of the GOS2 promoter are discussed .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: Why is golden rice golden ( yellow ) instead of red?
| | Author: Schaub P Al-Babili S Drake R Beyer P | | Journal: Plant Physiol .
Citation: V : 138 ( 1 ) P : 441-50 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15821145 Accession (PMID): 15821145 | | Abstract: The endosperm of Golden Rice ( Oryza sativa ) is yellow due to the accumulation of beta-carotene ( provitamin A ) and xanthophylls .
The product of the two carotenoid biosynthesis transgenes used in Golden Rice , phytoene synthase ( PSY ) and the bacterial carotene desaturase ( CRTI ) , is lycopene , which has a red color .
The absence of lycopene in Golden Rice shows that the pathway proceeds beyond the transgenic end point and thus that the endogenous pathway must also be acting .
By using TaqMan real-time PCR , we show in wild-type rice endosperm the mRNA expression of the relevant carotenoid biosynthetic enzymes encoding phytoene desaturase , zeta-carotene desaturase , carotene cis-trans-isomerase , beta-lycopene cyclase , and beta-carotene hydroxylase ; only PSY mRNA was virtually absent .
We show that the transgenic phenotype is not due to up-regulation of expression of the endogenous rice pathway in response to the transgenes , as was suggested to be the case in tomato ( Lycopersicon esculentum ) fruit , where CRTI expression resulted in a similar carotenoid phenomenon .
This means that beta-carotene and xanthophyll formation in Golden Rice relies on the activity of constitutively expressed intrinsic rice genes ( carotene cis-trans-isomerase , alpha/beta-lycopene cyclase , beta-carotene hydroxylase ) .
PSY needs to be supplemented and the need for the CrtI transgene in Golden Rice is presumably due to insufficient activity of the phytoene desaturase and/or zeta-carotene desaturase enzyme in endosperm .
The effect of CRTI expression was also investigated in leaves of transgenic rice and Arabidopsis ( Arabidopsis thaliana ) .
Here , again , the mRNA levels of intrinsic carotenogenic enzymes remained unaffected ; nevertheless , the carotenoid pattern changed , showing a decrease in lutein , while the beta-carotene-derived xanthophylls increased .
This shift correlated with CRTI-expression and is most likely governed at the enzyme level by lycopene-cis-trans-isomerism .
Possible implications are discussed . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The endosperm of Golden Rice ( Oryza sativa ) is yellow due to the accumulation of beta-carotene ( provitamin A ) and xanthophylls .
[ Sen. 2, subscore: 1.00 ]: The product of the two carotenoid biosynthesis transgenes used in Golden Rice , phytoene synthase ( PSY ) and the bacterial carotene desaturase ( CRTI ) , is lycopene , which has a red color .
[ Sen. 3, subscore: 1.00 ]: The absence of lycopene in Golden Rice shows that the pathway proceeds beyond the transgenic end point and thus that the endogenous pathway must also be acting .
[ Sen. 6, subscore: 1.00 ]: This means that beta-carotene and xanthophyll formation in Golden Rice relies on the activity of constitutively expressed intrinsic rice genes ( carotene cis-trans-isomerase , alpha/beta-lycopene cyclase , beta-carotene hydroxylase ) .
[ Sen. 7, subscore: 1.00 ]: PSY needs to be supplemented and the need for the CrtI transgene in Golden Rice is presumably due to insufficient activity of the phytoene desaturase and/or zeta-carotene desaturase enzyme in endosperm .
[ Sen. 10, subscore: 1.00 ]: This shift correlated with CRTI-expression and is most likely governed at the enzyme level by lycopene-cis-trans-isomerism .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: Ubiquitin C-terminal hydrolase-L1 ( Uch-L1 ) correlates with gonadal transformation in the rice field eel .
| | Author: Sun J Shang X Tian Y Zhao W He Y Chen K Cheng H Zhou R | | Journal: FEBS J Citation: V : 275 P : 242-9 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18076650 Accession (PMID): 18076650 | | Abstract: The ubiquitin-proteasome pathway is crucial for a variety of biological processes , including spermatogenesis .
Ubiquitin C-terminal hydrolase-L1 ( Uch-L1 ) is thought to associate with monoubiquitin to control ubiquitin levels .
Here , we report the identification of Uch-L1 cDNA from the testis of the rice field eel , a natural sex reversal vertebrate , by using cDNA microarray analysis .
Uch-L1 encodes a protein of 220 amino acids that shows high homology to Uch-L1 of vertebrates , especially fish species .
Both mRNA and protein are mainly expressed in testis , ovotestis and ovary , as well as in the brain .
Immunohistochemistry analysis revealed differential expression of Uch-L1 in three kinds of gonads .
In the ovary , expression of Uch-L1 was observed mainly in the developing ovary and slightly in the mature ovary .
In ovotestis during the intersex stage , Uch-L1 was expressed in the male gonad epithelium and degraded ovary .
In testis , expression was observed in developing germ cells , including spermatogonia and spermatocytes .
Furthermore , Uch-L1 was upregulated during gonadal transformation , especially from the beginning of the intersex stage onwards .
Native-PAGE showed that Uch-L1 underwent dimerization and oligomerization in gonads , and that the relative level of dimerization/oligomerization decreased during gonadal transformation .
Simultaneously , ubiquitin polypeptide expression was upregulated during this process .
These results suggest that Uch-L1 , via the ubiquitin-proteasome system , may play an important role not only in gametogenesis , but also in the gonadal transformation process in the rice field eel .
| Matching Sentences:
[ Sen. 11, subscore: 2.00 ]: Native-PAGE showed that Uch-L1 underwent dimerization and oligomerization in gonads , and that the relative level of dimerization/oligomerization decreased during gonadal transformation .
[ Sen. 6, subscore: 1.00 ]: Immunohistochemistry analysis revealed differential expression of Uch-L1 in three kinds of gonads .
[ Sen. 8, subscore: 1.00 ]: In ovotestis during the intersex stage , Uch-L1 was expressed in the male gonad epithelium and degraded ovary .
[ Sen. 10, subscore: 1.00 ]: Furthermore , Uch-L1 was upregulated during gonadal transformation , especially from the beginning of the intersex stage onwards .
[ Sen. 13, subscore: 1.00 ]: These results suggest that Uch-L1 , via the ubiquitin-proteasome system , may play an important role not only in gametogenesis , but also in the gonadal transformation process in the rice field eel .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: Regulation of gonad development and respiratory metabolism associated with food availability and reproductive diapause in the rice bug Leptocorisa chinensis .
| | Author: Tachibana S Watanabe T | | Journal: J Insect Physiol Citation: V : 54 P : 445-53 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18164027 Accession (PMID): 18164027 | | Abstract: Food has an influence on many life history traits related to dormancy in insects .
In our previous study with the rice bug Leptocorisa chinensis ( Dallas ) ( Hemiptera : Alydidae ) , diapausing females transferred to conditions physically favorable for promoting the gonad development required food intake to resume gonad development , whereas males did not .
These differences in response to food between males and females lead to two questions : ( 1 ) Was diapause in the starved females completed?
( 2 ) Were the starved males that resumed gonad development at the same physiological status as fed males?
We tested these questions with two physiological indicators : gonad status and respiratory rate .
Results indicate that starved females are able to complete diapause , but show depressed respiration relative to well-fed insects in diapause .
Similar to females , starved males that resumed postdiapause gonad development also had depressed respiratory rate , and hence physiological status is presumed to be different between starved and fed individuals .
In this study , it was also found that the photoperiodic signal is storable , whereas the food signal acts directly .
The adaptive significance of regulation of gonad development and respiratory metabolism in relation to phenology of suitable host plant and reproductive strategy is discussed in both sexes .
| Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: In our previous study with the rice bug Leptocorisa chinensis ( Dallas ) ( Hemiptera : Alydidae ) , diapausing females transferred to conditions physically favorable for promoting the gonad development required food intake to resume gonad development , whereas males did not .
[ Sen. 4, subscore: 1.00 ]: ( 2 ) Were the starved males that resumed gonad development at the same physiological status as fed males?
[ Sen. 5, subscore: 1.00 ]: We tested these questions with two physiological indicators : gonad status and respiratory rate .
[ Sen. 7, subscore: 1.00 ]: Similar to females , starved males that resumed postdiapause gonad development also had depressed respiratory rate , and hence physiological status is presumed to be different between starved and fed individuals .
[ Sen. 9, subscore: 1.00 ]: The adaptive significance of regulation of gonad development and respiratory metabolism in relation to phenology of suitable host plant and reproductive strategy is discussed in both sexes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology .
| | Author: Botton A Galla G Conesa A Bachem C Ramina A Barcaccia G | | Journal: BMC Genomics Citation: V : 9 P : 347 Year: 2008 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub18652646 Accession (PMID): 18652646 | | Abstract: ABSTRACT : BACKGROUND : After 10-year-use of AFLP ( Amplified Fragment Length Polymorphism ) technology for DNA fingerprinting and mRNA profiling , large repertories of genome and transcriptome-derived sequences are available in public databases for model , crop and tree species .
AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping , as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning .
The evaluation , annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants .
This may be achieved by means of the Gene Ontology ( GO ) , consisting in three structured vocabularies ( ie ontologies ) describing genes , transcripts and proteins of any organism in terms of their associated cellular component , biological process and molecular function in a species-independent manner .
In this paper , the functional annotation of about 8 , 000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology .
RESULTS : Descriptive statistics on the type , size and nature of gene sequences obtained by means of AFLP technology were calculated .
The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies .
A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice , respectively .
On the whole , the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results .
Such an exhaustive annotation may offer a suitable platform for functional genomics , particularly useful in non-model species .
CONCLUSIONS : Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted .
The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis .
According to the whole set of GO annotations , the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families .
The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome-anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments .
| Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: This may be achieved by means of the Gene Ontology ( GO ) , consisting in three structured vocabularies ( ie ontologies ) describing genes , transcripts and proteins of any organism in terms of their associated cellular component , biological process and molecular function in a species-independent manner .
[ Sen. 5, subscore: 1.00 ]: In this paper , the functional annotation of about 8 , 000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology .
[ Sen. 7, subscore: 1.00 ]: The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies .
[ Sen. 9, subscore: 1.00 ]: On the whole , the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results .
[ Sen. 11, subscore: 1.00 ]: CONCLUSIONS : Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted .
[ Sen. 13, subscore: 1.00 ]: According to the whole set of GO annotations , the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Phosphoethanolamine substitution of lipid A and resistance of Neisseria gonorrhoeae to cationic antimicrobial peptides and complement-mediated killing by normal human serum .
| | Author: Lewis LA Choudhury B Balthazar JT Martin LE Ram S Rice PA Stephens DS Carlson R Shafer WM | | Journal: Infect Immun Citation: V : 77 P : 1112-20 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19114544 Accession (PMID): 19114544 | | Abstract: The capacity of Neisseria gonorrhoeae to cause disseminated gonococcal infection requires that such strains resist the bactericidal action of normal human serum .
The bactericidal action of normal human serum against N gonorrhoeae is mediated by the classical complement pathway through an antibody-dependent mechanism .
The mechanism ( s ) by which certain strains of gonococci resist normal human serum is not fully understood , but alterations in lipooligosaccharide structure can affect such resistance .
During an investigation of the biological significance of phosphoethanolamine extensions from lipooligosaccharide , we found that phosphoethanolamine substitutions from the heptose II group of the lipooligosaccharide beta-chain did not impact levels of gonococcal ( strain FA19 ) resistance to normal human serum or polymyxin B However , loss of phosphoethanolamine substitution from the lipid A component of lipooligosaccharide , due to insertional inactivation of lptA , resulted in increased gonococcal susceptibility to polymyxin B , as reported previously for Neisseria meningitidis .
In contrast to previous reports with N meningitidis , loss of phosphoethanolamine attached to lipid A rendered strain FA19 susceptible to complement killing .
Serum killing of the lptA mutant occurred through the classical complement pathway .
Both serum and polymyxin B resistance as well as phosphoethanolamine decoration of lipid A were restored in the lptA-null mutant by complementation with wild-type lptA .
Our results support a role for lipid A phosphoethanolamine substitutions in resistance of this strict human pathogen to innate host defenses .
| Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: The capacity of Neisseria gonorrhoeae to cause disseminated gonococcal infection requires that such strains resist the bactericidal action of normal human serum .
[ Sen. 4, subscore: 2.00 ]: During an investigation of the biological significance of phosphoethanolamine extensions from lipooligosaccharide , we found that phosphoethanolamine substitutions from the heptose II group of the lipooligosaccharide beta-chain did not impact levels of gonococcal ( strain FA19 ) resistance to normal human serum or polymyxin B However , loss of phosphoethanolamine substitution from the lipid A component of lipooligosaccharide , due to insertional inactivation of lptA , resulted in increased gonococcal susceptibility to polymyxin B , as reported previously for Neisseria meningitidis .
[ Sen. 2, subscore: 1.00 ]: The bactericidal action of normal human serum against N gonorrhoeae is mediated by the classical complement pathway through an antibody-dependent mechanism .
[ Sen. 3, subscore: 1.00 ]: The mechanism ( s ) by which certain strains of gonococci resist normal human serum is not fully understood , but alterations in lipooligosaccharide structure can affect such resistance .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: GS2 : an efficiently computable measure of GO-based similarity of gene sets .
| | Author: Ruths T Ruths D Nakhleh L | | Journal: Bioinformatics Citation: V : 25 P : 1178-84 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19289444 Accession (PMID): 19289444 | | Abstract: MOTIVATION : The growing availability of genome-scale datasets has attracted increasing attention to the development of computational methods for automated inference of functional similarities among genes and their products .
One class of such methods measures the functional similarity of genes based on their distance in the Gene Ontology ( GO ) .
To measure the functional relatedness of a gene set , these measures consider every pair of genes in the set , and the average of all pairwise distances is calculated .
However , as more data becomes available and gene sets used for analysis become larger , such pair-based calculation becomes prohibitive .
RESULTS : In this article , we propose GS ( 2 ) ( GO-based similarity of gene sets ) , a novel GO-based measure of gene set similarity that is computable in linear time in the size of the gene set .
The measure quantifies the similarity of the GO annotations among a set of genes by averaging the contribution of each genes GO terms and their ancestor terms with respect to the GO vocabulary graph .
To study the performance of our method , we compared our measure with an established pair-based measure when run on gene sets with varying degrees of functional similarities .
In addition to a significant speed improvement , our method produced comparable similarity scores to the established method .
Our method is available as a web-based tool and an open-source Python library .
AVAILABILITY : The web-based tools and Python code are available at : http : //bioserver . cs . rice . edu/gs2 .
| Matching Sentences:
[ Sen. 6, subscore: 3.00 ]: The measure quantifies the similarity of the GO annotations among a set of genes by averaging the contribution of each genes GO terms and their ancestor terms with respect to the GO vocabulary graph .
[ Sen. 5, subscore: 2.00 ]: RESULTS : In this article , we propose GS ( 2 ) ( GO-based similarity of gene sets ) , a novel GO-based measure of gene set similarity that is computable in linear time in the size of the gene set .
[ Sen. 2, subscore: 1.00 ]: One class of such methods measures the functional similarity of genes based on their distance in the Gene Ontology ( GO ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Site selection and resource depletion in black-tailed godwits Limosa l . limosa eating rice during northward migration .
| | Author: Lourenco PM Mandema FS Hooijmeijer JC Granadeiro JP Piersma T | | Journal: J Anim Ecol Citation: V : 79 P : 522-8 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20070431 Accession (PMID): 20070431 | | Abstract: 1 .
During migratory stopovers , animals are under strong time stress and need to maximize intake rates .
We examine how foragers react to resource depletion by studying the foraging ecology and foraging site selection of black-tailed godwits Limosa l . limosa staging in rice fields during their northward migration stopover ( January-March 2007 ) .
2 .
We analysed godwit abundance and foraging behaviour , sampled the availability of rice in the fields and used the functional response model to predict the giving-up density ( GUD ) of rice kernels when godwits should give up a rice field .
Sightings of individually colour-marked birds were used to verify whether individuals moving between rice fields confirmed the predicted GUD .
3 .
Black-tailed godwit intake rates at different rice densities fitted Hollings functional response curve .
The predicted GUD of rice necessary to balance allometric estimates of daily energy expenditure ( DEE ) and measured time budgets were confirmed by GUD measured in the field .
4 .
Individually marked birds moved towards rice fields with higher rather than lower rice densities more often than randomly expected .
These birds increased the measured intake rates after this move .
5 .
Godwit foraging caused a decrease in the rice density of individual fields during the stopover period .
Despite this , overall intake rates remained constant as godwits reacted to resource depletion by moving to a new foraging site as soon as their intake rate falls below the required levels to achieve DEE .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: We analysed godwit abundance and foraging behaviour , sampled the availability of rice in the fields and used the functional response model to predict the giving-up density ( GUD ) of rice kernels when godwits should give up a rice field .
[ Sen. 3, subscore: 1.00 ]: We examine how foragers react to resource depletion by studying the foraging ecology and foraging site selection of black-tailed godwits Limosa l . limosa staging in rice fields during their northward migration stopover ( January-March 2007 ) .
[ Sen. 8, subscore: 1.00 ]: Black-tailed godwit intake rates at different rice densities fitted Hollings functional response curve .
[ Sen. 14, subscore: 1.00 ]: Godwit foraging caused a decrease in the rice density of individual fields during the stopover period .
[ Sen. 15, subscore: 1.00 ]: Despite this , overall intake rates remained constant as godwits reacted to resource depletion by moving to a new foraging site as soon as their intake rate falls below the required levels to achieve DEE .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: The private sectors role in public sector genetically engineered crop projects .
| | Author: Potrykus I | | Journal: N Biotechnol Citation: V : 27 P : 578-81 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20637908 Accession (PMID): 20637908 | | Abstract: There is widespread interest within academia to work on public good genetically engineered ( GE ) projects to the benefit of the poor , especially to use GE-technology to contribute to food security .
Not a single product from this work has reached the market .
The major cause is GE-regulation , which prevents use of the technology for public good beyond proof-of-concept ( Potrykus , I ( 2010 ) Lessons from the Humanitarian Golden Rice project : Regulation prevents development of public good GE-products ( these Proceedings ) ) .
There is , however , another key problem responsible for the lack of deployment of public good GE-plants : the public sector is incompetent and disinterested for work beyond proof-of-concept , and has neither capability nor funding to develop GE-plant products and introduce them to growers and consumers .
The private sector has the expertise for both and in the right circumstances can be ready to support the public sector in public good enterprises .
Public-private-partnerships are the best solution so far , to advance exploitation of GE-technology to the benefit of the poor .
Public-private-partnerships are viable , however , only , if there is mutual interest from the private sector and initiative and funding from the public sector .
| Matching Sentences:
[ Sen. 3, subscore: 3.00 ]: The major cause is GE-regulation , which prevents use of the technology for public good beyond proof-of-concept ( Potrykus , I ( 2010 ) Lessons from the Humanitarian Golden Rice project : Regulation prevents development of public good GE-products ( these Proceedings ) ) .
[ Sen. 1, subscore: 1.00 ]: There is widespread interest within academia to work on public good genetically engineered ( GE ) projects to the benefit of the poor , especially to use GE-technology to contribute to food security .
[ Sen. 4, subscore: 1.00 ]: There is , however , another key problem responsible for the lack of deployment of public good GE-plants : the public sector is incompetent and disinterested for work beyond proof-of-concept , and has neither capability nor funding to develop GE-plant products and introduce them to growers and consumers .
[ Sen. 5, subscore: 1.00 ]: The private sector has the expertise for both and in the right circumstances can be ready to support the public sector in public good enterprises .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: The small GTPase Rab5a is essential for intracellular transport of proglutelin from the Golgi apparatus to the protein storage vacuole and endosomal membrane organization in developing rice endosperm .
| | Author: Fukuda M Satoh-Cruz M Wen L Crofts AJ Sugino A Washida H Okita TW Ogawa M Kawagoe Y Maeshima M Kumamaru T | | Journal: Plant Physiol Citation: V : 157 P : 632-44 Year: 2011 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub21825104 Accession (PMID): 21825104 | | Abstract: Rice ( Oryza sativa ) glutelins are synthesized on the endoplasmic reticulum as larger precursors , which are then transported via the Golgi to the protein storage vacuole ( PSV ) , where they are processed into acidic and basic subunits .
Three independent glutelin precursor mutant4 ( glup4 ) rice lines , which accumulated elevated levels of proglutelin over the wild type , were identified as loss-of-function mutants of Rab5a , the small GTPase involved in vesicular membrane transport .
In addition to the plasma membrane , Rab5a colocalizes with glutelins on the Golgi apparatus , Golgi-derived dense vesicles , and the PSV , suggesting that Rab5a participates in the transport of the proglutelin from the Golgi to the PSV .
This spatial distribution pattern was dramatically altered in the glup4 mutants .
Numerous smaller protein bodies containing glutelin and alpha-globulin were evident , and the proteins were secreted extracellularly .
Moreover , all three independent glup4 allelic lines displayed the novel appearance of a large dilated , structurally complex paramural body containing proglutelins , alpha-globulins , membrane biomarkers for the Golgi apparatus , prevacuolar compartment , PSV , and the endoplasmic reticulum luminal chaperones BiP and protein disulfide isomerase as well as beta-glucan .
These results indicate that the formation of the paramural bodies in glup4 endosperm was due to a significant disruption of endocytosis and membrane vesicular transport by Rab5a loss of function .
Overall , Rab5a is required not only for the intracellular transport of proglutelins from the Golgi to the PSV in rice endosperm but also in the maintenance of the general structural organization of the endomembrane system in developing rice seeds .
| Matching Sentences:
[ Sen. 3, subscore: 3.00 ]: In addition to the plasma membrane , Rab5a colocalizes with glutelins on the Golgi apparatus , Golgi-derived dense vesicles , and the PSV , suggesting that Rab5a participates in the transport of the proglutelin from the Golgi to the PSV .
[ Sen. 1, subscore: 1.00 ]: Rice ( Oryza sativa ) glutelins are synthesized on the endoplasmic reticulum as larger precursors , which are then transported via the Golgi to the protein storage vacuole ( PSV ) , where they are processed into acidic and basic subunits .
[ Sen. 6, subscore: 1.00 ]: Moreover , all three independent glup4 allelic lines displayed the novel appearance of a large dilated , structurally complex paramural body containing proglutelins , alpha-globulins , membrane biomarkers for the Golgi apparatus , prevacuolar compartment , PSV , and the endoplasmic reticulum luminal chaperones BiP and protein disulfide isomerase as well as beta-glucan .
[ Sen. 8, subscore: 1.00 ]: Overall , Rab5a is required not only for the intracellular transport of proglutelins from the Golgi to the PSV in rice endosperm but also in the maintenance of the general structural organization of the endomembrane system in developing rice seeds .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Quantitative Analysis of Structure and Bandgap Changes in Graphene Oxide Nanoribbons during Thermal Annealing .
| | Author: Zhu Y Li X Cai Q Sun Z Casillas G Jose-Yacaman M Verduzco R Tour JM | | Journal: J Am Chem Soc Citation: V : 134 P : 11774-80 Year: 2012 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub22716929 Accession (PMID): 22716929 | | Abstract: Graphene oxide nanoribbons ( GONRs ) are wide bandgap semiconductors that can be reduced to metallic graphene nanoribbons .
The transformation of GONRs from their semiconductive to the metallic state by annealing has attracted significant interest due to its simplicity .
However , the detailed process by which GONRs transform from wide-bandgap semiconductors to semimetals with a near zero bandgap is unclear .
As a result , precise control of the bandgap between these two states is not currently achievable .
Here , we quantitatively examine the removal of oxygen-containing groups and changes in the bandgap during thermal annealing of GONRs .
X-ray photoelectron spectroscopy measurements show the progressive removal of oxygen-containing functional groups .
Aberration-corrected scanning transmission electron microscopy reveals that initially small graphene regions in GONRs become large stacked graphitic layers during thermal annealing .
These structural and chemical changes are correlated with progressive changes in the electrochemical bandgap , monitored by cyclic voltammetry .
These results show that small changes in the thermal annealing temperature result in significant changes to the bandgap and chemical composition of GONRs and provide a straightforward method for tuning the bandgap in oxidized graphene structures .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Graphene oxide nanoribbons ( GONRs ) are wide bandgap semiconductors that can be reduced to metallic graphene nanoribbons .
[ Sen. 2, subscore: 1.00 ]: The transformation of GONRs from their semiconductive to the metallic state by annealing has attracted significant interest due to its simplicity .
[ Sen. 3, subscore: 1.00 ]: However , the detailed process by which GONRs transform from wide-bandgap semiconductors to semimetals with a near zero bandgap is unclear .
[ Sen. 5, subscore: 1.00 ]: Here , we quantitatively examine the removal of oxygen-containing groups and changes in the bandgap during thermal annealing of GONRs .
[ Sen. 7, subscore: 1.00 ]: Aberration-corrected scanning transmission electron microscopy reveals that initially small graphene regions in GONRs become large stacked graphitic layers during thermal annealing .
[ Sen. 9, subscore: 1.00 ]: These results show that small changes in the thermal annealing temperature result in significant changes to the bandgap and chemical composition of GONRs and provide a straightforward method for tuning the bandgap in oxidized graphene structures .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Towards comprehensive malaria planning : The effect of government capacity , health policy , and land use variables on malaria incidence in India .
| | Author: Boussalis C Nelson HT Swaminathan S | | Journal: Soc Sci Med Citation: V : 75 P : 1213-21 Year: 2012 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub22770486 Accession (PMID): 22770486 | | Abstract: We present what we believe is the first empirical research that accounts for subnational government capacity in estimating malaria incidence .
After controlling for relevant extrinsic factors , we find evidence of a negative effect of state government capacity on reported malaria cases in Indian states over the period 1993-2002 .
Government capacity is more successful in predicting malaria incidence than potentially more direct indicators such as state public health expenditures and economic development levels .
We find that high government capacity can moderate the deleterious health effects of malaria in rice producing regions .
Our research also suggests that government capacity may have exacerbated the effectiveness of the World Bank Malaria Control Project in India over the period studied .
We conclude by proposing the integration of government capacity measures into existing planning efforts , including vulnerability mapping tools and disease surveillance efforts .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: We present what we believe is the first empirical research that accounts for subnational government capacity in estimating malaria incidence .
[ Sen. 2, subscore: 1.00 ]: After controlling for relevant extrinsic factors , we find evidence of a negative effect of state government capacity on reported malaria cases in Indian states over the period 1993-2002 .
[ Sen. 3, subscore: 1.00 ]: Government capacity is more successful in predicting malaria incidence than potentially more direct indicators such as state public health expenditures and economic development levels .
[ Sen. 4, subscore: 1.00 ]: We find that high government capacity can moderate the deleterious health effects of malaria in rice producing regions .
[ Sen. 5, subscore: 1.00 ]: Our research also suggests that government capacity may have exacerbated the effectiveness of the World Bank Malaria Control Project in India over the period studied .
[ Sen. 6, subscore: 1.00 ]: We conclude by proposing the integration of government capacity measures into existing planning efforts , including vulnerability mapping tools and disease surveillance efforts .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Transient and stable expression of gusA fusions with rice genes in rice , barley and perennial ryegrass .
| | Author: Hensgens LA de Bakker EP van Os-Ruygrok EP Rueb S van de Mark F van der Maas HM van der Veen S Kooman-Gersmann M Hart L Schilperoort RA .
| | Journal: Plant Mol . Biol . Citation: V : 23 ( 4 ) P : 643-69 Year: 1993 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub8251621 Accession (PMID): 8251621 | | Abstract: Transcriptional and translational fusions were made between the reading frame coding for beta-D-glucuronidase and sequences of either a constitutively expressed rice gene ( GOS2 ) involved in initiation of translation or a light-inducible rice gene ( GOS5 ) .
The transient expression of the fusions was studied via particle bombardment of seedling it issues of rice , perennial ryegrass and barley .
Furthermore , the results of transient and stable expression were compared for cell suspensions of four rice varieties , one barley variety and one perennial ryegrass variety .
The GOS2-gusA fusions were active in all three monocots studied .
Best results were obtained for a construct having both a transcriptional and a translational fusion as well as intron and exon sequences ( PORCEHyg ) .
The level of GUS activity was in the range of activities as obtained by the 35S CaMV promoter transcriptionally fused to gusA .
The gusA fusion with the light-inducible gene ( GOS5 ) was active in green seedling it issues of all monocots studied .
Also a weak expression compared to the GOS2 constructs was found in stably transformed rice callus .
The gusA fusions with the mannopine synthase promoters 1 and 2 of the TR-DNA were transiently expressed at lower levels in cell suspensions than PORCEHyg .
For stably transformed rice callus the expression of the GOS2-gusA fusion often decreased during prolonged subculture .
This decrease in GUS activity and the various GUS-staining phenotypes of transgenic calli are explained by the presence of different cell types in the suspensions used and in the calli .
It is presumed that the nature of the cells and their relative contribution in the calli change drastically upon further subculture . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Transcriptional and translational fusions were made between the reading frame coding for beta-D-glucuronidase and sequences of either a constitutively expressed rice gene ( GOS2 ) involved in initiation of translation or a light-inducible rice gene ( GOS5 ) .
[ Sen. 4, subscore: 1.00 ]: The GOS2-gusA fusions were active in all three monocots studied .
[ Sen. 7, subscore: 1.00 ]: The gusA fusion with the light-inducible gene ( GOS5 ) was active in green seedling it issues of all monocots studied .
[ Sen. 8, subscore: 1.00 ]: Also a weak expression compared to the GOS2 constructs was found in stably transformed rice callus .
[ Sen. 10, subscore: 1.00 ]: For stably transformed rice callus the expression of the GOS2-gusA fusion often decreased during prolonged subculture .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Cell-type specific expression of three rice genes GOS2 , GOS5 and GOS9 .
| | Author: Rey P Diaz C Schilperoort RA Hensgens LA .
| | Journal: Plant Mol . Biol . Citation: V : 23 ( 4 ) P : 889-94 Year: 1993 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub8251641 Accession (PMID): 8251641 | | Abstract: The cell-type-specific expression of three rice genes , GOS2 , GOS5 and GOS9 , was studied by mRNA in situ hybridization .
Previous northern blot analysis revealed that these genes were constitutive , green it issue-specific and root-specific , respectively .
In this study , GOS2 transcripts were observed in all leaf cell types .
In roots , a temporal and spatial expression pattern was noticed .
Higher mRNA levels were observed in lateral roots , especially in parenchymal cells of the vascular cylinder .
Expression of GOS5 was mainly found in chloroplast-containing cells .
For GOS9 , significant levels of signal were observed in root and leaf sections . | Matching Sentences:
[ Sen. 1, subscore: 3.00 ]: The cell-type-specific expression of three rice genes , GOS2 , GOS5 and GOS9 , was studied by mRNA in situ hybridization .
[ Sen. 3, subscore: 1.00 ]: In this study , GOS2 transcripts were observed in all leaf cell types .
[ Sen. 6, subscore: 1.00 ]: Expression of GOS5 was mainly found in chloroplast-containing cells .
[ Sen. 7, subscore: 1.00 ]: For GOS9 , significant levels of signal were observed in root and leaf sections .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
|---|
| Title: Transient and stable expression of gusA fusions with rice genes in rice , barley and perennial ryegrass .
| | Author: Hensgens LA de Bakker EP van Os-Ruygrok EP Rueb S van de Mark F van der Maas HM van der Veen S Kooman-Gersmann M Hart L Schilperoort RA .
| | Journal: Plant Mol . Biol . Citation: V : 22 ( 6 ) P : 1101-27 Year: 1993 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub8400127 Accession (PMID): 8400127 | | Abstract: Transcriptional and translational fusions were made between the reading frame coding for beta-D-glucuronidase and sequences of either a constitutively expressed rice gene ( GOS2 ) involved in initiation of translation or a light-inducible rice gene ( GOS5 ) .
The transient expression of the fusions was studied via particle bombardment of seedling it issues of rice , perennial ryegrass and barley .
Furthermore , the results of transient and stable expression were compared for cell suspensions of four rice varieties , one barley variety and one perennial ryegrass variety .
The GOS2-gusA fusions were active in all three monocots studied .
Best results were obtained for a construct having both a transcriptional and a translational fusion as well as intron and exon sequences ( PORCEHyg ) .
The level of GUS activity was in the range of activities as obtained by the 35S CaMV promoter transcriptionally fused to gusA .
The gusA fusion with the light-inducible gene ( GOS5 ) was active in green seedling it issues of all monocots studied .
Also a weak expression compared to the GOS2 constructs was found in stably transformed rice callus .
The gusA fusions with the mannopine synthase promoters 1 and 2 of the TR-DNA were transiently expressed at lower levels in cell suspensions than PORCEHyg .
For stably transformed rice callus the expression of the GOS2-gusA fusion often decreased during prolonged subculture .
This decrease in GUS activity and the various GUS-staining phenotypes of transgenic calli are explained by the presence of different cell types in the suspensions used and in the calli .
It is presumed that the nature of the cells and their relative contribution in the calli change drastically upon further subculture . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Transcriptional and translational fusions were made between the reading frame coding for beta-D-glucuronidase and sequences of either a constitutively expressed rice gene ( GOS2 ) involved in initiation of translation or a light-inducible rice gene ( GOS5 ) .
[ Sen. 4, subscore: 1.00 ]: The GOS2-gusA fusions were active in all three monocots studied .
[ Sen. 7, subscore: 1.00 ]: The gusA fusion with the light-inducible gene ( GOS5 ) was active in green seedling it issues of all monocots studied .
[ Sen. 8, subscore: 1.00 ]: Also a weak expression compared to the GOS2 constructs was found in stably transformed rice callus .
[ Sen. 10, subscore: 1.00 ]: For stably transformed rice callus the expression of the GOS2-gusA fusion often decreased during prolonged subculture .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: The yeast VRG4 gene is required for normal Golgi functions and defines a new family of related genes .
| | Author: Poster JB Dean N | | Journal: J Biol . Chem . Citation: V : 271 ( 7 ) P : 3837-45 Year: 1996 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub8632002 Accession (PMID): 8632002 | | Abstract: Sodium vanadate is an effective agent for the enrichment of yeast mutants with defects in glycosylation steps that occur in the Golgi complex ( Ballou , L , Hitzeman , R A , Lewis , M S , and Ballou , C E ( 1991 ) Proc . Natl . Acad . Sci . U S A 88 , 3209-3212 ) .
We isolated and screened vanadate-resistant glycosylation mutants in the budding yeast , Saccharomyces cerevisiae , to identify any that may be defective in the secretory pathway , since changes in normal glycosylation may reflect defects within the secretory pathway .
We identified one such mutant , allelic to vrg4/van2 , that is defective in processes that occur specifically in the Golgi complex Protein secreted from vrg4 mutants lacks the outer chain glycosylation that is normally extended during passage through the Golgi .
This mutant fails to retrieve soluble endoplasmic reticulum proteins from the Golgi and accumulates the Golgi-specific biosynthetic intermediate of the vacuolar protein , carboxypeptidase Y Analyses of intracellular membranes by staining with the fluorescent lipophilic dye , DiOC6 , and by electron microscopy reveals a dramatic alteration in the membrane morphology of vrg4 mutant cells .
The VRG4 gene encodes a 36 . 9-kDa membrane protein that is essential for cell viability .
A sequence homology search has identified five related genes , establishing that VRG4 is a founding member of a family of structurally similar genes .
Taken together , these results suggest that the VRG4 gene plays an important role in regulating Golgi functions and in maintaining the normal organization of intracellular membranes . | Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: We identified one such mutant , allelic to vrg4/van2 , that is defective in processes that occur specifically in the Golgi complex Protein secreted from vrg4 mutants lacks the outer chain glycosylation that is normally extended during passage through the Golgi .
[ Sen. 4, subscore: 2.00 ]: This mutant fails to retrieve soluble endoplasmic reticulum proteins from the Golgi and accumulates the Golgi-specific biosynthetic intermediate of the vacuolar protein , carboxypeptidase Y Analyses of intracellular membranes by staining with the fluorescent lipophilic dye , DiOC6 , and by electron microscopy reveals a dramatic alteration in the membrane morphology of vrg4 mutant cells .
[ Sen. 1, subscore: 1.00 ]: Sodium vanadate is an effective agent for the enrichment of yeast mutants with defects in glycosylation steps that occur in the Golgi complex ( Ballou , L , Hitzeman , R A , Lewis , M S , and Ballou , C E ( 1991 ) Proc . Natl . Acad . Sci . U S A 88 , 3209-3212 ) .
[ Sen. 7, subscore: 1.00 ]: Taken together , these results suggest that the VRG4 gene plays an important role in regulating Golgi functions and in maintaining the normal organization of intracellular membranes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Alternative splicing and differential expression of P450c17 ( CYP17 ) in gonads during sex transformation in the rice field eel .
| | Author: Yu H Cheng H Guo Y Xia L Zhou R | | Journal: Biochem . Biophys . Res . Commun . Citation: V : 307 ( 1 ) P : 165-71 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12849996 Accession (PMID): 12849996 | | Abstract: Several mechanisms were used in determination of the development of the male or female of vertebrates .
The genes for determination of sequential hermaphrodite sex are unknown .
Here , we reported cloning , alternative splicing , and expression patterns of the CYP17 gene of the rice field eel , a teleost fish with a characteristic of nature sex reversal The CYP17 gene of the rice field eel was clustered into the CYP17 gene group of all the other vertebrates , especially into the fish subgroup .
Four isoforms of the CYP17 were generated in gonads by alternative splicing and polyadenylation .
Alternative splicing events of all these isoforms occurred in 3 ( ) regions , which encoded three different sizes ( 517 , 512 , and 159aa ) of proteins .
RT-PCR results indicate specific expression in gonads of these isoforms .
Northern blot analysis shows that expression patterns of the CYP17 ( dominantly expressed in testis , less in ovary , and the least in ovotestis ) are consistent with the sex reversal process of the rice field eel .
In situ hybridization further shows its specific expression in germinal lamellae , the gonadal epithelium of the gonads .
These findings indicate that CYP17 is differentially regulated in a sex and developmentally specific manner , suggesting that the CYP17 potentially has important roles in gonad differentiation during sex reversal of the rice field eel .
| Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: In situ hybridization further shows its specific expression in germinal lamellae , the gonadal epithelium of the gonads .
[ Sen. 4, subscore: 1.00 ]: Four isoforms of the CYP17 were generated in gonads by alternative splicing and polyadenylation .
[ Sen. 6, subscore: 1.00 ]: RT-PCR results indicate specific expression in gonads of these isoforms .
[ Sen. 9, subscore: 1.00 ]: These findings indicate that CYP17 is differentially regulated in a sex and developmentally specific manner , suggesting that the CYP17 potentially has important roles in gonad differentiation during sex reversal of the rice field eel .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Micronutrient content of certain tropical conventional and unconventional feed resources of Southern India .
| | Author: Gowda NK Ramana JV Prasad CS Singh K | | Journal: Citation: V : 36 ( 1 ) P : 77-94 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub14979561 Accession (PMID): 14979561 | | Abstract: The ash , silica and certain important micronutrients were estimated in conventional and unconventional feed and fodder resources available in Southern India .
Commonly used dry roughages , such as paddy straw , ragi straw , maize kadbi/stalk , jowar kadbi/stalk , bajra stalk and wheat straw , were high in ash ( 9 . 9% +/- 0 . 77% ) and silica ( 6 . 4% +/- 0 . 65% ) and low in most of the other micronutrients , except iron , with paddy straw containing most silica ( >9% ) .
Cultivated non-leguminous ( maize , jowar ) and improved green crops ( hybrid napier , guinea , green panic , NB-21 , CO-1 ) were also high in ash ( 10 . 5% +/- 0 . 60% and 12 . 5% +/- 0 . 51% ) but were moderate sources of P , Mg and Cu and good sources of Zn ( 98 +/- 13 . 8 ppm and 55 +/- 6 . 7 ppm ) .
Leguminous green fodders ( stylosanthus , lucerne , cow pea , soyabean ) were excellent sources of Ca ( 1 . 9% +/- 0 . 16% ) , Mg ( 0 . 40% +/- 0 . 05% ) , Cu ( 30 +/- 5 . 2 ppm ) , Zn ( 121 +/- 14 . 7 ppm ) and Fe ( 1234 +/- 166 ppm ) and moderate sources of P Mixed local grasses and weeds were high in silica ( 6 . 9% +/- 1 . 00% ) but were good sources of Cu , Zn and Fe .
Cereal grains ( maize , wheat , rice , ragi ) were low in ash ( 2 . 9% +/- 0 . 33% ) and were relatively poor sources of Ca ( 0 . 22% +/- 0 . 03% ) , Mg ( 0 . 19% +/- 0 . 03% ) and Cu ( 13 +/- 3 . 1 ppm ) .
Pulses were low to medium sources of most minerals and good sources of Fe ( 1230 +/- 293 ppm ) .
Oil seed cake/extractions ( groundnut cake , cotton seed cake , soyabean meal , sunflower cake , safflower cake ) and cereal by-products ( rice polish , rice bran , wheat bran ) were excellent sources of P ( 1 . 1% +/- 0 . 47% and 2 . 3% +/- 0 . 19% ) and good sources of Zn ( 65 +/- 3 . 9 ppm and 66 +/- 10 . 7 ppm ) and Fe ( 938 +/- 130 ppm and 662 +/- 126 ppm ) .
Among the unconventional feeds screened , orange peel , sunflower heads , meat meal , rubber seed cake , spirulina algae and sea weeds contained plentiful Ca , Zn and Fe : tree leaves/top feeds ( mulberry , erythrina , glyricidia , banana , subabul , groundnut haulms ) were excellent sources of Ca ( 1 . 5% +/- 0 . 13% ) , Zn ( 120 +/- 22 . 9 ppm ) and Fe ( 1033 +/- 133 ppm ) but relatively poor sources of P Soyabean husk , cocoa seed husk , rubber seed cake and meat meal were moderate to good sources of P ( 1 . 0% and 0 . 33% ) .
The high Zn and Fe values of most feeds/fodders were probably due to soil contamination .
This account of the micronutrient content of feed/fodder resources should help in strategic supplementation intended to alleviate local deficiencies .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Cultivated non-leguminous ( maize , jowar ) and improved green crops ( hybrid napier , guinea , green panic , NB-21 , CO-1 ) were also high in ash ( 10 . 5% +/- 0 . 60% and 12 . 5% +/- 0 . 51% ) but were moderate sources of P , Mg and Cu and good sources of Zn ( 98 +/- 13 . 8 ppm and 55 +/- 6 . 7 ppm ) .
[ Sen. 4, subscore: 1.00 ]: Leguminous green fodders ( stylosanthus , lucerne , cow pea , soyabean ) were excellent sources of Ca ( 1 . 9% +/- 0 . 16% ) , Mg ( 0 . 40% +/- 0 . 05% ) , Cu ( 30 +/- 5 . 2 ppm ) , Zn ( 121 +/- 14 . 7 ppm ) and Fe ( 1234 +/- 166 ppm ) and moderate sources of P Mixed local grasses and weeds were high in silica ( 6 . 9% +/- 1 . 00% ) but were good sources of Cu , Zn and Fe .
[ Sen. 6, subscore: 1.00 ]: Pulses were low to medium sources of most minerals and good sources of Fe ( 1230 +/- 293 ppm ) .
[ Sen. 7, subscore: 1.00 ]: Oil seed cake/extractions ( groundnut cake , cotton seed cake , soyabean meal , sunflower cake , safflower cake ) and cereal by-products ( rice polish , rice bran , wheat bran ) were excellent sources of P ( 1 . 1% +/- 0 . 47% and 2 . 3% +/- 0 . 19% ) and good sources of Zn ( 65 +/- 3 . 9 ppm and 66 +/- 10 . 7 ppm ) and Fe ( 938 +/- 130 ppm and 662 +/- 126 ppm ) .
[ Sen. 8, subscore: 1.00 ]: Among the unconventional feeds screened , orange peel , sunflower heads , meat meal , rubber seed cake , spirulina algae and sea weeds contained plentiful Ca , Zn and Fe : tree leaves/top feeds ( mulberry , erythrina , glyricidia , banana , subabul , groundnut haulms ) were excellent sources of Ca ( 1 . 5% +/- 0 . 13% ) , Zn ( 120 +/- 22 . 9 ppm ) and Fe ( 1033 +/- 133 ppm ) but relatively poor sources of P Soyabean husk , cocoa seed husk , rubber seed cake and meat meal were moderate to good sources of P ( 1 . 0% and 0 . 33% ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Identification of a Golgi-localised GRIP domain protein from Arabidopsis thaliana .
| | Author: Gilson PR Vergara CE Kjer-Nielsen L Teasdale RD Bacic A Gleeson PA .
| | Journal: Planta Citation: V : 219 ( 6 ) P : 1050-6 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15605178 Accession (PMID): 15605178 | | Abstract: A family of Golgi-localised molecules was recently described in animals and fungi possessing extensive coiled regions and a short ( approximately 40 residues ) conserved C-terminal domain , called the GRIP domain , which is responsible for their location to this organelle .
Using the model plant Arabidopsis thaliana , we identified a gene ( AtGRIP ) encoding a putative GRIP protein .
We demonstrated that the C-terminal domain from AtGRIP functions as a Golgi-targeting sequence in plant cells .
Localisation studies in living cells expressing the AtGRIP fused to a DsRed2 fluorescent probe , showed extensive co-location with the Golgi marker alpha-mannosidase I in transformed tobacco protoplasts .
GRIP-like sequences were also found in genomic databases of rice , maize , wheat and alfalfa , suggesting that this domain may be a useful Golgi marker for immunolocalisation studies .
Despite low sequence identity amongst GRIP domains , the plant GRIP sequence was able to target to the Golgi of mammalian cells .
Taken together , these data indicate that GRIP domain proteins might be implicated in a targeting mechanism that is conserved amongst eukaryotes .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A family of Golgi-localised molecules was recently described in animals and fungi possessing extensive coiled regions and a short ( approximately 40 residues ) conserved C-terminal domain , called the GRIP domain , which is responsible for their location to this organelle .
[ Sen. 3, subscore: 1.00 ]: We demonstrated that the C-terminal domain from AtGRIP functions as a Golgi-targeting sequence in plant cells .
[ Sen. 4, subscore: 1.00 ]: Localisation studies in living cells expressing the AtGRIP fused to a DsRed2 fluorescent probe , showed extensive co-location with the Golgi marker alpha-mannosidase I in transformed tobacco protoplasts .
[ Sen. 5, subscore: 1.00 ]: GRIP-like sequences were also found in genomic databases of rice , maize , wheat and alfalfa , suggesting that this domain may be a useful Golgi marker for immunolocalisation studies .
[ Sen. 6, subscore: 1.00 ]: Despite low sequence identity amongst GRIP domains , the plant GRIP sequence was able to target to the Golgi of mammalian cells .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Multiple alternative splicing and differential expression of dmrt1 during gonad transformation of the rice field eel .
| | Author: Huang X Guo Y Shui Y Gao S Yu H Cheng H Zhou R | | Journal: Biol . Reprod . Citation: V : 73 ( 5 ) P : 1017-24 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16014815 Accession (PMID): 16014815 | | Abstract: Morphologically distinct males and females are observed throughout the animal kingdom .
Why and how sex evolved and is maintained in most living organisms remains a key question in cellular and evolutionary biology .
Here we report that four isoforms of dmrt1 ( dsx and mab3-related transcription factor 1 ) are generated in testis , ovotestis , and ovary by alternative splicing in the rice field eel , a fresh water fish that undergoes natural sex reversal from female to male during its life cycle .
These transcripts encode four different size proteins with 301 , 196 , 300 , and 205 amino acids .
Like fly doublesex splicing , the dmrt1 of the rice field eel is also alternatively spliced at the 3 region , which generates diverse isoforms in gonads by alternative use of 3 sequences .
Not only is dmrt1 expressed specifically in gonads , but its multiple isoforms are differentially coexpressed in gonadal epithelium during gonad transformation .
Expression levels of a and b isoforms of dmrt1 ranged from low to high ( ovary < ovotestis I < ovotestis II < ovotestis III < testis ) , based on comparisons of mean values from real-time fluorescent quantitative reverse transcription-polymerase chain reaction analysis .
The overall expression level of dmrt1 b was much lower than that of dmrt1 a .
Expression of dmrt1 d was not only low , but it also did not change significantly during sex transformation .
The differential expression of dmrt1 isoforms may also be regulated by their 3 untranslated regions ( UTRs ) , although these 3 UTRs do not contribute to intracellular localization of the Dmrt1 protein .
These results provide new insight into roles of regulation at the level of splicing of dmrt1 in governing the sex differentiation cascade .
| Matching Sentences:
[ Sen. 6, subscore: 3.00 ]: Not only is dmrt1 expressed specifically in gonads , but its multiple isoforms are differentially coexpressed in gonadal epithelium during gonad transformation .
[ Sen. 5, subscore: 1.00 ]: Like fly doublesex splicing , the dmrt1 of the rice field eel is also alternatively spliced at the 3 region , which generates diverse isoforms in gonads by alternative use of 3 sequences .
[ Sen. 11, subscore: 1.00 ]: These results provide new insight into roles of regulation at the level of splicing of dmrt1 in governing the sex differentiation cascade .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Holding it all together?
Candidate proteins for the plant Golgi matrix .
| | Author: Latijnhouwers M Hawes C Carvalho C | | Journal: Curr . Opin . Plant Biol .
Citation: V : 8 ( 6 ) P : 632-9 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16194619 Accession (PMID): 16194619 | | Abstract: A combination of electron microscopy and fluorescence microscopy has provided us with a global picture of the structure of the plant Golgi apparatus .
However , the components that shape this structure remain elusive .
In other organisms , members of the golgin family of coiled-coil proteins are essential for Golgi structure and organisation .
Putative Arabidopsis and rice homologues of some golgin family members can be identified using database searches .
Likewise , the heterogeneous group of multi-subunit-tethering complexes is responsible for crucial transport steps that affect Golgi structure and cisternal organisation in animals and yeasts .
The Arabidopsis genome harbours possible homologues for the majority of the subunits of these complexes , suggesting that they also operate in the plant kingdom .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: In other organisms , members of the golgin family of coiled-coil proteins are essential for Golgi structure and organisation .
[ Sen. 1, subscore: 1.00 ]: A combination of electron microscopy and fluorescence microscopy has provided us with a global picture of the structure of the plant Golgi apparatus .
[ Sen. 4, subscore: 1.00 ]: Putative Arabidopsis and rice homologues of some golgin family members can be identified using database searches .
[ Sen. 5, subscore: 1.00 ]: Likewise , the heterogeneous group of multi-subunit-tethering complexes is responsible for crucial transport steps that affect Golgi structure and cisternal organisation in animals and yeasts .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Golden Rice--five years on the road--five years to go?
| | Author: Al-Babili S Beyer P | | Journal: Trends Plant Sci .
Citation: V : 10 ( 12 ) P : 565-73 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16297656 Accession (PMID): 16297656 | | Abstract: Provitamin A accumulates in the grain of Golden Rice as a result of genetic transformation .
In developing countries , where vitamin A deficiency prevails , grain from Golden Rice is expected to provide this important micronutrient sustainably through agriculture .
Since its original production , the prototype Golden Rice has undergone intense research to increase the provitamin A content , to establish the scientific basis for its carotenoid complement , and to better comply with regulatory requirements .
Today , the current focus is on how to get Golden Rice effectively into the hands of farmers , which is a novel avenue for public sector research , carried out with the aid of international research consortia .
Additional new research is underway to further increase the nutritional value of Golden Rice . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Provitamin A accumulates in the grain of Golden Rice as a result of genetic transformation .
[ Sen. 2, subscore: 1.00 ]: In developing countries , where vitamin A deficiency prevails , grain from Golden Rice is expected to provide this important micronutrient sustainably through agriculture .
[ Sen. 3, subscore: 1.00 ]: Since its original production , the prototype Golden Rice has undergone intense research to increase the provitamin A content , to establish the scientific basis for its carotenoid complement , and to better comply with regulatory requirements .
[ Sen. 4, subscore: 1.00 ]: Today , the current focus is on how to get Golden Rice effectively into the hands of farmers , which is a novel avenue for public sector research , carried out with the aid of international research consortia .
[ Sen. 5, subscore: 1.00 ]: Additional new research is underway to further increase the nutritional value of Golden Rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Interaction of rice dwarf virus outer capsid P8 protein with rice glycolate oxidase mediates relocalization of P8 .
| | Author: Zhou F Wu G Deng W Pu Y Wei C Li Y | | Journal: FEBS Lett .
Citation: V : 581 ( 1 ) P : 34-40 Year: 2007 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17174956 Accession (PMID): 17174956 | | Abstract: Yeast two-hybrid and coimmunoprecipitation assays indicated that P8 , an outer capsid protein of Rice dwarf phytoreovirus ( RDV ) , interacts with rice glycolate oxidase ( GOX ) , a typical enzyme of peroxisomes .
Confocal immunofluorescence microscopy revealed that P8 was colocalized with GOX in peroxisomes .
Time course analysis demonstrated that the localization of P8 in Spodoptera frugiperda cells changed from diffuse to discrete , punctuate inclusions during expression from 24 to 48 h post inoculation .
Coexpression of GOX with P8 may target P8 into peroxisomes , which serve as replication sites for a number of viruses .
Therefore , we conclude that the interaction of P8 with the GOX of host cells leads to translocation of P8 into peroxisomes and we further propose that the interaction between P8 and GOX may play important roles in RDV targeting into the replication site of host cells .
Our findings have broad significance in studying the mechanisms whereby viruses target appropriate replication sites and begin their replication .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: Therefore , we conclude that the interaction of P8 with the GOX of host cells leads to translocation of P8 into peroxisomes and we further propose that the interaction between P8 and GOX may play important roles in RDV targeting into the replication site of host cells .
[ Sen. 1, subscore: 1.00 ]: Yeast two-hybrid and coimmunoprecipitation assays indicated that P8 , an outer capsid protein of Rice dwarf phytoreovirus ( RDV ) , interacts with rice glycolate oxidase ( GOX ) , a typical enzyme of peroxisomes .
[ Sen. 2, subscore: 1.00 ]: Confocal immunofluorescence microscopy revealed that P8 was colocalized with GOX in peroxisomes .
[ Sen. 4, subscore: 1.00 ]: Coexpression of GOX with P8 may target P8 into peroxisomes , which serve as replication sites for a number of viruses .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
