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Score: 15.00
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 13.00
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
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
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
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
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