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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 .
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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 .
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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 .
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[ 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 | |
