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Score: 17.00
Title: Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection .
Author: Guo B Chen X Dang P Scully BT Liang X Holbrook CC Yu J Culbreath AK
Journal: BMC Dev Biol Citation: V : 8 P : 12 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18248674 Accession (PMID): 18248674
Abstract: BACKGROUND : Peanut ( Arachis hypogaea L ) is an important crop economically and nutritionally , and is one of the most susceptible host crops to colonization of Aspergillus parasiticus and subsequent aflatoxin contamination . Knowledge from molecular genetic studies could help to devise strategies in alleviating this problem ; however , few peanut DNA sequences are available in the public database . In order to understand the molecular basis of host resistance to aflatoxin contamination , a large-scale project was conducted to generate expressed sequence tags ( ESTs ) from developing seeds to identify resistance-related genes involved in defense response against Aspergillus infection and subsequent aflatoxin contamination . RESULTS : We constructed six different cDNA libraries derived from developing peanut seeds at three reproduction stages ( R5 , R6 and R7 ) from a resistant and a susceptible cultivated peanut genotypes , Tifrunner ( susceptible to Aspergillus infection with higher aflatoxin contamination and resistant to TSWV ) and GT-C20 ( resistant to Aspergillus with reduced aflatoxin contamination and susceptible to TSWV ) . The developing peanut seed it issues were challenged by A parasiticus and drought stress in the field . A total of 24 , 192 randomly selected cDNA clones from six libraries were sequenced . After removing vector sequences and quality trimming , 21 , 777 high-quality EST sequences were generated . Sequence clustering and assembling resulted in 8 , 689 unique EST sequences with 1 , 741 tentative consensus EST sequences ( TCs ) and 6 , 948 singleton ESTs . Functional classification was performed according to MIPS functional catalogue criteria . The unique EST sequences were divided into twenty-two categories . A similarity search against the non-redundant protein database available from NCBI indicated that 84 . 78% of total ESTs showed significant similarity to known proteins , of which 165 genes had been previously reported in peanuts . There were differences in overall expression patterns in different libraries and genotypes . A number of sequences were expressed throughout all of the libraries , representing constitutive expressed sequences . In order to identify resistance-related genes with significantly differential expression , a statistical analysis to estimate the relative abundance ( R ) was used to compare the relative abundance of each gene transcripts in each cDNA library . Thirty six and forty seven unique EST sequences with threshold of R > 4 from libraries of GT-C20 and Tifrunner , respectively , were selected for examination of temporal gene expression patterns according to EST frequencies . Nine and eight resistance-related genes with significant up-regulation were obtained in GT-C20 and Tifrunner libraries , respectively . Among them , three genes were common in both genotypes . Furthermore , a comparison of our EST sequences with other plant sequences in the TIGR Gene Indices libraries showed that the percentage of peanut EST matched to Arabidopsis thaliana , maize ( Zea mays ) , Medicago truncatula , rapeseed ( Brassica napus ) , rice ( Oryza sativa ) , soybean ( Glycine max ) and wheat ( Triticum aestivum ) ESTs ranged from 33 . 84% to 79 . 46% with the sequence identity >/= 80% . These results revealed that peanut ESTs are more closely related to legume species than to cereal crops , and more homologous to dicot than to monocot plant species . CONCLUSION : The developed ESTs can be used to discover novel sequences or genes , to identify resistance-related genes and to detect the differences among alleles or markers between these resistant and susceptible peanut genotypes . Additionally , this large collection of cultivated peanut EST sequences will make it possible to construct microarrays for gene expression studies and for further characterization of host resistance mechanisms . It will be a valuable genomic resource for the peanut community . The 21 , 777 ESTs have been deposited to the NCBI GenBank database with accession numbers ES702769 to ES724546 .
Matching Sentences:
[ Sen. 8, subscore: 3.00 ]: Sequence clustering and assembling resulted in 8 , 689 unique EST sequences with 1 , 741 tentative consensus EST sequences ( TCs ) and 6 , 948 singleton ESTs .
[ Sen. 18, subscore: 3.00 ]: Furthermore , a comparison of our EST sequences with other plant sequences in the TIGR Gene Indices libraries showed that the percentage of peanut EST matched to Arabidopsis thaliana , maize ( Zea mays ) , Medicago truncatula , rapeseed ( Brassica napus ) , rice ( Oryza sativa ) , soybean ( Glycine max ) and wheat ( Triticum aestivum ) ESTs ranged from 33 . 84% to 79 . 46% with the sequence identity >/= 80% .
[ Sen. 15, subscore: 2.00 ]: Thirty six and forty seven unique EST sequences with threshold of R > 4 from libraries of GT-C20 and Tifrunner , respectively , were selected for examination of temporal gene expression patterns according to EST frequencies .
[ Sen. 3, subscore: 1.00 ]: In order to understand the molecular basis of host resistance to aflatoxin contamination , a large-scale project was conducted to generate expressed sequence tags ( ESTs ) from developing seeds to identify resistance-related genes involved in defense response against Aspergillus infection and subsequent aflatoxin contamination .
[ Sen. 7, subscore: 1.00 ]: After removing vector sequences and quality trimming , 21 , 777 high-quality EST sequences were generated .
[ Sen. 10, subscore: 1.00 ]: The unique EST sequences were divided into twenty-two categories .
[ Sen. 11, subscore: 1.00 ]: A similarity search against the non-redundant protein database available from NCBI indicated that 84 . 78% of total ESTs showed significant similarity to known proteins , of which 165 genes had been previously reported in peanuts .
[ Sen. 14, subscore: 1.00 ]: In order to identify resistance-related genes with significantly differential expression , a statistical analysis to estimate the relative abundance ( R ) was used to compare the relative abundance of each gene transcripts in each cDNA library .
[ Sen. 19, subscore: 1.00 ]: These results revealed that peanut ESTs are more closely related to legume species than to cereal crops , and more homologous to dicot than to monocot plant species .
[ Sen. 20, subscore: 1.00 ]: CONCLUSION : The developed ESTs can be used to discover novel sequences or genes , to identify resistance-related genes and to detect the differences among alleles or markers between these resistant and susceptible peanut genotypes .
[ Sen. 21, subscore: 1.00 ]: Additionally , this large collection of cultivated peanut EST sequences will make it possible to construct microarrays for gene expression studies and for further characterization of host resistance mechanisms .
[ Sen. 23, subscore: 1.00 ]: The 21 , 777 ESTs have been deposited to the NCBI GenBank database with accession numbers ES702769 to ES724546 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 14.00
Title: The in vitro hydrolysis of phytosterol conjugates in food matrices by mammalian digestive enzymes .
Author: Moreau RA Hicks KB .
Journal: Lipids Citation: V : 39 ( 8 ) P : 769-76 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15638245 Accession (PMID): 15638245
Abstract: All fruits , vegetables , and grains contain phytosterols . Numerous clinical studies have documented that phytosterols lower LDL-cholesterol levels and thereby reduce the risk of cardiovascular disease . Most experts believe that the cholesterol-lowering mechanism of phytosterols requires that they be in their "free" form . In addition to their occurrence in the free form , phytosterols also occur as four common phytosterol conjugates : ( i ) fatty acyl esters , ( ii ) hydroxycinnamate esters , ( iii ) steryl glycosides , and ( iv ) fatty acylated steryl glycosides . This study was undertaken to investigate the extent of hydrolysis of four common phytosterol conjugates by mammalian digestive enzymes ( cholesterol esterase and pancreatin , a mixture of pancreatic enzymes ) and for comparison purposes , by KOH . Two types of purified hydroxycinnamate esters ( sitostanyl ferulate and oryzanol , a mixture of hydroxycinnamate esters purified from rice bran oil ) were hydrolyzed by cholesterol esterase and by pancreatin . Both cholesterol esterase and pancreatin hydrolyzed the phytosteryl esters in two functional food matrices , and they hydrolyzed the hydroxycinnamate esters in corn fiber oil . This is the first report to demonstrate that phytostanyl ferulate esters ( which are present at levels of 3-6% in corn fiber oil ) are hydrolyzed by pancreatic cholesterol esterase . It is also the first report that pancreatin contains enzymes that hydrolyze the fatty acyl moiety of fatty acylated steryl glycoside , converting it to steryl glycoside . Pancreatin had no effect on steryl glycosides . The ability of pancreatin to hydrolyze three other types of lipid conjugates was also evaluated . Phospholipids were completely hydrolyzed . About half of the galactolipids were hydrolyzed , and less than 10% of the polyamine conjugates were hydrolyzed . The extents of hydrolysis of phytosteryl esters by base ( saponification ) were also studied , and conditions commonly used for the saponification of acyl lipids ( 1 . 5 N methanolic KOH , 30 min at 70 degrees C ) , were found to result in a nearly 100% hydrolysis of TAG but only about 35-45% hydrolysis of the phytosteryl fatty acyl esters or phytosteryl hydroxycinnamate esters .
Matching Sentences:
[ Sen. 6, subscore: 3.00 ]: Two types of purified hydroxycinnamate esters ( sitostanyl ferulate and oryzanol , a mixture of hydroxycinnamate esters purified from rice bran oil ) were hydrolyzed by cholesterol esterase and by pancreatin .
[ Sen. 7, subscore: 3.00 ]: Both cholesterol esterase and pancreatin hydrolyzed the phytosteryl esters in two functional food matrices , and they hydrolyzed the hydroxycinnamate esters in corn fiber oil .
[ Sen. 14, subscore: 3.00 ]: The extents of hydrolysis of phytosteryl esters by base ( saponification ) were also studied , and conditions commonly used for the saponification of acyl lipids ( 1 . 5 N methanolic KOH , 30 min at 70 degrees C ) , were found to result in a nearly 100% hydrolysis of TAG but only about 35-45% hydrolysis of the phytosteryl fatty acyl esters or phytosteryl hydroxycinnamate esters .
[ Sen. 4, subscore: 2.00 ]: In addition to their occurrence in the free form , phytosterols also occur as four common phytosterol conjugates : ( i ) fatty acyl esters , ( ii ) hydroxycinnamate esters , ( iii ) steryl glycosides , and ( iv ) fatty acylated steryl glycosides .
[ Sen. 8, subscore: 2.00 ]: This is the first report to demonstrate that phytostanyl ferulate esters ( which are present at levels of 3-6% in corn fiber oil ) are hydrolyzed by pancreatic cholesterol esterase .
[ Sen. 5, subscore: 1.00 ]: This study was undertaken to investigate the extent of hydrolysis of four common phytosterol conjugates by mammalian digestive enzymes ( cholesterol esterase and pancreatin , a mixture of pancreatic enzymes ) and for comparison purposes , by KOH .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 14.00
Title: A comparison of plotless density estimators using Monte Carlo simulation on totally enumerated field data sets .
Author: White NA Engeman RM Sugihara RT Krupa HW
Journal: BMC Ecol Citation: V : 8 P : 6 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18416853 Accession (PMID): 18416853
Abstract: BACKGROUND : Plotless density estimators are those that are based on distance measures rather than counts per unit area ( quadrats or plots ) to estimate the density of some usually stationary event , eg burrow openings , damage to plant stems , etc These estimators typically use distance measures between events and from random points to events to derive an estimate of density . The error and bias of these estimators for the various spatial patterns found in nature have been examined using simulated populations only . In this study we investigated eight plotless density estimators to determine which were robust across a wide range of data sets from fully mapped field sites . They covered a wide range of situations including animal damage to rice and corn , nest locations , active rodent burrows and distribution of plants . Monte Carlo simulations were applied to sample the data sets , and in all cases the error of the estimate ( measured as relative root mean square error ) was reduced with increasing sample size . The method of calculation and ease of use in the field were also used to judge the usefulness of the estimator . Estimators were evaluated in their original published forms , although the variable area transect ( VAT ) and ordered distance methods have been the subjects of optimization studies . RESULTS : An estimator that was a compound of three basic distance estimators was found to be robust across all spatial patterns for sample sizes of 25 or greater . The same field methodology can be used either with the basic distance formula or the formula used with the Kendall-Moran estimator in which case a reduction in error may be gained for sample sizes less than 25 , however , there is no improvement for larger sample sizes . The variable area transect ( VAT ) method performed moderately well , is easy to use in the field , and its calculations easy to undertake . CONCLUSION : Plotless density estimators can provide an estimate of density in situations where it would not be practical to layout a plot or quadrat and can in many cases reduce the workload in the field .
Matching Sentences:
[ Sen. 1, subscore: 4.00 ]: BACKGROUND : Plotless density estimators are those that are based on distance measures rather than counts per unit area ( quadrats or plots ) to estimate the density of some usually stationary event , eg burrow openings , damage to plant stems , etc These estimators typically use distance measures between events and from random points to events to derive an estimate of density .
[ Sen. 8, subscore: 2.00 ]: RESULTS : An estimator that was a compound of three basic distance estimators was found to be robust across all spatial patterns for sample sizes of 25 or greater .
[ Sen. 11, subscore: 2.00 ]: CONCLUSION : Plotless density estimators can provide an estimate of density in situations where it would not be practical to layout a plot or quadrat and can in many cases reduce the workload in the field .
[ Sen. 2, subscore: 1.00 ]: The error and bias of these estimators for the various spatial patterns found in nature have been examined using simulated populations only .
[ Sen. 3, subscore: 1.00 ]: In this study we investigated eight plotless density estimators to determine which were robust across a wide range of data sets from fully mapped field sites .
[ Sen. 5, subscore: 1.00 ]: Monte Carlo simulations were applied to sample the data sets , and in all cases the error of the estimate ( measured as relative root mean square error ) was reduced with increasing sample size .
[ Sen. 6, subscore: 1.00 ]: The method of calculation and ease of use in the field were also used to judge the usefulness of the estimator .
[ Sen. 7, subscore: 1.00 ]: Estimators were evaluated in their original published forms , although the variable area transect ( VAT ) and ordered distance methods have been the subjects of optimization studies .
[ Sen. 9, subscore: 1.00 ]: The same field methodology can be used either with the basic distance formula or the formula used with the Kendall-Moran estimator in which case a reduction in error may be gained for sample sizes less than 25 , however , there is no improvement for larger sample sizes .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 13.00
Title: Prevalence of autism spectrum disorders--Autism and Developmental Disabilities Monitoring Network , 14 sites , United States , 2008 .
Author:
Journal: MMWR Surveill Summ Citation: V : 61 P : 1-19 Year: 2012 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub22456193 Accession (PMID): 22456193
Abstract: PROBLEM/CONDITION : Autism spectrum disorders ( ASDs ) are a group of developmental disabilities characterized by impairments in social interaction and communication and by restricted , repetitive , and stereotyped patterns of behavior . Symptoms typically are apparent before age 3 years . The complex nature of these disorders , coupled with a lack of biologic markers for diagnosis and changes in clinical definitions over time , creates challenges in monitoring the prevalence of ASDs . Accurate reporting of data is essential to understand the prevalence of ASDs in the population and can help direct research . PERIOD COVERED : 2008 . DESCRIPTION OF SYSTEM : The Autism and Developmental Disabilities Monitoring ( ADDM ) Network is an active surveillance system that estimates the prevalence of ASDs and describes other characteristics among children aged 8 years whose parents or guardians reside within 14 ADDM sites in the United States . ADDM does not rely on professional or family reporting of an existing ASD diagnosis or classification to ascertain case status . Instead , information is obtained from childrens evaluation records to determine the presence of ASD symptoms at any time from birth through the end of the year when the child reaches age 8 years . ADDM focuses on children aged 8 years because a baseline study conducted by CDC demonstrated that this is the age of identified peak prevalence . A child is included as meeting the surveillance case definition for an ASD if he or she displays behaviors ( as described on a comprehensive evaluation completed by a qualified professional ) consistent with the American Psychiatric Associations Diagnostic and Statistical Manual-IV , Text Revision ( DSM-IV-TR ) diagnostic criteria for any of the following conditions : Autistic Disorder ; Pervasive Developmental Disorder-Not Otherwise Specified ( PDD-NOS , including Atypical Autism ) ; or Asperger Disorder . The first phase of the ADDM methodology involves screening and abstraction of comprehensive evaluations completed by professional providers at multiple data sources in the community . Multiple data sources are included , ranging from general pediatric health clinics to specialized programs for children with developmental disabilities . In addition , many ADDM sites also review and abstract records of children receiving special education services in public schools . In the second phase of the study , all abstracted evaluations are reviewed by trained clinicians to determine ASD case status . Because the case definition and surveillance methods have remained consistent across all ADDM surveillance years to date , comparisons to results for earlier surveillance years can be made . This report provides updated ASD prevalence estimates from the 2008 surveillance year , representing 14 ADDM areas in the United States . In addition to prevalence estimates , characteristics of the population of children with ASDs are described , as well as detailed comparisons of the 2008 surveillance year findings with those for the 2002 and 2006 surveillance years . RESULTS : For 2008 , the overall estimated prevalence of ASDs among the 14 ADDM sites was 11 . 3 per 1 , 000 ( one in 88 ) children aged 8 years who were living in these communities during 2008 . Overall ASD prevalence estimates varied widely across all sites ( range : 4 . 8-21 . 2 per 1 , 000 children aged 8 years ) . ASD prevalence estimates also varied widely by sex and by racial/ethnic group . Approximately one in 54 boys and one in 252 girls living in the ADDM Network communities were identified as having ASDs . Comparison of 2008 findings with those for earlier surveillance years indicated an increase in estimated ASD prevalence of 23% when the 2008 data were compared with the data for 2006 ( from 9 . 0 per 1 , 000 children aged 8 years in 2006 to 11 . 0 in 2008 for the 11 sites that provided data for both surveillance years ) and an estimated increase of 78% when the 2008 data were compared with the data for 2002 ( from 6 . 4 per 1 , 000 children aged 8 years in 2002 to 11 . 4 in 2008 for the 13 sites that provided data for both surveillance years ) . Because the ADDM Network sites do not make up a nationally representative sample , these combined prevalence estimates should not be generalized to the United States as a whole . INTERPRETATION : These data confirm that the estimated prevalence of ASDs identified in the ADDM network surveillance populations continues to increase . The extent to which these increases reflect better case ascertainment as a result of increases in awareness and access to services or true increases in prevalence of ASD symptoms is not known . ASDs continue to be an important public health concern in the United States , underscoring the need for continued resources to identify potential risk factors and to provide essential supports for persons with ASDs and their families . PUBLIC HEALTH ACTION : Given substantial increases in ASD prevalence estimates over a relatively short period , overall and within various subgroups of the population , continued monitoring is needed to quantify and understand these patterns . With 5 biennial surveillance years completed in the past decade , the ADDM Network continues to monitor prevalence and characteristics of ASDs and other developmental disabilities for the 2010 surveillance year . Further work is needed to evaluate multiple factors contributing to increases in estimated ASD prevalence over time . ADDM Network investigators continue to explore these factors , with a focus on understanding disparities in the identification of ASDs among certain subgroups and on how these disparities have contributed to changes in the estimated prevalence of ASDs . CDC is partnering with other federal and private partners in a coordinated response to identify risk factors for ASDs and to meet the needs of persons with ASDs and their families .
Matching Sentences:
[ Sen. 22, subscore: 2.00 ]: Comparison of 2008 findings with those for earlier surveillance years indicated an increase in estimated ASD prevalence of 23% when the 2008 data were compared with the data for 2006 ( from 9 . 0 per 1 , 000 children aged 8 years in 2006 to 11 . 0 in 2008 for the 11 sites that provided data for both surveillance years ) and an estimated increase of 78% when the 2008 data were compared with the data for 2002 ( from 6 . 4 per 1 , 000 children aged 8 years in 2002 to 11 . 4 in 2008 for the 13 sites that provided data for both surveillance years ) .
[ Sen. 6, subscore: 1.00 ]: DESCRIPTION OF SYSTEM : The Autism and Developmental Disabilities Monitoring ( ADDM ) Network is an active surveillance system that estimates the prevalence of ASDs and describes other characteristics among children aged 8 years whose parents or guardians reside within 14 ADDM sites in the United States .
[ Sen. 16, subscore: 1.00 ]: This report provides updated ASD prevalence estimates from the 2008 surveillance year , representing 14 ADDM areas in the United States .
[ Sen. 17, subscore: 1.00 ]: In addition to prevalence estimates , characteristics of the population of children with ASDs are described , as well as detailed comparisons of the 2008 surveillance year findings with those for the 2002 and 2006 surveillance years .
[ Sen. 18, subscore: 1.00 ]: RESULTS : For 2008 , the overall estimated prevalence of ASDs among the 14 ADDM sites was 11 . 3 per 1 , 000 ( one in 88 ) children aged 8 years who were living in these communities during 2008 .
[ Sen. 19, subscore: 1.00 ]: Overall ASD prevalence estimates varied widely across all sites ( range : 4 . 8-21 . 2 per 1 , 000 children aged 8 years ) .
[ Sen. 20, subscore: 1.00 ]: ASD prevalence estimates also varied widely by sex and by racial/ethnic group .
[ Sen. 23, subscore: 1.00 ]: Because the ADDM Network sites do not make up a nationally representative sample , these combined prevalence estimates should not be generalized to the United States as a whole .
[ Sen. 24, subscore: 1.00 ]: INTERPRETATION : These data confirm that the estimated prevalence of ASDs identified in the ADDM network surveillance populations continues to increase .
[ Sen. 27, subscore: 1.00 ]: PUBLIC HEALTH ACTION : Given substantial increases in ASD prevalence estimates over a relatively short period , overall and within various subgroups of the population , continued monitoring is needed to quantify and understand these patterns .
[ Sen. 29, subscore: 1.00 ]: Further work is needed to evaluate multiple factors contributing to increases in estimated ASD prevalence over time .
[ Sen. 30, subscore: 1.00 ]: ADDM Network investigators continue to explore these factors , with a focus on understanding disparities in the identification of ASDs among certain subgroups and on how these disparities have contributed to changes in the estimated prevalence of ASDs .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 12.00
Title: Characterization of Esterase A , a Pseudomonas stutzeri A15 Autotransporter .
Author: Nicolay T Devleeschouwer K Vanderleyden J Spaepen S
Journal: Appl Environ Microbiol Citation: V : 78 P : 2533-42 Year: 2012 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub22307303 Accession (PMID): 22307303
Abstract: Autotransporters are a widespread family of proteins , generally known as virulence factors produced by Gram-negative bacteria . In this study , the esterase A ( EstA ) autotransporter of the rice root-colonizing beneficial bacterium Pseudomonas stutzeri A15 was characterized . A multiple sequence alignment identified EstA as belonging to clade II of the GDSL esterase family . Autologous overexpression allowed the investigation of several features of both autotransporter proteins and GDSL esterases . First , the correctly folded autotransporter was shown to be present in the membrane fraction . Unexpectedly , after separation of the membrane fraction , EstA was detected in the N-laurylsarcosine soluble fraction . However , evidence is presented for the surface exposure of EstA based on fluorescent labeling with EstA specific antibodies . Another remarkable feature is the occurrence of a C-terminal leucine residue instead of the canonical phenylalanine or tryptophan residue . Replacement of this residue with a phenylalanine residue reduced the stability of the beta-barrel . Regarding the esterase passenger domain , we show the importance of the catalytic triad residues , with the serine and histidine residues being more critical than the aspartate residue . Furthermore , the growth of an estA-negative mutant was not impaired and cell mobility was not disabled compared to the wild type . No specific phenotype was detected for an estA-negative mutant . Overall , P stutzeri A15 EstA is a new candidate for the surface display of proteins in environmentally relevant biotechnological applications .
Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: In this study , the esterase A ( EstA ) autotransporter of the rice root-colonizing beneficial bacterium Pseudomonas stutzeri A15 was characterized .
[ Sen. 3, subscore: 2.00 ]: A multiple sequence alignment identified EstA as belonging to clade II of the GDSL esterase family .
[ Sen. 7, subscore: 2.00 ]: However , evidence is presented for the surface exposure of EstA based on fluorescent labeling with EstA specific antibodies .
[ Sen. 4, subscore: 1.00 ]: Autologous overexpression allowed the investigation of several features of both autotransporter proteins and GDSL esterases .
[ Sen. 6, subscore: 1.00 ]: Unexpectedly , after separation of the membrane fraction , EstA was detected in the N-laurylsarcosine soluble fraction .
[ Sen. 10, subscore: 1.00 ]: Regarding the esterase passenger domain , we show the importance of the catalytic triad residues , with the serine and histidine residues being more critical than the aspartate residue .
[ Sen. 11, subscore: 1.00 ]: Furthermore , the growth of an estA-negative mutant was not impaired and cell mobility was not disabled compared to the wild type .
[ Sen. 12, subscore: 1.00 ]: No specific phenotype was detected for an estA-negative mutant .
[ Sen. 13, subscore: 1.00 ]: Overall , P stutzeri A15 EstA is a new candidate for the surface display of proteins in environmentally relevant biotechnological applications .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 11.00
Title: Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis .
Author: Peng JH Zadeh H Lazo GR Gustafson JP Chao S Anderson OD Qi LL Echalier B Gill BS Dilbirligi M Sandhu D Gill KS Greene RA Sorrells ME Akhunov ED Dvork J Linkiewicz AM Dubcovsky J Hossain KG Kalavacharla V Kianian SF Mahmoud AA Miftahudin Conley EJ Anderson JA Pathan MS Nguyen HT McGuire PE Qualset CO Lapitan NL .
Journal: Genetics Citation: V : 168 ( 2 ) P : 609-23 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15514039 Accession (PMID): 15514039
Abstract: A total of 944 expressed sequence tags ( ESTs ) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat ( Triticum aestivum L ) . EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution . EST loci were unevenly distributed among chromosomes 1A , 1B , and 1D with 660 , 826 , and 726 , respectively . The number of EST loci was greater on the long arms than on the short arms for all three chromosomes . The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms . Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35 . 5% . Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences ( E < or = e ( -10 ) ) , where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10 . Only 9 . 5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences . The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses .
Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: A total of 944 expressed sequence tags ( ESTs ) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat ( Triticum aestivum L ) .
[ Sen. 2, subscore: 2.00 ]: EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution .
[ Sen. 5, subscore: 2.00 ]: The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms .
[ Sen. 3, subscore: 1.00 ]: EST loci were unevenly distributed among chromosomes 1A , 1B , and 1D with 660 , 826 , and 726 , respectively .
[ Sen. 4, subscore: 1.00 ]: The number of EST loci was greater on the long arms than on the short arms for all three chromosomes .
[ Sen. 6, subscore: 1.00 ]: Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35 . 5% .
[ Sen. 7, subscore: 1.00 ]: Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences ( E < or = e ( -10 ) ) , where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10 .
[ Sen. 8, subscore: 1.00 ]: Only 9 . 5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences .
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Score: 11.00
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. 2, subscore: 1.00 ]: DNA content estimates from about half of the species indicate over a 3-fold variation exists .
[ Sen. 3, subscore: 1.00 ]: However , the nine DNA content estimates for G hirsutum reveal over a 2-fold difference for this species alone .
[ Sen. 4, subscore: 1.00 ]: Recent reports have shown that several plant compounds can bias DNA content estimates obtained by commonly used methods .
[ Sen. 5, subscore: 1.00 ]: 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. 7, subscore: 1.00 ]: Fluorescence values were converted to DNA content estimates based on the nuclear fluorescence of standard genotypes of barley , corn and rice .
[ Sen. 8, subscore: 1.00 ]: Various combinations of nuclei preparations relative to the standards were evaluated for their influence on the estimates .
[ 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. 10, subscore: 1.00 ]: Internal standardization with Hordeum vulgare Sultan resulted in a high estimate of DNA content .
[ Sen. 11, subscore: 1.00 ]: Nuclear DNA content estimates were generated for 37 Gossypium species using external standardization .
[ Sen. 12, subscore: 1.00 ]: Estimates of ancestral genome sizes reveal that both increases and decreases in nuclear DNA content have occurred .
[ Sen. 15, subscore: 1.00 ]: The current DNA content estimates support accepted cytogenetic divisions of the genus .
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Score: 11.00
Title: Structural and functional analyses of the wheat genomes based on expressed sequence tags ( ESTs ) related to abiotic stresses .
Author: Ramalingam J Pathan MS Feril O Ross K Ma XF Mahmoud AA Layton J Rodriguez-Milla MA Chikmawati T Valliyodan B Skinner R Matthews DE Gustafson JP Nguyen HT .
Journal: Genome Citation: V : 49 ( 10 ) P : 1324-40 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub17218960 Accession (PMID): 17218960
Abstract: To gain insights into the structure and function of the wheat ( Triticum aestivum L ) genomes , we identified 278 ESTs related to abiotic stress ( cold , heat , drought , salinity , and aluminum ) from 7671 ESTs previously mapped to wheat chromosomes . Of the 278 abiotic stress related ESTs , 259 ( 811 loci ) were assigned to chromosome deletion bins and analyzed for their distribution pattern among the 7 homoeologous chromosome groups . Distribution of abiotic stress related EST loci were not uniform throughout the different regions of the chromosomes of the 3 wheat genomes . Both the short and long arms of group 4 chromosomes showed a higher number of loci in their distal regions compared with proximal regions . Of the 811 loci , the number of mapped loci on the A , B , and D genomes were 258 , 281 , and 272 , respectively . The highest number of abiotic stress related loci were found in homoeologous chromosome group 2 ( 142 loci ) and the lowest number were found in group 6 ( 94 loci ) . When considering the genome-specific ESTs , the B genome showed the highest number of unique ESTs ( 7 loci ) , while none were found in the D genome . Similarly , considering homoeologous group-specific ESTs , group 2 showed the highest number with 16 unique ESTs ( 58 loci ) , followed by group 4 with 9 unique ESTs ( 33 loci ) . Many of the classified proteins fell into the biological process categories associated with metabolism , cell growth , and cell maintenance . Most of the mapped ESTs fell into the category of enzyme activity ( 28% ) , followed by binding activity ( 27% ) . Enzymes related to abiotic stress such as beta-galactosidase , peroxidase , glutathione reductase , and trehalose-6-phosphate synthase were identified . The comparison of stress-responsive ESTs with genomic sequences of rice ( Oryza sativa L ) chromosomes revealed the complexities of colinearity . This bin map provides insight into the structural and functional details of wheat genomic regions in relation to abiotic stress .
Matching Sentences:
[ Sen. 8, subscore: 3.00 ]: Similarly , considering homoeologous group-specific ESTs , group 2 showed the highest number with 16 unique ESTs ( 58 loci ) , followed by group 4 with 9 unique ESTs ( 33 loci ) .
[ Sen. 1, subscore: 2.00 ]: To gain insights into the structure and function of the wheat ( Triticum aestivum L ) genomes , we identified 278 ESTs related to abiotic stress ( cold , heat , drought , salinity , and aluminum ) from 7671 ESTs previously mapped to wheat chromosomes .
[ Sen. 7, subscore: 2.00 ]: When considering the genome-specific ESTs , the B genome showed the highest number of unique ESTs ( 7 loci ) , while none were found in the D genome .
[ Sen. 2, subscore: 1.00 ]: Of the 278 abiotic stress related ESTs , 259 ( 811 loci ) were assigned to chromosome deletion bins and analyzed for their distribution pattern among the 7 homoeologous chromosome groups .
[ Sen. 3, subscore: 1.00 ]: Distribution of abiotic stress related EST loci were not uniform throughout the different regions of the chromosomes of the 3 wheat genomes .
[ Sen. 10, subscore: 1.00 ]: Most of the mapped ESTs fell into the category of enzyme activity ( 28% ) , followed by binding activity ( 27% ) .
[ Sen. 12, subscore: 1.00 ]: The comparison of stress-responsive ESTs with genomic sequences of rice ( Oryza sativa L ) chromosomes revealed the complexities of colinearity .
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Score: 11.00
Title: Estradiol and SERM Treatments Influence Estrogen Receptor Coregulator Gene Expression in Human Skeletal Muscle Cells .
Author: Dieli-Conwright CM Spektor TM Rice JC Todd Schroeder E
Journal: Acta Physiol ( Oxf ) Citation: V : P : Year: 2009 Type: Publisher
Literature: oryza Field: abstract Doc ID: pub19432593 Accession (PMID): 19432593
Abstract: Aim : Estrogen receptors are present in human skeletal muscle ; however , the function of the receptor is currently unknown . We investigated the influence of estradiol and selective estrogen receptor modulators ( tamoxifen , raloxifene ) on estrogen receptor coregulator mRNA expression in human skeletal muscle cells . Methods : Human skeletal muscle cells were treated with the following conditions over a 24-hour period : 10 nM estradiol ; 5 muM of tamoxifen ; and 10muM raloxifene . Following the treatment period , mRNA expression was quantified using real-time PCR to detect changes in ER-alpha , ER-beta , SRC , SMRT , MyoD , GLUT4 and c-fos . Results : ER-alpha mRNA expression increased with all 3 drug treatments ( p< 0 . 05 ) while there was no change in mRNA expression of ER-beta in human skeletal muscle cells . mRNA expression of SRC increased and SMRT decreased with estradiol , tamoxifen , and raloxifene in human skeletal muscle cells ( p< 0 . 05 ) . Importantly , mRNA expression of MyoD increased with estradiol and decreased with tamoxifen and raloxifene in human skeletal muscle cells ( p < 0 . 05 ) . mRNA expression of GLUT4 increased with estradiol and raloxifene and decreased with tamoxifen in human skeletal muscle cells ( p < 0 . 05 ) . Conclusions : These findings are novel in that they provide the first evidence that estradiol and selective estrogen receptor modulators influence ER-alpha function in human skeletal muscle . This demonstrates the importance of the estrogen receptor and alterations in its coregulators , to potentially prevent sarcopenia and promote muscle growth in postmenopausal women using these forms of hormone replacement therapy .
Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: We investigated the influence of estradiol and selective estrogen receptor modulators ( tamoxifen , raloxifene ) on estrogen receptor coregulator mRNA expression in human skeletal muscle cells .
[ Sen. 6, subscore: 2.00 ]: Importantly , mRNA expression of MyoD increased with estradiol and decreased with tamoxifen and raloxifene in human skeletal muscle cells ( p < 0 . 05 ) . mRNA expression of GLUT4 increased with estradiol and raloxifene and decreased with tamoxifen in human skeletal muscle cells ( p < 0 . 05 ) .
[ Sen. 7, subscore: 2.00 ]: Conclusions : These findings are novel in that they provide the first evidence that estradiol and selective estrogen receptor modulators influence ER-alpha function in human skeletal muscle .
[ Sen. 1, subscore: 1.00 ]: Aim : Estrogen receptors are present in human skeletal muscle ; however , the function of the receptor is currently unknown .
[ Sen. 3, subscore: 1.00 ]: Methods : Human skeletal muscle cells were treated with the following conditions over a 24-hour period : 10 nM estradiol ; 5 muM of tamoxifen ; and 10muM raloxifene .
[ Sen. 5, subscore: 1.00 ]: Results : ER-alpha mRNA expression increased with all 3 drug treatments ( p< 0 . 05 ) while there was no change in mRNA expression of ER-beta in human skeletal muscle cells . mRNA expression of SRC increased and SMRT decreased with estradiol , tamoxifen , and raloxifene in human skeletal muscle cells ( p< 0 . 05 ) .
[ Sen. 8, subscore: 1.00 ]: This demonstrates the importance of the estrogen receptor and alterations in its coregulators , to potentially prevent sarcopenia and promote muscle growth in postmenopausal women using these forms of hormone replacement therapy .
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Score: 10.00
Title: A comprehensive rice transcript map containing 6591 expressed sequence tag sites .
Author: Wu J Maehara T Shimokawa T Yamamoto S Harada C Takazaki Y Ono N Mukai Y Koike K Yazaki J Fujii F Shomura A Ando T Kono I Waki K Yamamoto K Yano M Matsumoto T Sasaki T
Journal: Plant Cell Citation: V : 14 ( 3 ) P : 525-35 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11910001 Accession (PMID): 11910001
Abstract: To determine the chromosomal positions of expressed rice genes , we have performed an expressed sequence tag ( EST ) mapping project by polymerase chain reaction-based yeast artificial chromosome ( YAC ) screening . Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis . Here , we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80 . 8% of the rice genome . Chromosomes 1 , 2 , and 3 have relatively high EST densities , approximately twice those of chromosomes 11 and 12 , and contain 41% of the total EST sites on the map . Most of the EST-dense regions are distributed on the distal regions of each chromosome arm . Genomic regions flanking the centromeres for most of the chromosomes have lower EST density . Recombination frequency in these regions is suppressed significantly . Our EST mapping also shows that 40% of the assigned ESTs occupy only approximately 21% of the entire genome . The rice transcript map has been a valuable resource for genetic study , gene isolation , and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals .
Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: Here , we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80 . 8% of the rice genome .
[ Sen. 4, subscore: 2.00 ]: Chromosomes 1 , 2 , and 3 have relatively high EST densities , approximately twice those of chromosomes 11 and 12 , and contain 41% of the total EST sites on the map .
[ Sen. 8, subscore: 2.00 ]: Our EST mapping also shows that 40% of the assigned ESTs occupy only approximately 21% of the entire genome .
[ Sen. 1, subscore: 1.00 ]: To determine the chromosomal positions of expressed rice genes , we have performed an expressed sequence tag ( EST ) mapping project by polymerase chain reaction-based yeast artificial chromosome ( YAC ) screening .
[ Sen. 2, subscore: 1.00 ]: Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis .
[ Sen. 5, subscore: 1.00 ]: Most of the EST-dense regions are distributed on the distal regions of each chromosome arm .
[ Sen. 6, subscore: 1.00 ]: Genomic regions flanking the centromeres for most of the chromosomes have lower EST density .
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Score: 10.00
Title: Annotation and BAC/PAC localization of nonredundant ESTs from drought-stressed seedlings of an indica rice .
Author: Babu PR Sekhar AC Ithal N Markandeya G Reddy AR .
Journal: J Genet . Citation: V : 81 ( 1 ) P : 25-44 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12357076 Accession (PMID): 12357076
Abstract: To decipher the genes associated with drought stress response and to identify novel genes in rice , we utilized 1540 high-quality expressed sequence tags ( ESTs ) for functional annotation and mapping to rice genomic sequences . These ESTs were generated earlier by 3-end single-pass sequencing of 2000 cDNA clones from normalized cDNA libraries constructed form drought-stressed seedlings of an indica rice . A rice UniGene set of 1025 transcripts was constructed from this collection through the BLASTN algorithm . Putative functions of 559 nonredundant ESTs were identified by BLAST similarity search against public databases . Putative functions were assigned at a stringency E value of 10 ( -6 ) in BLASTN and BLASTX algorithms . To understand the gene structure and function further , we have utilized the publicly available finished and unfinished rice BAC/PAC ( BAC , bacterial artificial chromosome ; PAC , P1 artificial chromosome ) sequences for similarity search using the BLASTN algorithm . Further , 603 nonredundant ESTs have been mapped to BAC/PAC clones . BAC clones were assigned by a homology of above 95% identity along 90% of EST sequence length in the aligned region . In all , 700 ESTs showed rice EST hits in GenBank . Of the 325 novel ESTs , 128 were localized to BAC clones . In addition , 127 ESTs with identified putative functions but with no homology in IRGSP ( International Rice Genome Sequencing Program ) BAC/PAC sequences were mapped to the Chinese WGS ( whole genome shotgun contigs ) draft sequence of the rice genome . Functional annotation uncovered about a hundred candidate ESTs associated with abiotic stress in rice and Arabidopsis that were previously reported based on microarray analysis and other studies . This study is a major effort in identifying genes associated with drought stress response and will serve as a resource to rice geneticists and molecular biologists .
Matching Sentences:
[ Sen. 9, subscore: 2.00 ]: In all , 700 ESTs showed rice EST hits in GenBank .
[ Sen. 1, subscore: 1.00 ]: To decipher the genes associated with drought stress response and to identify novel genes in rice , we utilized 1540 high-quality expressed sequence tags ( ESTs ) for functional annotation and mapping to rice genomic sequences .
[ Sen. 2, subscore: 1.00 ]: These ESTs were generated earlier by 3-end single-pass sequencing of 2000 cDNA clones from normalized cDNA libraries constructed form drought-stressed seedlings of an indica rice .
[ Sen. 4, subscore: 1.00 ]: Putative functions of 559 nonredundant ESTs were identified by BLAST similarity search against public databases .
[ Sen. 7, subscore: 1.00 ]: Further , 603 nonredundant ESTs have been mapped to BAC/PAC clones .
[ Sen. 8, subscore: 1.00 ]: BAC clones were assigned by a homology of above 95% identity along 90% of EST sequence length in the aligned region .
[ Sen. 10, subscore: 1.00 ]: Of the 325 novel ESTs , 128 were localized to BAC clones .
[ Sen. 11, subscore: 1.00 ]: In addition , 127 ESTs with identified putative functions but with no homology in IRGSP ( International Rice Genome Sequencing Program ) BAC/PAC sequences were mapped to the Chinese WGS ( whole genome shotgun contigs ) draft sequence of the rice genome .
[ Sen. 12, subscore: 1.00 ]: Functional annotation uncovered about a hundred candidate ESTs associated with abiotic stress in rice and Arabidopsis that were previously reported based on microarray analysis and other studies .
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Score: 10.00
Title: [ A new method for EST clustering ]
Author: Zhang LD Yuan DJ Zhang JW Wang SP Zhang QF .
Journal: Yi Chuan Xue Bao Citation: V : 30 ( 2 ) P : 147-53 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12776603 Accession (PMID): 12776603
Abstract: We developed an EST ( expressed sequence tag ) clustering method , ESTClustering , to generate high-quality unique expressed sequence based on large-scale EST sequencing . The method uses consensus sequences to sequence analyze with megablast and assemble each cluster with phrap in clustering process . The clustering strategy can efficiently identify gene family and alternate splicing forms of expressed sequences . It can also reduce the adverse effects caused by sequence errors . The ESTClustering method tends to provide more expressed gene forms comparing with the UniGene clustering method of the National Center for Biotechnology Information . Analysis of the 112 , 256 ESTs of Arabidopsis with ESTClustering produced 23 , 581 EST clusters . Among these Arabidopsis EST clusters , 13 , 597 have corresponding genome coding sequences and this number is close to the number of genes predicted with Arabidopsis ESTs . Using this clustering method , a total of 147 , 191 rice ESTs were clustered into 33 , 896 groups .
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[ Sen. 1, subscore: 3.00 ]: We developed an EST ( expressed sequence tag ) clustering method , ESTClustering , to generate high-quality unique expressed sequence based on large-scale EST sequencing .
[ Sen. 6, subscore: 3.00 ]: Analysis of the 112 , 256 ESTs of Arabidopsis with ESTClustering produced 23 , 581 EST clusters .
[ Sen. 7, subscore: 2.00 ]: Among these Arabidopsis EST clusters , 13 , 597 have corresponding genome coding sequences and this number is close to the number of genes predicted with Arabidopsis ESTs .
[ Sen. 5, subscore: 1.00 ]: The ESTClustering method tends to provide more expressed gene forms comparing with the UniGene clustering method of the National Center for Biotechnology Information .
[ Sen. 8, subscore: 1.00 ]: Using this clustering method , a total of 147 , 191 rice ESTs were clustered into 33 , 896 groups .
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Score: 10.00
Title: Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags .
Author: Randhawa HS Dilbirligi M Sidhu D Erayman M Sandhu D Bondareva S Chao S Lazo GR Anderson OD Miftahudin Gustafson JP Echalier B Qi LL Gill BS Akhunov ED Dvork J Linkiewicz AM Ratnasiri A Dubcovsky J Bermudez-Kandianis CE Greene RA Sorrells ME Conley EJ Anderson JA Peng JH Lapitan NL Hossain KG Kalavacharla V Kianian SF Pathan MS Nguyen HT Endo TR Close TJ McGuire PE Qualset CO Gill KS .
Journal: Genetics Citation: V : 168 ( 2 ) P : 677-86 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15514044 Accession (PMID): 15514044
Abstract: To localize wheat ( Triticum aestivum L ) ESTs on chromosomes , 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome , arm , and sub-arm aneuploid and deletion stocks . The 882 ESTs were physically mapped to 25 regions ( bins ) flanked by 23 deletion breakpoints . Of the 5154 restriction fragments detected by 882 ESTs , 2043 ( loci ) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups . The number of loci mapped was greatest on chromosome 6B and least on 6D . The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map . The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms . About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences . Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes . Even within the group 6 bins , rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes . These rice-block contigs were used to resolve the order of wheat ESTs within each bin .
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[ Sen. 1, subscore: 2.00 ]: To localize wheat ( Triticum aestivum L ) ESTs on chromosomes , 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome , arm , and sub-arm aneuploid and deletion stocks .
[ Sen. 2, subscore: 1.00 ]: The 882 ESTs were physically mapped to 25 regions ( bins ) flanked by 23 deletion breakpoints .
[ Sen. 3, subscore: 1.00 ]: Of the 5154 restriction fragments detected by 882 ESTs , 2043 ( loci ) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups .
[ Sen. 5, subscore: 1.00 ]: The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map .
[ Sen. 6, subscore: 1.00 ]: The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms .
[ Sen. 7, subscore: 1.00 ]: About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences .
[ Sen. 8, subscore: 1.00 ]: Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes .
[ Sen. 9, subscore: 1.00 ]: Even within the group 6 bins , rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes .
[ Sen. 10, subscore: 1.00 ]: These rice-block contigs were used to resolve the order of wheat ESTs within each bin .
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Score: 10.00
Title: Production of low-estrogen goldfish diet for in vivo endocrine disrupter test
Author: Kobayashi M Ishibashi H Moriwaki T Koshiishi T Ogawa S Matsumoto T Arizono K Watabe S
Journal: Citation: V : 13 ( 2 ) P : 125-36 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16788564 Accession (PMID): 16788564
Abstract: A low-estrogenic diet for goldfish Carassius auatus was produced for an in vivo estrogen activity test , because commercial fish feed has estrogenic activity and may affect the results of estrogen assays . The newly produced diet ( FD5 ) was formulated with defatted rice bran and casein , and did not contain any soybean meal or fish meal Phytoestrogen contents ( genistein , daidzein , equol , and coumestrol ) of FD5 were measured by liquid chromatography-mass spectroscopy/mass spectroscopy ( LC-MS/MS ) and compared with those of the commercial trout diet ( TD ) and carp diet ( CD ) . The genistein , daidzein , and coumestrol contents of TD and CD were much higher ( 5-2000 times ) than those of FD5 , but equol was detected only in FD5 . Estrogenic activity of the fish diets was estimated in vitro by the yeast estrogen-screen assay ( YES assay ) . The estrogenic activity was detected in TD and CD , but not in FD5 . The in vivo estrogenic activity of the diets was examined by determining the production of vitellogenin in male goldfish . When male goldfish were fed TD or CD , plasma vitellogenin levels increased , but fish that were fed FD5 maintained low vitellogenin levels . These results indicate that FD5 produced in the present study has a low estrogenic activity , and FD5 would be suitable for the in vivo estrogen activity test using goldfish .
Matching Sentences:
[ Sen. 1, subscore: 3.00 ]: A low-estrogenic diet for goldfish Carassius auatus was produced for an in vivo estrogen activity test , because commercial fish feed has estrogenic activity and may affect the results of estrogen assays .
[ Sen. 4, subscore: 3.00 ]: Estrogenic activity of the fish diets was estimated in vitro by the yeast estrogen-screen assay ( YES assay ) .
[ Sen. 8, subscore: 2.00 ]: These results indicate that FD5 produced in the present study has a low estrogenic activity , and FD5 would be suitable for the in vivo estrogen activity test using goldfish .
[ Sen. 5, subscore: 1.00 ]: The estrogenic activity was detected in TD and CD , but not in FD5 .
[ Sen. 6, subscore: 1.00 ]: The in vivo estrogenic activity of the diets was examined by determining the production of vitellogenin in male goldfish .
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Score: 10.00
Title: A robust estimator of mutation rates .
Author: Wu X Strome ED Meng Q Hastings PJ Plon SE Kimmel M
Journal: Mutat Res Citation: V : 661 P : 101-9 Year: 2009 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub19100753 Accession (PMID): 19100753
Abstract: Fluctuation analysis is an established and widely used technique of estimating mutation rates in cultured cells . This paper presents a modified median estimator of mutation rates , which is novel because it allows for unequal population sizes N ( t ) of the parallel cultures , and helps to detect and reduce the estimation variability . Simulation results show a good accuracy and robustness of the modified median estimator compared with the median estimator and the maximum likelihood estimator . The proposed estimator , based on the Luria-Delbruck model , is applied to 20 yeast datasets collected during 3 different days for a study of chromosome loss and recombination in wild-type Saccharomyces cerevisiae strains . The estimates obtained display among-experiment variability , which is inflated with respect to the model predictions on simulated data . Further investigation in S cerevisiae and Escherichia coli uncovers an empirical inverse relationship between the population sizes N ( t ) and the mutation rate estimates under certain experimental conditions . The impact of these effects on the practice of fluctuation analysis is discussed .
Matching Sentences:
[ Sen. 3, subscore: 3.00 ]: Simulation results show a good accuracy and robustness of the modified median estimator compared with the median estimator and the maximum likelihood estimator .
[ Sen. 1, subscore: 2.00 ]: Fluctuation analysis is an established and widely used technique of estimating mutation rates in cultured cells .
[ Sen. 2, subscore: 2.00 ]: This paper presents a modified median estimator of mutation rates , which is novel because it allows for unequal population sizes N ( t ) of the parallel cultures , and helps to detect and reduce the estimation variability .
[ Sen. 4, subscore: 1.00 ]: The proposed estimator , based on the Luria-Delbruck model , is applied to 20 yeast datasets collected during 3 different days for a study of chromosome loss and recombination in wild-type Saccharomyces cerevisiae strains .
[ Sen. 5, subscore: 1.00 ]: The estimates obtained display among-experiment variability , which is inflated with respect to the model predictions on simulated data .
[ Sen. 6, subscore: 1.00 ]: Further investigation in S cerevisiae and Escherichia coli uncovers an empirical inverse relationship between the population sizes N ( t ) and the mutation rate estimates under certain experimental conditions .
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Score: 10.00
Title: The first set of EST resource for gene discovery and marker development in pigeonpea ( Cajanus cajan L ) .
Author: Raju NL Gnanesh BN Lekha P Jayashree B Pande S Hiremath PJ Byregowda M Singh NK Varshney RK
Journal: BMC Plant Biol Citation: V : 10 P : 45 Year: 2010 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub20222972 Accession (PMID): 20222972
Abstract: BACKGROUND : Pigeonpea ( Cajanus cajan ( L ) Millsp ) is one of the major grain legume crops of the tropics and subtropics , but biotic stresses [ Fusarium wilt ( FW ) , sterility mosaic disease ( SMD ) , etc ] are serious challenges for sustainable crop production . Modern genomic tools such as molecular markers and candidate genes associated with resistance to these stresses offer the possibility of facilitating pigeonpea breeding for improving biotic stress resistance . Availability of limited genomic resources , however , is a serious bottleneck to undertake molecular breeding in pigeonpea to develop superior genotypes with enhanced resistance to above mentioned biotic stresses . With an objective of enhancing genomic resources in pigeonpea , this study reports generation and analysis of comprehensive resource of FW and SMD responsive expressed sequence tags ( ESTs ) . RESULTS : A total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ( ICPL 20102 and ICP 2376 ) and SMD ( ICP 7035 and TTB 7 ) and a total of 9 , 888 ( 9 , 468 high quality ) ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231 . Clustering and assembly analyses of these ESTs resulted into 4 , 557 unique sequences ( unigenes ) including 697 contigs and 3 , 860 singletons . BLASTN analysis of 4 , 557 unigenes showed a significant identity with ESTs of different legumes ( 23 . 2-60 . 3% ) , rice ( 28 . 3% ) , Arabidopsis ( 33 . 7% ) and poplar ( 35 . 4% ) . As expected , pigeonpea ESTs are more closely related to soybean ( 60 . 3% ) and cowpea ESTs ( 43 . 6% ) than other plant ESTs . Similarly , BLASTX similarity results showed that only 1 , 603 ( 35 . 1% ) out of 4 , 557 total unigenes correspond to known proteins in the UniProt database ( ESTs were compiled together with 908 ESTs available in public domain , at the time of analysis , and a set of 5 , 085 unigenes were defined that were used for identification of molecular markers in pigeonpea . For instance , 3 , 583 simple sequence repeat ( SSR ) motifs were identified in 1 , 365 unigenes and 383 primer pairs were designed . Assessment of a set of 84 primer pairs on 40 elite pigeonpea lines showed polymorphism with 15 ( 28 . 8% ) markers with an average of four alleles per marker and an average polymorphic information content ( PIC ) value of 0 . 40 . Similarly , in silico mining of 133 contigs with >or= 5 sequences detected 102 single nucleotide polymorphisms ( SNPs ) in 37 contigs . As an example , a set of 10 contigs were used for confirming in silico predicted SNPs in a set of four genotypes using wet lab experiments . Occurrence of SNPs were confirmed for all the 6 contigs for which scorable and sequenceable amplicons were generated . PCR amplicons were not obtained in case of 4 contigs . Recognition sites for restriction enzymes were identified for 102 SNPs in 37 contigs that indicates possibility of assaying SNPs in 37 genes using cleaved amplified polymorphic sequences ( CAPS ) assay . CONCLUSION : The pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance . Sequence analyses of this dataset have showed conservation of a considerable number of pigeonpea transcripts across legume and model plant species analysed as well as some putative pigeonpea specific genes . Validation of identified biotic stress responsive genes should provide candidate genes for allele mining as well as candidate markers for molecular breeding .
Matching Sentences:
[ Sen. 8, subscore: 3.00 ]: As expected , pigeonpea ESTs are more closely related to soybean ( 60 . 3% ) and cowpea ESTs ( 43 . 6% ) than other plant ESTs .
[ Sen. 12, subscore: 2.00 ]: Generated ESTs were compiled together with 908 ESTs available in public domain , at the time of analysis , and a set of 5 , 085 unigenes were defined that were used for identification of molecular markers in pigeonpea .
[ Sen. 4, subscore: 1.00 ]: With an objective of enhancing genomic resources in pigeonpea , this study reports generation and analysis of comprehensive resource of FW and SMD responsive expressed sequence tags ( ESTs ) .
[ Sen. 5, subscore: 1.00 ]: RESULTS : A total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ( ICPL 20102 and ICP 2376 ) and SMD ( ICP 7035 and TTB 7 ) and a total of 9 , 888 ( 9 , 468 high quality ) ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231 .
[ Sen. 6, subscore: 1.00 ]: Clustering and assembly analyses of these ESTs resulted into 4 , 557 unique sequences ( unigenes ) including 697 contigs and 3 , 860 singletons .
[ Sen. 7, subscore: 1.00 ]: BLASTN analysis of 4 , 557 unigenes showed a significant identity with ESTs of different legumes ( 23 . 2-60 . 3% ) , rice ( 28 . 3% ) , Arabidopsis ( 33 . 7% ) and poplar ( 35 . 4% ) .
[ Sen. 20, subscore: 1.00 ]: CONCLUSION : The pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance .
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Score: 9.00
Title: Quantitative determination of hydroxycinnamic acids in wheat , rice , rye , and barley straws , maize stems , oil palm frond fiber , and fast-growing poplar wood .
Author: Sun RC Sun XF Zhang SH .
Journal: J Agric . Food Chem . Citation: V : 49 ( 11 ) P : 5122-9 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11714291 Accession (PMID): 11714291
Abstract: A new method has been developed for the quantitative determination of hydroxycinnamic acids participating in ester or ether linkages to the cell wall polymers . The method is based on mild alkaline hydrolysis followed by acid hydrolysis or mild alkaline hydrolysis , which partially removed esterified phenolic acids , and high-temperature concentrated alkaline treatment , which cleaved both the ester and ether linkages . It was found that traditional mild alkaline hydrolysis and acid hydrolysis released only part of the ester and ether-linked phenolic acids , respectively . Approximately half ( 44 . 0-47 . 9% ) of the total ester-linked p-coumaric acid and 18 . 2-32 . 6% of the total esterified ferulic acid remained ester-linked to the mild alkali-soluble lignin polymers , and 55 . 0-72 . 0% of the total ether-linked p-coumaric acid and 37 . 5-53 . 8% of the total ether-linked ferulic acid remained ether-linked to the solubilized lignin molecules after the acid hydrolysis . To correct this , a second mild alkaline hydrolysis of the alkali-soluble lignin preparations and acid hydrolysis of the solubilized lignin fractions , obtained from the first acid hydrolysis of the cell wall materials , was investigated . On the basis of this new method , a majority of the cell wall p-coumaric acid ( 55 . 8-81 . 5% ) was found to be ester-linked to cell wall components , mainly to lignin , and about half of the cell wall ferulic acid is etherified through its phenolic oxygen to the cell wall lignin component , whereas the remainder is esterified to the cell wall hemicelluloses and/or lignin in different plant materials .
Matching Sentences:
[ Sen. 4, subscore: 3.00 ]: Approximately half ( 44 . 0-47 . 9% ) of the total ester-linked p-coumaric acid and 18 . 2-32 . 6% of the total esterified ferulic acid remained ester-linked to the mild alkali-soluble lignin polymers , and 55 . 0-72 . 0% of the total ether-linked p-coumaric acid and 37 . 5-53 . 8% of the total ether-linked ferulic acid remained ether-linked to the solubilized lignin molecules after the acid hydrolysis .
[ Sen. 2, subscore: 2.00 ]: The method is based on mild alkaline hydrolysis followed by acid hydrolysis or mild alkaline hydrolysis , which partially removed esterified phenolic acids , and high-temperature concentrated alkaline treatment , which cleaved both the ester and ether linkages .
[ Sen. 6, subscore: 2.00 ]: On the basis of this new method , a majority of the cell wall p-coumaric acid ( 55 . 8-81 . 5% ) was found to be ester-linked to cell wall components , mainly to lignin , and about half of the cell wall ferulic acid is etherified through its phenolic oxygen to the cell wall lignin component , whereas the remainder is esterified to the cell wall hemicelluloses and/or lignin in different plant materials .
[ Sen. 1, subscore: 1.00 ]: A new method has been developed for the quantitative determination of hydroxycinnamic acids participating in ester or ether linkages to the cell wall polymers .
[ Sen. 3, subscore: 1.00 ]: It was found that traditional mild alkaline hydrolysis and acid hydrolysis released only part of the ester and ether-linked phenolic acids , respectively .
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Score: 9.00
Title: Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus .
Author: Brendel V Xing L Zhu W
Journal: Bioinformatics Citation: V : 20 ( 7 ) P : 1157-69 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14764557 Accession (PMID): 14764557
Abstract: MOTIVATION : Accurate gene structure annotation is a challenging computational problem in genomics . The best results are achieved with spliced alignment of full-length cDNAs or multiple expressed sequence tags ( ESTs ) with sufficient overlap to cover the entire gene . For most species , cDNA and EST collections are far from comprehensive . We sought to overcome this bottleneck by exploring the possibility of using combined EST resources from fairly diverged species that still share a common gene space . Previous spliced alignment tools were found inadequate for this task because they rely on very high sequence similarity between the ESTs and the genomic DNA . RESULTS : We have developed a computer program , GeneSeqer , which is capable of aligning thousands of ESTs with a long genomic sequence in a reasonable amount of time . The algorithm is uniquely designed to tolerate a high percentage of mismatches and insertions or deletions in the EST relative to the genomic template . This feature allows use of non-cognate ESTs for gene structure prediction , including ESTs derived from duplicated genes and homologous genes from related species . The increased gene prediction sensitivity results in part from novel splice site prediction models that are also available as a stand-alone splice site prediction tool . We assessed GeneSeqer performance relative to a standard Arabidopsis thaliana gene set and demonstrate its utility for plant genome annotation . In particular , we propose that this method provides a timely tool for the annotation of the rice genome , using abundant ESTs from other cereals and plants . AVAILABILITY : The source code is available for download at http : //bioinformatics . iastate . edu/bioinformatics2go/gs/download . html . Web servers for Arabidopsis and other plant species are accessible at http : //www . plantgdb . org/cgi-bin/AtGeneSeqer . cgi and http : //www . plantgdb . org/cgi-bin/GeneSeqer . cgi , respectively . For non-plant species , use http : //bioinformatics . iastate . edu/cgi-bin/gs . cgi . The splice site prediction tool ( SplicePredictor ) is distributed with the GeneSeqer code . A SplicePredictor web server is available at http : //bioinformatics . iastate . edu/cgi-bin/sp . cgi
Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: This feature allows use of non-cognate ESTs for gene structure prediction , including ESTs derived from duplicated genes and homologous genes from related species .
[ Sen. 2, subscore: 1.00 ]: The best results are achieved with spliced alignment of full-length cDNAs or multiple expressed sequence tags ( ESTs ) with sufficient overlap to cover the entire gene .
[ Sen. 3, subscore: 1.00 ]: For most species , cDNA and EST collections are far from comprehensive .
[ Sen. 4, subscore: 1.00 ]: We sought to overcome this bottleneck by exploring the possibility of using combined EST resources from fairly diverged species that still share a common gene space .
[ Sen. 5, subscore: 1.00 ]: Previous spliced alignment tools were found inadequate for this task because they rely on very high sequence similarity between the ESTs and the genomic DNA .
[ Sen. 6, subscore: 1.00 ]: RESULTS : We have developed a computer program , GeneSeqer , which is capable of aligning thousands of ESTs with a long genomic sequence in a reasonable amount of time .
[ Sen. 7, subscore: 1.00 ]: The algorithm is uniquely designed to tolerate a high percentage of mismatches and insertions or deletions in the EST relative to the genomic template .
[ Sen. 11, subscore: 1.00 ]: In particular , we propose that this method provides a timely tool for the annotation of the rice genome , using abundant ESTs from other cereals and plants .
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Score: 9.00
Title: EST analysis in Ginkgo biloba : an assessment of conserved developmental regulators and gymnosperm specific genes .
Author: Brenner ED Katari MS Stevenson DW Rudd SA Douglas AW Moss WN Twigg RW Runko SJ Stellari GM McCombie WR Coruzzi GM .
Journal: BMC Genomics Citation: V : 6 ( ) P : 143 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16225698 Accession (PMID): 16225698
Abstract: BACKGROUND : Ginkgo biloba L is the only surviving member of one of the oldest living seed plant groups with medicinal , spiritual and horticultural importance worldwide . As an evolutionary relic , it displays many characters found in the early , extinct seed plants and extant cycads . To establish a molecular base to understand the evolution of seeds and pollen , we created a cDNA library and EST dataset from the reproductive structures of male ( microsporangiate ) , female ( megasporangiate ) , and vegetative organs ( leaves ) of Ginkgo biloba . RESULTS : RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6 , 434 ESTs were generated . These 6 , 434 ESTs from Ginkgo biloba were clustered into 3 , 830 unigenes . A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis , and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants--many with multiple matches to genes in non-angiosperm plants . Conversely , another group of unigenes in Gingko had highly significant homology to transcription factors in angiosperms involved in development , including MADS box genes as well as post-transcriptional regulators . Several of the conserved developmental genes found in Ginkgo had top BLAST homology to cycad genes . We also note here the presence of ESTs in G biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads . CONCLUSION : Our analysis of an EST dataset from G biloba revealed genes potentially unique to gymnosperms . Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms . Other Ginkgo ESTs are similar to developmental regulators in higher plants . This work sets the stage for future studies on Ginkgo to better understand seed and pollen evolution , and to resolve the ambiguous phylogenetic relationship of G biloba among the gymnosperms .
Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: To establish a molecular base to understand the evolution of seeds and pollen , we created a cDNA library and EST dataset from the reproductive structures of male ( microsporangiate ) , female ( megasporangiate ) , and vegetative organs ( leaves ) of Ginkgo biloba .
[ Sen. 4, subscore: 1.00 ]: RESULTS : RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6 , 434 ESTs were generated .
[ Sen. 5, subscore: 1.00 ]: These 6 , 434 ESTs from Ginkgo biloba were clustered into 3 , 830 unigenes .
[ Sen. 6, subscore: 1.00 ]: A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis , and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants--many with multiple matches to genes in non-angiosperm plants .
[ Sen. 9, subscore: 1.00 ]: We also note here the presence of ESTs in G biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads .
[ Sen. 10, subscore: 1.00 ]: CONCLUSION : Our analysis of an EST dataset from G biloba revealed genes potentially unique to gymnosperms .
[ Sen. 11, subscore: 1.00 ]: Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms .
[ Sen. 12, subscore: 1.00 ]: Other Ginkgo ESTs are similar to developmental regulators in higher plants .
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Score: 9.00
Title: Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja .
Author: Ji W Li Y Li J Dai CH Wang X Bai X Cai H Yang L Zhu YM .
Journal: BMC Plant Biol . Citation: V : 6 ( ) P : 4 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16504061 Accession (PMID): 16504061
Abstract: BACKGROUND : Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture . Wild soybean ( Glycine soja ) can survive in highly saline conditions , therefore provides an ideal candidate plant system for salt tolerance gene mining . RESULTS : As a first step towards the characterization of genes that contribute to combating salinity stress , we constructed a full-length cDNA library of Glycine soja ( 50109 ) leaf treated with 150 mM NaCl , using the SMART technology . Random expressed sequence tag ( EST ) sequencing of 2 , 219 clones produced 2 , 003 cleaned ESTs for gene expression analysis . The average read length of cleaned ESTs was 454 bp , with an average GC content of 40% . These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets . The resulting unigenes were categorized according to the Gene Ontology ( GO ) hierarchy . The potential roles of gene products associated with stress related ESTs were discussed . We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm . Most expressed sequences from wild soybean exhibited similarity with soybean . All our EST data are available on the Internet ( GenBank_Accn : DT082443-DT084445 ) . CONCLUSION : The Glycine soja ESTs will be used to mine salt tolerance gene , whose full-length cDNAs will be obtained easily from the full-length cDNA library . Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybeans expression profile using the soybeans gene chip . This will provide opportunities to understand the genetic mechanisms underlying stress response of plants .
Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: Random expressed sequence tag ( EST ) sequencing of 2 , 219 clones produced 2 , 003 cleaned ESTs for gene expression analysis .
[ Sen. 5, subscore: 1.00 ]: The average read length of cleaned ESTs was 454 bp , with an average GC content of 40% .
[ Sen. 6, subscore: 1.00 ]: These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets .
[ Sen. 8, subscore: 1.00 ]: The potential roles of gene products associated with stress related ESTs were discussed .
[ Sen. 9, subscore: 1.00 ]: We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm .
[ Sen. 11, subscore: 1.00 ]: All our EST data are available on the Internet ( GenBank_Accn : DT082443-DT084445 ) .
[ Sen. 12, subscore: 1.00 ]: CONCLUSION : The Glycine soja ESTs will be used to mine salt tolerance gene , whose full-length cDNAs will be obtained easily from the full-length cDNA library .
[ Sen. 13, subscore: 1.00 ]: Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybeans expression profile using the soybeans gene chip .
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Score: 9.00
Title: Frequency , type , and distribution of EST-SSRs from three genotypes of Lolium perenne , and their conservation across orthologous sequences of Festuca arundinacea , Brachypodium distachyon , and Oryza sativa .
Author: Asp T Frei UK Didion T Nielsen KK Lubberstedt T
Journal: BMC Plant Biol Citation: V : 7 P : 36 Year: 2007 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17626623 Accession (PMID): 17626623
Abstract: BACKGROUND : Simple sequence repeat ( SSR ) markers are highly informative and widely used for genetic and breeding studies in several plant species . They are used for cultivar identification , variety protection , as anchor markers in genetic mapping , and in marker-assisted breeding . Currently , a limited number of SSR markers are publicly available for perennial ryegrass ( Lolium perenne ) . We report on the exploitation of a comprehensive EST collection in L perenne for SSR identification . The objectives of this study were 1 ) to analyse the frequency , type , and distribution of SSR motifs in ESTs derived from three genotypes of L perenne , 2 ) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences , 3 ) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of L perenne , Festuca arundinacea , Brachypodium distachyon , and O sativa , 4 ) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding . RESULTS : From 25 , 744 ESTs , representing 8 . 53 megabases of nucleotide information from three genotypes of L perenne , 1 , 458 ESTs ( 5 . 7% ) contained one or more SSRs . Of these SSRs , 955 ( 3 . 7% ) were non-redundant . Tri-nucleotide repeats were the most abundant type of repeats followed by di and tetra-nucleotide repeats . The EST-SSRs from the three genotypes were analysed for allelic and/or genotypic SSR motif polymorphisms . Most of the SSR motifs ( 97 . 7% ) showed no polymorphisms , whereas 22 EST-SSRs showed allelic and/or genotypic polymorphisms . All polymorphisms identified were changes in the number of repeat units . Comparative analysis of the L perenne EST-SSRs with sequences of Festuca arundinacea , Brachypodium distachyon , and Oryza sativa identified 19 clusters of orthologous sequences between these four species . Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species F arundinacea , but often differs in length of the SSR motif . In contrast , SSR motifs are often lost in the more distant related species B distachyon and O sativa . CONCLUSION : The results indicate that the L perenne EST-SSR markers are a valuable resource for genetic mapping , as well as evaluation of co-location between QTLs and functionally associated markers .
Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: The objectives of this study were 1 ) to analyse the frequency , type , and distribution of SSR motifs in ESTs derived from three genotypes of L perenne , 2 ) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences , 3 ) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of L perenne , Festuca arundinacea , Brachypodium distachyon , and O sativa , 4 ) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding .
[ Sen. 6, subscore: 2.00 ]: RESULTS : From 25 , 744 ESTs , representing 8 . 53 megabases of nucleotide information from three genotypes of L perenne , 1 , 458 ESTs ( 5 . 7% ) contained one or more SSRs .
[ Sen. 4, subscore: 1.00 ]: We report on the exploitation of a comprehensive EST collection in L perenne for SSR identification .
[ Sen. 9, subscore: 1.00 ]: The EST-SSRs from the three genotypes were analysed for allelic and/or genotypic SSR motif polymorphisms .
[ Sen. 10, subscore: 1.00 ]: Most of the SSR motifs ( 97 . 7% ) showed no polymorphisms , whereas 22 EST-SSRs showed allelic and/or genotypic polymorphisms .
[ Sen. 12, subscore: 1.00 ]: Comparative analysis of the L perenne EST-SSRs with sequences of Festuca arundinacea , Brachypodium distachyon , and Oryza sativa identified 19 clusters of orthologous sequences between these four species .
[ Sen. 15, subscore: 1.00 ]: CONCLUSION : The results indicate that the L perenne EST-SSR markers are a valuable resource for genetic mapping , as well as evaluation of co-location between QTLs and functionally associated markers .
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Score: 8.00
Title: New experimental and computational approaches to the analysis of gene expression .
Author: Rafalski JA Hanafey M Miao GH Ching A Lee JM Dolan M Tingey S
Journal: Acta Biochim . Pol . Citation: V : 45 ( 4 ) P : 929-34 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10397340 Accession (PMID): 10397340
Abstract: Public and private EST ( Expressed Sequence Tag ) programs provide access to a large number of ESTs from a number of plant species , including Arabidopsis , corn , soybean , rice , wheat . In addition to the homology of each EST to genes in GenBank , information about homology to all other ESTs in the data base can be obtained . To estimate expression levels of genes represented in the DuPont EST data base we count the number of times each gene has been seen in different cDNA libraries , from different it issues , developmental stages or induction conditions . This quantitation of message levels is quite accurate for highly expressed messages and , unlike conventional Northern blots , allows comparison of expression levels between different genes . Lists of most highly expresses genes in different libraries can be compiled . Also , if EST data is available for cDNA libraries derived from different developmental stages , gene expression profiles across development can be assembled . We present an example of such a profile for soybean seed development . Gene expression data obtained from Electronic Northern analysis can be confirmed and extended beyond the realm of highly expressed genes by using high density DNA arrays . The ESTs identified as interesting can be arrayed on nylon or glass and probed with total labeled cDNA first strand from the it issue of interest Two-color fluorescent labeling allows accurate mRNA ratio measurements . We are currently using the DNA array technology to study chemical induction of gene expression and the biosynthesis of oil , carbohydrate and protein in developing seeds .
Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Public and private EST ( Expressed Sequence Tag ) programs provide access to a large number of ESTs from a number of plant species , including Arabidopsis , corn , soybean , rice , wheat .
[ Sen. 2, subscore: 2.00 ]: In addition to the homology of each EST to genes in GenBank , information about homology to all other ESTs in the data base can be obtained .
[ Sen. 3, subscore: 2.00 ]: To estimate expression levels of genes represented in the DuPont EST data base we count the number of times each gene has been seen in different cDNA libraries , from different it issues , developmental stages or induction conditions .
[ Sen. 6, subscore: 1.00 ]: Also , if EST data is available for cDNA libraries derived from different developmental stages , gene expression profiles across development can be assembled .
[ Sen. 9, subscore: 1.00 ]: The ESTs identified as interesting can be arrayed on nylon or glass and probed with total labeled cDNA first strand from the it issue of interest Two-color fluorescent labeling allows accurate mRNA ratio measurements .
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Score: 8.00
Title: Effects of dietary rice bran , lasalocid , and sex of calf on postpartum reproduction in Brahman cows .
Author: Webb SM Lewis AW Neuendorff DA Randel RD .
Journal: J Anim . Sci . Citation: V : 79 ( 12 ) P : 2968-74 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11811449 Accession (PMID): 11811449
Abstract: To determine the effects of dietary lasalocid and increased dietary fat on reproduction , multiparous Brahman cows ( n = 68 ) , body condition score ( BCS ) of 6 . 2 +/- 0 . 7 and BW of 500 . 9 +/- 42 . 6 kg , were randomly assigned within sex of calf to receive one of four rations . All treatment groups grazed Coastal bermudagrass overseeded with rye-ryegrass and were given ad libitum access to hay and water . The control ( n = 17 ) group received 4 . 17 kg x d ( -1 ) x cow ( -1 ) of 4 : 1 corn : soybean meal The rice bran ( n = 17 ) group received 4 . 35 kg x d ( -1 ) x cow ( -1 ) of 3 : 1 : 1 corn : soybean meal : rice bran ( 5 . 2% dietary fat ) . The lasalocid ( n = 17 ) group received the Control diet with the addition of 200 mg of lasalocid x d ( -1 ) x cow ( -1 ) . The rice bran-lasalocid ( n = 17 ) group received the rice bran diet with the addition of 200 mg of lasalocid x d ( -1 ) x cow ( -1 ) . Diets were fed once daily from d 1 after parturition through the detection of first estrus . Weight and BCS of cows and BW of calves were recorded at 14-d intervals from d 1 after parturition through detection of first estrus and at weaning . Cows were bled on d 1 , 3 , 5 , 7 , and 14 and at weekly intervals until estrus and on d 7 and d 10 after estrus . Ovarian follicular populations were monitored by transrectal ultrasonography weekly from d 14 after parturition through detection of first estrus . Plasma 13-14-dihydro-15-ketoprostaglandin-F2alpha ( PGFM ) and progesterone ( P4 ) concentrations were quantified using RIA . Concentrations of PGFM from d 1 to 7 and P4 concentrations on d 7 and 10 after estrus were not influenced ( P > 0 . 10 ) by diet or sex of calf . Changes in BW and BCS were not affected ( P > 0 . 10 ) by diet . The number of medium-sized follicles tended to be greater ( P < 0 . 06 ) in Controls than in cows on lasalocid or rice bran + lasalocid treatments on d 21 . Cumulative return to estrus with a functional corpus luteum by d 60 postpartum was greater ( P < 0 . 02 ) in the rice bran ( 70 . 6% ) and lasalocid groups ( 76 . 5% ) than in Controls ( 52 . 9% ) or the group given rice bran + lasalocid ( 25 . 0% ) . Normal first estrous cycles were less likely ( P < 0 . 07 ) to be exhibited in cows given rice bran + lasalocid than in other groups . Intervals from calving to corpus luteum formation , functional corpus luteum , and first P4 > or = 1 ng/mL were longer ( P < 0 . 02 ) in cows given rice bran + lasalocid than in other cows . Combining increased dietary fat ( 5 . 2% ) with lasalocid lengthened the time to reproductively important events .
Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: Cows were bled on d 1 , 3 , 5 , 7 , and 14 and at weekly intervals until estrus and on d 7 and d 10 after estrus .
[ Sen. 6, subscore: 1.00 ]: Diets were fed once daily from d 1 after parturition through the detection of first estrus .
[ Sen. 7, subscore: 1.00 ]: Weight and BCS of cows and BW of calves were recorded at 14-d intervals from d 1 after parturition through detection of first estrus and at weaning .
[ Sen. 9, subscore: 1.00 ]: Ovarian follicular populations were monitored by transrectal ultrasonography weekly from d 14 after parturition through detection of first estrus .
[ Sen. 11, subscore: 1.00 ]: Concentrations of PGFM from d 1 to 7 and P4 concentrations on d 7 and 10 after estrus were not influenced ( P > 0 . 10 ) by diet or sex of calf .
[ Sen. 14, subscore: 1.00 ]: Cumulative return to estrus with a functional corpus luteum by d 60 postpartum was greater ( P < 0 . 02 ) in the rice bran ( 70 . 6% ) and lasalocid groups ( 76 . 5% ) than in Controls ( 52 . 9% ) or the group given rice bran + lasalocid ( 25 . 0% ) .
[ Sen. 15, subscore: 1.00 ]: Normal first estrous cycles were less likely ( P < 0 . 07 ) to be exhibited in cows given rice bran + lasalocid than in other groups .
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Score: 8.00
Title: Effect of esterified 4-desmethylsterols and -stanols or 4 , 4-dimethylsterols on cholesterol and bile acid metabolism in hamsters .
Author: Trautwein EA Schulz C Rieckhoff D Kunath-Rau A Erbersdobler HF de Groot WA Meijer GW .
Journal: Br . J Nutr . Citation: V : 87 ( 3 ) P : 227-37 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12064331 Accession (PMID): 12064331
Abstract: 4-Desmethylsterols and -stanols reduce plasma total cholesterol ( TC ) and LDL cholesterol by inhibition of intestinal cholesterol absorption , while the cholesterol-lowering potential of 4 , 4-dimethylsterols is less well defined . The present study aimed to compare the effects of 4-desmethylsterols , -stanols , and 4 , 4-dimethylsterols on plasma and hepatic cholesterol , sterol excretion and bile acid metabolism . Male golden Syrian hamsters were fed diets containing 13 g/100 g fat , 008 g/100 g cholesterol and 0 ( control ) , 0 . 24 or 0 . 48% ( w/w ) esterified 4-desmethylsterols ( sterols ) and esterified hydrogenated 4-desmethylsterols ( stanols ) from common vegetable oils or esterified 4 , 4-dimethylsterols from rice bran oil for 5 weeks . Sterol and stanol esters at the dose of 0 . 24% were equally effective and significantly ( P<0 . 05 ) lowered TC by 15% , while 0 . 24% 4 , 4-dimethylsterols reduced TC by 10% . Liver total and esterified cholesterol concentrations were significantly ( P<0 . 05 ) lowered by 40 , 22 , 43 and 31% in hamsters fed 0 . 48% sterols , 0 . 24% stanols , 0 . 48% stanols or 0 . 48% dimethylsterols , respectively . Daily faecal bile acid excretion and hepatic cholesterol 7alpha-hydroxylase activity were not altered , indicating that sterols , stanols and dimethylsterols had no effect on the intestinal re-absorption of bile acids or on hepatic bile acid synthesis . Daily excretion of cholesterol was significantly higher in hamsters fed esterified sterols and stanols , but was only slightly increased in those fed dimethylsterols . The results indicate that esterified sterols and stanols were equally effective in lowering plasma TC and LDL cholesterol , while dimethylsterol esters caused a weaker cholesterol-lowering effect . Sterols and stanols achieve their cholesterol-lowering effect by stimulating faecal cholesterol excretion through inhibiting intestinal cholesterol absorption , but do not affect bile acid excretion . Other mechanisms need to be considered to explain the effect on plasma and hepatic cholesterol of dimethylsterols .
Matching Sentences:
[ Sen. 3, subscore: 3.00 ]: Male golden Syrian hamsters were fed diets containing 13 g/100 g fat , 008 g/100 g cholesterol and 0 ( control ) , 0 . 24 or 0 . 48% ( w/w ) esterified 4-desmethylsterols ( sterols ) and esterified hydrogenated 4-desmethylsterols ( stanols ) from common vegetable oils or esterified 4 , 4-dimethylsterols from rice bran oil for 5 weeks .
[ Sen. 8, subscore: 2.00 ]: The results indicate that esterified sterols and stanols were equally effective in lowering plasma TC and LDL cholesterol , while dimethylsterol esters caused a weaker cholesterol-lowering effect .
[ Sen. 4, subscore: 1.00 ]: Sterol and stanol esters at the dose of 0 . 24% were equally effective and significantly ( P<0 . 05 ) lowered TC by 15% , while 0 . 24% 4 , 4-dimethylsterols reduced TC by 10% .
[ Sen. 5, subscore: 1.00 ]: Liver total and esterified cholesterol concentrations were significantly ( P<0 . 05 ) lowered by 40 , 22 , 43 and 31% in hamsters fed 0 . 48% sterols , 0 . 24% stanols , 0 . 48% stanols or 0 . 48% dimethylsterols , respectively .
[ Sen. 7, subscore: 1.00 ]: Daily excretion of cholesterol was significantly higher in hamsters fed esterified sterols and stanols , but was only slightly increased in those fed dimethylsterols .
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Score: 8.00
Title: Analysis of expressed sequence tag loci on wheat chromosome group 4 .
Author: Miftahudin Ross K Ma XF Mahmoud AA Layton J Milla MA Chikmawati T Ramalingam J Feril O Pathan MS Momirovic GS Kim S Chema K Fang P Haule L Struxness H Birkes J Yaghoubian C Skinner R McAllister J Nguyen V Qi LL Echalier B Gill BS Linkiewicz AM Dubcovsky J Akhunov ED Dvork J Dilbirligi M Gill KS Peng JH Lapitan NL Bermudez-Kandianis CE Sorrells ME Hossain KG Kalavacharla V Kianian SF Lazo GR Chao S Anderson OD Gonzalez-Hernandez J Conley EJ Anderson JA Choi DW Fenton RD Close TJ McGuire PE Qualset CO Nguyen HT Gustafson JP .
Journal: Genetics Citation: V : 168 ( 2 ) P : 651-63 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15514042 Accession (PMID): 15514042
Abstract: A total of 1918 loci , detected by the hybridization of 938 expressed sequence tag unigenes ( ESTs ) from 26 Triticeae cDNA libraries , were mapped to wheat ( Triticum aestivum L ) homoeologous group 4 chromosomes using a set of deletion , ditelosomic , and nulli-tetrasomic lines . The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes ; 41 , 28 , and 31% mapped to chromosomes 4A , 4B , and 4D , respectively . This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups , as reported elsewhere , that found the highest proportion of loci mapped to the B genome . Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes , while 35% mapped to the short arms . The distal regions of chromosome arms showed higher numbers of loci than the proximal regions , with the exception of 4DL . This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions , previously identified . An additional inversion in the centromeric region of 4A was revealed . A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4 . Forty-nine percent of these ESTs were found to be homoeologous to sequences on rice chromosome 3 , 12% had matches with sequences on other rice chromosomes , and 39% had no matches with rice sequences at all . Limited homology ( only 26 of the 119 consensus ESTs ) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome . Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases .
Matching Sentences:
[ Sen. 10, subscore: 2.00 ]: Limited homology ( only 26 of the 119 consensus ESTs ) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome .
[ Sen. 1, subscore: 1.00 ]: A total of 1918 loci , detected by the hybridization of 938 expressed sequence tag unigenes ( ESTs ) from 26 Triticeae cDNA libraries , were mapped to wheat ( Triticum aestivum L ) homoeologous group 4 chromosomes using a set of deletion , ditelosomic , and nulli-tetrasomic lines .
[ Sen. 2, subscore: 1.00 ]: The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes ; 41 , 28 , and 31% mapped to chromosomes 4A , 4B , and 4D , respectively .
[ Sen. 3, subscore: 1.00 ]: This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups , as reported elsewhere , that found the highest proportion of loci mapped to the B genome .
[ Sen. 8, subscore: 1.00 ]: A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4 .
[ Sen. 9, subscore: 1.00 ]: Forty-nine percent of these ESTs were found to be homoeologous to sequences on rice chromosome 3 , 12% had matches with sequences on other rice chromosomes , and 39% had no matches with rice sequences at all .
[ Sen. 11, subscore: 1.00 ]: Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases .
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Score: 8.00
Title: Gene discovery and gene expression in the rice blast fungus , Magnaporthe grisea : analysis of expressed sequence tags .
Author: Ebbole DJ Jin Y Thon M Pan H Bhattarai E Thomas T Dean R
Journal: Mol . Plant Microbe Interact . Citation: V : 17 ( 12 ) P : 1337-47 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15597739 Accession (PMID): 15597739
Abstract: Over 28 , 000 expressed sequence tags ( ESTs ) were produced from cDNA libraries representing a variety of growth conditions and cell types . Several Magnaporthe grisea strains were used to produce the libraries , including a nonpathogenic strain bearing a mutation in the PMK1 mitogen-activated protein kinase . Approximately 23 , 000 of the ESTs could be clustered into 3 , 050 contigs , leaving 5 , 127 singleton sequences . The estimate of 8 , 177 unique sequences indicates that over half of the genes of the fungus are represented in the ESTs . Analysis of EST frequency reveals growth and cell type-specific patterns of gene expression . This analysis establishes criteria for identification of fungal genes involved in pathogenesis . A large fraction of the genes represented by ESTs have no known function or described homologs . Manual annotation of the most abundant cDNAs with no known homologs allowed us to identify a family of metallothionein proteins present in M grisea , Neurospora crassa , and Fusarium graminearum . In addition , multiply represented ESTs permitted the identification of alternatively spliced mRNA species . Alternative splicing was rare , and in most cases , the alternate mRNA forms were unspliced , although alternative 5 splice sites were also observed .
Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: The estimate of 8 , 177 unique sequences indicates that over half of the genes of the fungus are represented in the ESTs .
[ Sen. 1, subscore: 1.00 ]: Over 28 , 000 expressed sequence tags ( ESTs ) were produced from cDNA libraries representing a variety of growth conditions and cell types .
[ Sen. 3, subscore: 1.00 ]: Approximately 23 , 000 of the ESTs could be clustered into 3 , 050 contigs , leaving 5 , 127 singleton sequences .
[ Sen. 5, subscore: 1.00 ]: Analysis of EST frequency reveals growth and cell type-specific patterns of gene expression .
[ Sen. 6, subscore: 1.00 ]: This analysis establishes criteria for identification of fungal genes involved in pathogenesis .
[ Sen. 7, subscore: 1.00 ]: A large fraction of the genes represented by ESTs have no known function or described homologs .
[ Sen. 9, subscore: 1.00 ]: In addition , multiply represented ESTs permitted the identification of alternatively spliced mRNA species .
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Score: 8.00
Title: Gene identification and expression analysis of 86 , 136 Expressed Sequence Tags ( EST ) from the rice genome .
Author: Zhou Y Tang J Walker MG Zhang X Wang J Hu S Xu H Deng Y Dong J Ye L Lin L Li J Wang X Xu H Pan Y Lin W Tian W Liu J Wei L Liu S Yang H Yu J Wang J
Journal: Genomics Proteomics Bioinformatics Citation: V : 1 ( 1 ) P : 26-42 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15626331 Accession (PMID): 15626331
Abstract: Expressed Sequence Tag ( EST ) analysis has pioneered genome-wide gene discovery and expression profiling . In order to establish a gene expression index in the rice cultivar indica , we sequenced and analyzed 86 , 136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars . We assembled these ESTs into 13 , 232 contigs and leave 8 , 976 singletons . Overall , 7 , 497 sequences were found similar to existing sequences in GenBank and 14 , 711 are novel . These sequences are classified by molecular function , biological process and pathways according to the Gene Ontology . We compared our sequenced ESTs with the publicly available 95 , 000 ESTs from japonica , and found little sequence variation , despite the large difference between genome sequences . We then assembled the combined 173 , 000 rice ESTs for further analysis . Using the pooled ESTs , we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG . We further profiled gene expression patterns in different it issues , developmental stages , and in a conditional sterile mutant , after checking the libraries are comparable by means of sequence coverage . We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development .
Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: In order to establish a gene expression index in the rice cultivar indica , we sequenced and analyzed 86 , 136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars .
[ Sen. 6, subscore: 2.00 ]: We compared our sequenced ESTs with the publicly available 95 , 000 ESTs from japonica , and found little sequence variation , despite the large difference between genome sequences .
[ Sen. 1, subscore: 1.00 ]: Expressed Sequence Tag ( EST ) analysis has pioneered genome-wide gene discovery and expression profiling .
[ Sen. 3, subscore: 1.00 ]: We assembled these ESTs into 13 , 232 contigs and leave 8 , 976 singletons .
[ Sen. 7, subscore: 1.00 ]: We then assembled the combined 173 , 000 rice ESTs for further analysis .
[ Sen. 8, subscore: 1.00 ]: Using the pooled ESTs , we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG .
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Score: 8.00
Title: Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction .
Author: Jantasuriyarat C Gowda M Haller K Hatfield J Lu G Stahlberg E Zhou B Li H Kim H Yu Y Dean RA Wing RA Soderlund C Wang GL .
Journal: Plant Physiol . Citation: V : 138 ( 1 ) P : 105-15 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15888683 Accession (PMID): 15888683
Abstract: To better understand the molecular basis of the defense response against the rice blast fungus ( Magnaporthe grisea ) , a large-scale expressed sequence tag ( EST ) sequencing approach was used to identify genes involved in the early infection stages in rice ( Oryza sativa ) . Six cDNA libraries were constructed using infected leaf it issues harvested from 6 conditions : resistant , partially resistant , and susceptible reactions at both 6 and 24 h after inoculation . Two additional libraries were constructed using uninoculated leaves and leaves from the lesion mimic mutant spl11 . A total of 68 , 920 ESTs were generated from 8 libraries . Clustering and assembly analyses resulted in 13 , 570 unique sequences from 10 , 934 contigs and 2 , 636 singletons . Gene function classification showed that 42% of the ESTs were predicted to have putative gene function . Comparison of the pathogen-challenged libraries with the uninoculated control library revealed an increase in the percentage of genes in the functional categories of defense and signal transduction mechanisms and cell cycle control , cell division , and chromosome partitioning . In addition , hierarchical clustering analysis grouped the eight libraries based on their disease reactions . A total of 7 , 748 new and unique ESTs were identified from our collection compared with the KOME full-length cDNA collection . Interestingly , we found that rice ESTs are more closely related to sorghum ( Sorghum bicolor ) ESTs than to barley ( Hordeum vulgare ) , wheat ( Triticum aestivum ) , and maize ( Zea mays ) ESTs . The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies .
Matching Sentences:
[ Sen. 10, subscore: 3.00 ]: Interestingly , we found that rice ESTs are more closely related to sorghum ( Sorghum bicolor ) ESTs than to barley ( Hordeum vulgare ) , wheat ( Triticum aestivum ) , and maize ( Zea mays ) ESTs .
[ Sen. 1, subscore: 1.00 ]: To better understand the molecular basis of the defense response against the rice blast fungus ( Magnaporthe grisea ) , a large-scale expressed sequence tag ( EST ) sequencing approach was used to identify genes involved in the early infection stages in rice ( Oryza sativa ) .
[ Sen. 4, subscore: 1.00 ]: A total of 68 , 920 ESTs were generated from 8 libraries .
[ Sen. 6, subscore: 1.00 ]: Gene function classification showed that 42% of the ESTs were predicted to have putative gene function .
[ Sen. 9, subscore: 1.00 ]: A total of 7 , 748 new and unique ESTs were identified from our collection compared with the KOME full-length cDNA collection .
[ Sen. 11, subscore: 1.00 ]: The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies .
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Score: 8.00
Title: High-resolution mapping of the barley leaf rust resistance gene Rph5 using barley expressed sequence tags ( ESTs ) and synteny with rice .
Author: Mammadov JA Steffenson BJ Maroof MA .
Journal: Theor . Appl . Genet . Citation: V : 111 ( 8 ) P : 1651-60 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16195886 Accession (PMID): 16195886
Abstract: The rapidly growing expressed sequence tag ( EST ) resources of species representing the Poacea family and availability of comprehensive sequence information for the rice ( Oryza sativa ) genome create an excellent opportunity for comparative genome analysis . Extensive synteny between rice chromosome 1 and barley ( Hordeum vulgare L ) chromosome 3 has proven extremely useful for saturation mapping of chromosomal regions containing target genes of large-genome barley with conserved orthologous genes from the syntenic regions of the rice genome . Rph5 is a gene conferring resistance to the barley leaf rust pathogen Puccinia hordei . It was mapped to chromosome 3HS , which is syntenic with rice chromosome 1S . The objective of this study was to increase marker density within the sub-centimorgan region around Rph5 , using sequence-tagged site ( STS ) markers that were developed based on barley ESTs syntenic to the phage ( P1 ) -derived artificial chromosome ( PAC ) clones comprising the distal region of rice chromosome 1S . Five rice PAC clones were used as queries in a blastn search to screen 375 , 187 barley ESTs . Ninety-four non-redundant EST sequences were identified from the EST database and used as templates to design 174 pairs of primer combinations . As a result , 9 barley EST-based STS markers were incorporated into the Bowman x Magnif 102 high-resolution map of the Rph5 region . More importantly , six markers , including five EST-derived STS sequences , were found to co-segregate with Rph5 . The results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley ESTs for marker saturation of targeted barley genomic regions .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: Ninety-four non-redundant EST sequences were identified from the EST database and used as templates to design 174 pairs of primer combinations .
[ Sen. 1, subscore: 1.00 ]: The rapidly growing expressed sequence tag ( EST ) resources of species representing the Poacea family and availability of comprehensive sequence information for the rice ( Oryza sativa ) genome create an excellent opportunity for comparative genome analysis .
[ Sen. 5, subscore: 1.00 ]: The objective of this study was to increase marker density within the sub-centimorgan region around Rph5 , using sequence-tagged site ( STS ) markers that were developed based on barley ESTs syntenic to the phage ( P1 ) -derived artificial chromosome ( PAC ) clones comprising the distal region of rice chromosome 1S .
[ Sen. 6, subscore: 1.00 ]: Five rice PAC clones were used as queries in a blastn search to screen 375 , 187 barley ESTs .
[ Sen. 8, subscore: 1.00 ]: As a result , 9 barley EST-based STS markers were incorporated into the Bowman x Magnif 102 high-resolution map of the Rph5 region .
[ Sen. 9, subscore: 1.00 ]: More importantly , six markers , including five EST-derived STS sequences , were found to co-segregate with Rph5 .
[ Sen. 10, subscore: 1.00 ]: The results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley ESTs for marker saturation of targeted barley genomic regions .
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Score: 8.00
Title: A Kunitz trypsin inhibitor of Entada scandens seeds : another member with single disulfide bridge .
Author: Lingaraju MH Gowda LR
Journal: Biochim Biophys Acta Citation: V : 1784 P : 850-5 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18359299 Accession (PMID): 18359299
Abstract: Sword bean ( Entada scandens ) is a tree climber that belongs to Mimosoideae , a subfamily of Leguminosae . A potent Kunitz type trypsin inhibitor ( ESTI ) was purified to homogeneity from Entada scandens seeds by sequential ammonium sulfate precipitation , affinity chromatography on trypsin-Sepharose and DEAE-Sephacel ion-exchange chromatography . ESTI is a single polypeptide chain of 19 , 766 Da . Both native PAGE as well as isoelectric focusing showed a single inhibitor species with a pI of 7 . 43 . MALDI-TOF analysis also confirmed the monomeric nature . The amino-terminal sequence of ESTI reveals significant homology to the Kunitz-type protease inhibitors of legume plants . ESTI is unique in that it contains a single disulfide bridge , and unlike other inhibitors from Mimosoideae species is a single chain polypeptide . ESTI inhibited bovine trypsin with a stoichiometry of 1 : 1 and the apparent K ( i ) was 4 . 9 x 10 ( -9 ) M In vitro assay showed that ESTI inhibited the midgut proteinase of the fifth instar larvae of Rice moth ( Corcyra cephalonica ) with an IC ( 50 ) of 26 . 4+/-0 . 01 nM . ESTI exhibits a mixed type competitive inhibition at lower concentration and pure competitive at higher inhibitor concentrations . Phylogenetic analyses depicted a clear divergence of single disulfide containing inhibitors from other tree legume Kunitz inhibitors . The homology of ESTI to Kunitz inhibitors together with the absence of Bowman-Birk type inhibitors in sword bean further supports the theory that there exists an evolutionary relationship between the families of inhibitors found in Leguminosae .
Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: ESTI inhibited bovine trypsin with a stoichiometry of 1 : 1 and the apparent K ( i ) was 4 . 9 x 10 ( -9 ) M In vitro assay showed that ESTI inhibited the midgut proteinase of the fifth instar larvae of Rice moth ( Corcyra cephalonica ) with an IC ( 50 ) of 26 . 4+/-0 . 01 nM .
[ Sen. 2, subscore: 1.00 ]: A potent Kunitz type trypsin inhibitor ( ESTI ) was purified to homogeneity from Entada scandens seeds by sequential ammonium sulfate precipitation , affinity chromatography on trypsin-Sepharose and DEAE-Sephacel ion-exchange chromatography .
[ Sen. 3, subscore: 1.00 ]: ESTI is a single polypeptide chain of 19 , 766 Da .
[ Sen. 6, subscore: 1.00 ]: The amino-terminal sequence of ESTI reveals significant homology to the Kunitz-type protease inhibitors of legume plants .
[ Sen. 7, subscore: 1.00 ]: ESTI is unique in that it contains a single disulfide bridge , and unlike other inhibitors from Mimosoideae species is a single chain polypeptide .
[ Sen. 9, subscore: 1.00 ]: ESTI exhibits a mixed type competitive inhibition at lower concentration and pure competitive at higher inhibitor concentrations .
[ Sen. 11, subscore: 1.00 ]: The homology of ESTI to Kunitz inhibitors together with the absence of Bowman-Birk type inhibitors in sword bean further supports the theory that there exists an evolutionary relationship between the families of inhibitors found in Leguminosae .
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Score: 8.00
Title: Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags .
Author: Senthilvel S Jayashree B Mahalakshmi V Sathish Kumar P Nakka S Nepolean T Hash CT
Journal: BMC Plant Biol Citation: V : 8 P : 119 Year: 2008 Type: Publisher
Literature: oryza Field: abstract Doc ID: pub19038016 Accession (PMID): 19038016
Abstract: ABSTRACT : BACKGROUND : Pearl millet [ Pennisetum glaucum ( L ) R Br . ] is a staple food and fodder crop of marginal agricultural lands of sub-Saharan Africa and the Indian subcontinent . It is also a summer forage crop in the southern USA , Australia and Latin America , and is the preferred mulch in Brazilian no-till soybean production systems . Use of molecular marker technology for pearl millet genetic improvement has been limited . Progress is hampered by insufficient numbers of PCR-compatible co-dominant markers that can be used readily in applied breeding programmes . Therefore , we sought to develop additional SSR markers for the pearl millet research community . RESULTS : A set of new pearl millet SSR markers were developed using available sequence information from 3520 expressed sequence tags ( ESTs ) . After clustering , unigene sequences ( 2175 singlets and 317 contigs ) were searched for the presence of SSRs . We detected 164 sequences containing SSRs ( at least 14 bases in length ) , with a density of one per 1 . 75 kb of EST sequence . Di-nucleotide repeats were the most abundant followed by tri-nucleotide repeats . Ninety primer pairs were designed and tested for their ability to detect polymorphism across a panel of 11 pairs of pearl millet mapping population parental lines . Clear amplification products were obtained for 58 primer pairs . Of these , 15 were monomorphic across the panel . A subset of 21 polymorphic EST-SSRs and 6 recently developed genomic SSR markers were mapped using existing mapping populations . Linkage map positions of these EST-SSR were compared by homology search with mapped rice genomic sequences on the basis of pearl millet-rice synteny . Most new EST-SSR markers mapped to distal regions of linkage groups , often to previous gaps in these linkage maps . These new EST-SSRs are now used by ICRISAT in pearl millet diversity assessment and marker-aided breeding programs . CONCLUSIONS : This study has demonstrated the potential of EST-derived SSR primer pairs in pearl millet . As reported for other crops , EST-derived SSRs provide a cost-saving marker development option in pearl millet . Resources developed in this study have added a sizeable number of useful SSRs to the existing repertoire of circa 100 genomic SSRs that were previously available to pearl millet researchers .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: RESULTS : A set of new pearl millet SSR markers were developed using available sequence information from 3520 expressed sequence tags ( ESTs ) .
[ Sen. 8, subscore: 1.00 ]: We detected 164 sequences containing SSRs ( at least 14 bases in length ) , with a density of one per 1 . 75 kb of EST sequence .
[ Sen. 13, subscore: 1.00 ]: A subset of 21 polymorphic EST-SSRs and 6 recently developed genomic SSR markers were mapped using existing mapping populations .
[ Sen. 14, subscore: 1.00 ]: Linkage map positions of these EST-SSR were compared by homology search with mapped rice genomic sequences on the basis of pearl millet-rice synteny .
[ Sen. 15, subscore: 1.00 ]: Most new EST-SSR markers mapped to distal regions of linkage groups , often to previous gaps in these linkage maps .
[ Sen. 16, subscore: 1.00 ]: These new EST-SSRs are now used by ICRISAT in pearl millet diversity assessment and marker-aided breeding programs .
[ Sen. 17, subscore: 1.00 ]: CONCLUSIONS : This study has demonstrated the potential of EST-derived SSR primer pairs in pearl millet .
[ Sen. 18, subscore: 1.00 ]: As reported for other crops , EST-derived SSRs provide a cost-saving marker development option in pearl millet .
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Score: 8.00
Title: Parent-reported prevalence of autism spectrum disorders in US-born children : an assessment of changes within birth cohorts from the 2003 to the 2007 National Survey of Childrens Health .
Author: Schieve LA Rice C Yeargin-Allsopp M Boyle CA Kogan MD Drews C Devine O
Journal: Matern Child Health J Citation: V : 16 Suppl 1 P : S151-7 Year: 2012 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub22476793 Accession (PMID): 22476793
Abstract: The prevalence of autism spectrum disorders ( ASD ) from the 2007 National Survey of Childrens Health ( NSCH ) was twice the 2003 NSCH estimate for autism . From each NSCH , we selected children born in the US from 1990 to 2000 . We estimated autism prevalence within each 1-year birth cohort to hold genetic and non-genetic prenatal factors constant . Prevalence differences across surveys thus reflect survey measurement changes and/or external identification effects . In 2003 , parents were asked whether their child was ever diagnosed with autism . In 2007 , parents were asked whether their child was ever diagnosed with an ASD and whether s/he currently had an ASD . For the 1997-2000 birth cohorts ( children aged 3-6 years in 2003 and 7-10 years in 2007 ) , relative increases between 2003 autism estimates and 2007 ASD estimates were 200-600 % . For the 1990-1996 birth cohorts ( children aged 7-13 years in 2003 ) increases were lower ; nonetheless , differences between 2003 estimates and 2007 "ever ASD" estimates were >100 % for 6 cohorts and differences between 2003 estimates and 2007 "current ASD" estimates were >80 % for 3 cohorts . The magnitude of most birth cohort-specific differences suggests continuing diagnosis of children in the community played a sizable role in the 2003-2007 ASD prevalence increase . While some increase was expected for 1997-2000 cohorts , because some children have later diagnoses coinciding with school entry , increases were also observed for children ages >/= 7 years in 2003 . Given past ASD subtype studies , the 2003 "autism" question might have missed a modest amount (
Matching Sentences:
[ Sen. 8, subscore: 4.00 ]: For the 1990-1996 birth cohorts ( children aged 7-13 years in 2003 ) increases were lower ; nonetheless , differences between 2003 estimates and 2007 "ever ASD" estimates were >100 % for 6 cohorts and differences between 2003 estimates and 2007 "current ASD" estimates were >80 % for 3 cohorts .
[ Sen. 7, subscore: 2.00 ]: For the 1997-2000 birth cohorts ( children aged 3-6 years in 2003 and 7-10 years in 2007 ) , relative increases between 2003 autism estimates and 2007 ASD estimates were 200-600 % .
[ Sen. 1, subscore: 1.00 ]: The prevalence of autism spectrum disorders ( ASD ) from the 2007 National Survey of Childrens Health ( NSCH ) was twice the 2003 NSCH estimate for autism .
[ Sen. 3, subscore: 1.00 ]: We estimated autism prevalence within each 1-year birth cohort to hold genetic and non-genetic prenatal factors constant .
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Score: 8.00
Title: Fat supplementation influences postpartum reproductive performance in Brahman cows .
Author: De Fries CA Neuendorff DA Randel RD .
Journal: J Anim . Sci . Citation: V : 76 ( 3 ) P : 864-70 Year: 1998 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9535349 Accession (PMID): 9535349
Abstract: Multiparous Brahman cows ( n = 40 ) in excellent body condition ( 6 . 5+/- . 1 ) were randomly assigned to receive either 5 . 2 ( rice bran ) or 3 . 7% ( control ) dietary fat after calving . The experimental diets were formulated to be isocaloric and isonitrogenous . The experimental diets were fed twice daily from d 1 after calving through the first normal estrous cycle . Cows were weighed , scored for body condition , and bled at weekly intervals from d 1 through 50 after calving . Weekly bleedings continued until the first detectable estrus . Blood samples were collected daily throughout the first normal estrous cycle . All cows were exposed to a fertile bull at the estrus following the first normal estrous cycle and for a 60-d breeding season . Ovarian follicular populations were recorded weekly by transrectal ultrasonography from d 15 to 50 after calving . Calf weights were recorded at 14-d intervals from d 1 to 43 after birth and at weaning ( 205 d ) . Cows receiving rice bran gained more body condition ( P < . 05 ) than cows receiving the control supplement . The numbers of small ( < 4 . 0 mm , P < . 05 ) , medium ( 4 . 0 to 7 . 9 mm , P < . 05 ) and total follicles ( P < . 05 ) were greater in the rice bran than in the control group from 15 to 29 d after calving , and large follicles ( > or = 8 . 0 mm ) increased in number ( P < . 05 ) and the largest follicle increased in size ( P < . 001 ) over time regardless of the level of dietary fat . Fat supplementation increased the numbers of medium ( P < . 01 ) , large ( P < . 05 ) , and total ( P < . 01 ) follicles and size of the largest follicle ( P < . 05 ) during the 3 wk before the first normal estrous cycle . The intervals from parturition to reproductively important end points were similar ( P > . 10 ) between dietary treatments as well as the percentage of cows showing normal or abnormal estrous cyclic activity . Treatment did not affect ( P > . 10 ) daily serum progesterone ( P4 ) concentrations . However , there was a tendency ( P = . 09 ) for more rice bran-supplemented cows to be pregnant ( 94 . 1 vs 71 . 4% ) after being exposed to a fertile bull for 60 d . Calf weight gain tended to be higher ( P = . 08 ) in calves nursing rice bran-supplemented dams . In conclusion , using rice bran , with high concentrations of oleic and linoleic acids , as a fat supplement for postpartum cows enhanced ovarian follicular growth before normal estrous cycles resumed and increased body condition scores and pregnancy rates without altering postpartum interval or serum P4 concentrations .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: All cows were exposed to a fertile bull at the estrus following the first normal estrous cycle and for a 60-d breeding season .
[ Sen. 3, subscore: 1.00 ]: The experimental diets were fed twice daily from d 1 after calving through the first normal estrous cycle .
[ Sen. 5, subscore: 1.00 ]: Weekly bleedings continued until the first detectable estrus .
[ Sen. 6, subscore: 1.00 ]: Blood samples were collected daily throughout the first normal estrous cycle .
[ Sen. 12, subscore: 1.00 ]: Fat supplementation increased the numbers of medium ( P < . 01 ) , large ( P < . 05 ) , and total ( P < . 01 ) follicles and size of the largest follicle ( P < . 05 ) during the 3 wk before the first normal estrous cycle .
[ Sen. 13, subscore: 1.00 ]: The intervals from parturition to reproductively important end points were similar ( P > . 10 ) between dietary treatments as well as the percentage of cows showing normal or abnormal estrous cyclic activity .
[ Sen. 17, subscore: 1.00 ]: In conclusion , using rice bran , with high concentrations of oleic and linoleic acids , as a fat supplement for postpartum cows enhanced ovarian follicular growth before normal estrous cycles resumed and increased body condition scores and pregnancy rates without altering postpartum interval or serum P4 concentrations .
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Score: 7.00
Title: Cytochrome c oxidase inhibition in the rice weevil Sitophilus oryzae ( L ) by formate , the toxic metabolite of volatile alkyl formates .
Author: Haritos VS Dojchinov G
Journal: Comp . Biochem . Physiol . C Toxicol . Pharmacol . Citation: V : 136 ( 2 ) P : 135-43 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14559295 Accession (PMID): 14559295
Abstract: Volatile alkyl formates are potential replacements for the ozone-depleting fumigant , methyl bromide , as postharvest insecticides and here we have investigated their mode of insecticidal action . Firstly , a range of alkyl esters , ethanol and formic acid were tested in mortality bioassays with adults of the rice weevil , Sitophilus oryzae ( L ) and the grain borer , Rhyzopertha dominica ( F ) to determine whether the intact ester or one of its components was the toxic moiety . Volatile alkyl formates and formic acid caused similar levels of mortality ( LC ( 50 ) 131-165 micromol l ( -1 ) ) to S oryzae and were more potent than non-formate containing alkyl esters and ethanol ( LC ( 50 ) >275 micromol l ( -1 ) ) . The order of potency was the same in R dominica . Ethyl formate was rapidly metabolised in vitro to formic acid when incubated with insect homogenates , presumably through the action of esterases . S oryzae and R dominica fumigated with a lethal dose of ethyl formate had eight and 17-fold higher concentrations of formic acid , respectively , in their bodies than untreated controls . When tested against isolated mitochondria from S oryzae , alkyl esters , alcohols , acetate and propionate salts were not inhibitory towards cytochrome c oxidase ( EC 1 . 9 . 3 . 1 ) , but sodium cyanide and sodium formate were inhibitory with IC ( 50 ) values of 0 . 0015 mM and 59 mM , respectively . Volatile formate esters were more toxic than other alkyl esters , and this was found to be due , at least in part , to their hydrolysis to formic acid and its inhibition of cytochrome c oxidase .
Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: Firstly , a range of alkyl esters , ethanol and formic acid were tested in mortality bioassays with adults of the rice weevil , Sitophilus oryzae ( L ) and the grain borer , Rhyzopertha dominica ( F ) to determine whether the intact ester or one of its components was the toxic moiety .
[ Sen. 8, subscore: 2.00 ]: Volatile formate esters were more toxic than other alkyl esters , and this was found to be due , at least in part , to their hydrolysis to formic acid and its inhibition of cytochrome c oxidase .
[ Sen. 3, subscore: 1.00 ]: Volatile alkyl formates and formic acid caused similar levels of mortality ( LC ( 50 ) 131-165 micromol l ( -1 ) ) to S oryzae and were more potent than non-formate containing alkyl esters and ethanol ( LC ( 50 ) >275 micromol l ( -1 ) ) .
[ Sen. 5, subscore: 1.00 ]: Ethyl formate was rapidly metabolised in vitro to formic acid when incubated with insect homogenates , presumably through the action of esterases .
[ Sen. 7, subscore: 1.00 ]: When tested against isolated mitochondria from S oryzae , alkyl esters , alcohols , acetate and propionate salts were not inhibitory towards cytochrome c oxidase ( EC 1 . 9 . 3 . 1 ) , but sodium cyanide and sodium formate were inhibitory with IC ( 50 ) values of 0 . 0015 mM and 59 mM , respectively .
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Score: 7.00
Title: A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice .
Author: Conley EJ Nduati V Gonzalez-Hernandez JL Mesfin A Trudeau-Spanjers M Chao S Lazo GR Hummel DD Anderson OD Qi LL Gill BS Echalier B Linkiewicz AM Dubcovsky J Akhunov ED Dvork J Peng JH Lapitan NL Pathan MS Nguyen HT Ma XF Miftahudin Gustafson JP Greene RA Sorrells ME Hossain KG Kalavacharla V Kianian SF Sidhu D Dilbirligi M Gill KS Choi DW Fenton RD Close TJ McGuire PE Qualset CO Anderson JA .
Journal: Genetics Citation: V : 168 ( 2 ) P : 625-37 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15514040 Accession (PMID): 15514040
Abstract: The complex hexaploid wheat genome offers many challenges for genomics research . Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms . The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs , construct a consensus map of group 2 ESTs , investigate synteny , examine patterns of duplication , and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map . A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks . A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome . Regions of high gene density in distal bins and low gene density in proximal bins were found . Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered . The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B . Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7 .
Matching Sentences:
[ Sen. 3, subscore: 4.00 ]: The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs , construct a consensus map of group 2 ESTs , investigate synteny , examine patterns of duplication , and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map .
[ Sen. 4, subscore: 1.00 ]: A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks .
[ Sen. 5, subscore: 1.00 ]: A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome .
[ Sen. 8, subscore: 1.00 ]: The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B .
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Score: 7.00
Title: Nitrogen metabolism and excretion in the swamp eel , Monopterus albus , during 6 or 40 days of estivation in mud .
Author: Chew SF Gan J Ip YK .
Journal: Physiol . Biochem . Zool . Citation: V : 78 ( 4 ) P : 620-9 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15957116 Accession (PMID): 15957116
Abstract: Monopterus albus inhabits muddy ponds , swamps , canals , and rice fields , where it can burrow into the moist earth , and it survives for long periods during the dry summer season . However , it had been reported previously that mortality increased when M albus was exposed to air for 8 d or more . Thus , the objective of this study was to elucidate the strategies adopted by M albus to defend against ammonia toxicity during 6 or 40 d of estivation in mud and to evaluate whether these strategies were different from those adopted by fish to survive 6 d of aerial exposure . Ammonia and glutamine accumulations occurred in the muscle and liver of fish exposed to air ( normoxia ) for 6 d , indicating that ammonia was detoxified to glutamine under such conditions . In contrast , ammonia accumulation occurred only in the muscle , with no increases in glutamine or glutamate contents in all it issues , of fish estivated in mud for 6 d . Similar results were obtained from fish estivated in mud for 40 d . While estivating in mud prevented excessive water loss through evaporation , M albus was exposed to hypoxia , as indicated by significant decreases in blood P ( O ( 2 ) ) , muscle energy charge , and ATP content in fish estivated in mud for 6 d . Glutamine synthesis is energy intensive , and that could be the reason why M albus did not depend on glutamine synthesis to defend against ammonia toxicity when a decrease in ATP supply occurred . Instead , suppression of endogenous ammonia production was adopted as the major strategy to ameliorate ammonia toxicity when M albus estivated in mud . Our results suggest that a decrease in O ( 2 ) level in the mud could be a more effective signal than an increase in internal ammonia level during aerial exposure to induce a suppression of ammonia production in M albus . This might explain why M albus is able to estivate in mud for long periods ( 40 d ) but can survive in air for only <10 d .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: While estivating in mud prevented excessive water loss through evaporation , M albus was exposed to hypoxia , as indicated by significant decreases in blood P ( O ( 2 ) ) , muscle energy charge , and ATP content in fish estivated in mud for 6 d .
[ Sen. 3, subscore: 1.00 ]: Thus , the objective of this study was to elucidate the strategies adopted by M albus to defend against ammonia toxicity during 6 or 40 d of estivation in mud and to evaluate whether these strategies were different from those adopted by fish to survive 6 d of aerial exposure .
[ Sen. 5, subscore: 1.00 ]: In contrast , ammonia accumulation occurred only in the muscle , with no increases in glutamine or glutamate contents in all it issues , of fish estivated in mud for 6 d .
[ Sen. 6, subscore: 1.00 ]: Similar results were obtained from fish estivated in mud for 40 d .
[ Sen. 9, subscore: 1.00 ]: Instead , suppression of endogenous ammonia production was adopted as the major strategy to ameliorate ammonia toxicity when M albus estivated in mud .
[ Sen. 11, subscore: 1.00 ]: This might explain why M albus is able to estivate in mud for long periods ( 40 d ) but can survive in air for only <10 d .
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Score: 7.00
Title: Estrogenic effect of yam ingestion in healthy postmenopausal women .
Author: Wu WH Liu LY Chung CJ Jou HJ Wang TA .
Journal: Citation: V : 24 ( 4 ) P : 235-43 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16093400 Accession (PMID): 16093400
Abstract: OBJECTIVE : Yam ( Dioscorea ) has been used to treat menopausal symptom folklorically . This study was to investigate the effects of yam ingestion on lipids , antioxidant status , and sex hormones in postmenopausal women . METHODS : Twenty-four apparently healthy postmenopausal women were recruited to replace their staple food ( rice for the most part ) with 390 g of yam ( Dioscorea alata ) in 2 of 3 meals per day for 30 days and 22 completed the study . Fasting blood and first morning urine samples were collected before and after yam intervention for the analyses of blood lipids , sex hormones , urinary estrogen metabolites and oxidant stress biomarker . The design was a one arm , pre-post study . A similar study of postmenopausal women ( n = 19 ) fed 240 g of sweet potato for 41 days was included as a control study . Serum levels of estrone , estradiol and SHBG were analyzed for this control group . RESULTS : After yam ingestion , there were significant increases in serum concentrations of estrone ( 26% ) , sex hormone binding globulin ( SHBG ) ( 9 . 5% ) , and near significant increase in estradiol ( 27% ) . No significant changes were observed in serum concentrations of dehydroepiandrosterone sulfate , androstenedione , testosterone , follicular stimulating hormone , and luteinizing hormone . Free androgen index estimated from the ratio of serum concentrations of total testosterone to SHBG decreased . Urinary concentrations of the genotoxic metabolite of estrogen , 16alpha-hydroxyestrone decreased significantly by 37% . Plasma cholesterol concentration decreased significantly by 5 . 9% . Lag time of low-density lipoprotein oxidation prolonged significantly by 5 . 8% and urinary isoprostane levels decreased significantly by 42% . For the control subjects fed with sweet potato , all three hormone parameters measured were not changed after intervention . CONCLUSION : Although the exact mechanism is not clear , replacing two thirds of staple food with yam for 30 days improves the status of sex hormones , lipids , and antioxidants . These effects might reduce the risk of breast cancer and cardiovascular diseases in postmenopausal women .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: Serum levels of estrone , estradiol and SHBG were analyzed for this control group .
[ Sen. 8, subscore: 2.00 ]: RESULTS : After yam ingestion , there were significant increases in serum concentrations of estrone ( 26% ) , sex hormone binding globulin ( SHBG ) ( 9 . 5% ) , and near significant increase in estradiol ( 27% ) .
[ Sen. 4, subscore: 1.00 ]: Fasting blood and first morning urine samples were collected before and after yam intervention for the analyses of blood lipids , sex hormones , urinary estrogen metabolites and oxidant stress biomarker .
[ Sen. 10, subscore: 1.00 ]: Free androgen index estimated from the ratio of serum concentrations of total testosterone to SHBG decreased .
[ Sen. 11, subscore: 1.00 ]: Urinary concentrations of the genotoxic metabolite of estrogen , 16alpha-hydroxyestrone decreased significantly by 37% .
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Score: 7.00
Title: Gene evolution at the ends of wheat chromosomes .
Author: See DR Brooks S Nelson JC Brown-Guedira G Friebe B Gill BS .
Journal: Proc . Natl . Acad . Sci . USA Citation: V : 103 ( 11 ) P : 4162-7 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16537502 Accession (PMID): 16537502
Abstract: Wheat ESTs mapped to deletion bins in the distal 42% of the long arm of chromosome 4B ( 4BL ) were ordered in silico based on blastn homology against rice pseudochromosome 3 . The ESTs spanned 29 cM on the short arm of rice chromosome 3 , which is known to be syntenic to long arms of group-4 chromosomes of wheat . Fine-scale deletion-bin and genetic mapping revealed that 83% of ESTs were syntenic between wheat and rice , a far higher level of synteny than previously reported , and 6% were nonsyntenic ( not located on rice chromosome 3 ) . One inversion spanning a 5-cM region in rice and three deletion bins in wheat was identified . The remaining 11% of wheat ESTs showed no sequence homology in rice and mapped to the terminal 5% of the wheat chromosome 4BL . In this region , 27% of ESTs were duplicated , and it accounted for 70% of the recombination in the 4BL arm . Globally in wheat , no sequence homology ESTs mapped to the terminal bins , and ESTs rarely mapped to interstitial chromosomal regions known to be recombination hot spots . The wheat-rice comparative genomics analysis indicated that gene evolution occurs preferentially at the ends of chromosomes , driven by duplication and divergence associated with high rates of recombination .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: Globally in wheat , no sequence homology ESTs mapped to the terminal bins , and ESTs rarely mapped to interstitial chromosomal regions known to be recombination hot spots .
[ Sen. 1, subscore: 1.00 ]: Wheat ESTs mapped to deletion bins in the distal 42% of the long arm of chromosome 4B ( 4BL ) were ordered in silico based on blastn homology against rice pseudochromosome 3 .
[ Sen. 2, subscore: 1.00 ]: The ESTs spanned 29 cM on the short arm of rice chromosome 3 , which is known to be syntenic to long arms of group-4 chromosomes of wheat .
[ Sen. 3, subscore: 1.00 ]: Fine-scale deletion-bin and genetic mapping revealed that 83% of ESTs were syntenic between wheat and rice , a far higher level of synteny than previously reported , and 6% were nonsyntenic ( not located on rice chromosome 3 ) .
[ Sen. 5, subscore: 1.00 ]: The remaining 11% of wheat ESTs showed no sequence homology in rice and mapped to the terminal 5% of the wheat chromosome 4BL .
[ Sen. 6, subscore: 1.00 ]: In this region , 27% of ESTs were duplicated , and it accounted for 70% of the recombination in the 4BL arm .
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Score: 7.00
Title: [ A strategy based on comparative genomics to align ESTs of maize ]
Author: Zhang ZX Zhang SP Zheng YL .
Journal: Yi Chuan Citation: V : 28 ( 3 ) P : 339-44 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16551603 Accession (PMID): 16551603
Abstract: In this study , a new strategy to locate ESTs on maize linkage groups was described . In the strategy , the rice ( Oryza sativa L ) genomic sequence database of was employed to locate maize EST on rice linkage groups , and then to locate on maize linkage group by comparative genetics mapping between rice and maize genome . The aligned ESTs information should available for further study on genomics and gene cloning . As an example , 139 ESTs of maize were assayed , and 96 maize ESTs ( 69% ) were homologous with rice genomic sequence , 55% ( 77/139 ) ESTs were located on maize linkage groups based on the strategy , indicating that the locating approach of ESTs is feasible and available .
Matching Sentences:
[ Sen. 4, subscore: 4.00 ]: As an example , 139 ESTs of maize were assayed , and 96 maize ESTs ( 69% ) were homologous with rice genomic sequence , 55% ( 77/139 ) ESTs were located on maize linkage groups based on the strategy , indicating that the locating approach of ESTs is feasible and available .
[ Sen. 1, subscore: 1.00 ]: In this study , a new strategy to locate ESTs on maize linkage groups was described .
[ Sen. 2, subscore: 1.00 ]: In the strategy , the rice ( Oryza sativa L ) genomic sequence database of was employed to locate maize EST on rice linkage groups , and then to locate on maize linkage group by comparative genetics mapping between rice and maize genome .
[ Sen. 3, subscore: 1.00 ]: The aligned ESTs information should available for further study on genomics and gene cloning .
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Score: 7.00
Title: A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico : survey and evaluation .
Author: Jayashree B Punna R Prasad P Bantte K Hash CT Chandra S Hoisington DA Varshney RK
Journal: In Silico Biol Citation: V : 6 P : 607-20 Year: 2006 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17518768 Accession (PMID): 17518768
Abstract: Simple sequence repeats ( SSRs ) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications . In this paper , the SSR distributions within ESTs from the legumes soybean ( Glycine max , representing 135 . 86 Mb ) , medicago ( Medicago truncatula , 121 . 1 Mb ) and lotus ( Lotus japonicus , 45 . 4 Mb ) have been studied relative to the distributions in cereals such as sorghum ( Sorghum bicolor , 98 . 9 Mb ) , rice ( Oryza sativa , 143 . 9 Mb ) and maize ( Zea mays , 183 . 7 Mb ) . The relative abundance , density , composition and putative annotations of di- , tri- , tetra and penta-nucleotide repeats have been compared and SSR containing ESTs ( SSR-ESTs ) have been clustered to give a non-redundant set of EST-SSRs , available in a database . Further , a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible , stay-green drought tolerant mapping population parent E 36-1 and its Striga-resistant , non-stay-green counterpart N13 . Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines . Over half of these markers have been genotyped on 94 RILs from the ( N13 x E 36-1 ) -based mapping population , with 42 markers mapping onto the ten sorghum linkage groups . This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding . The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database ( http : //intranet . icrisat . org/gt1/ssr/ssrdatabase . html ) .
Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: The relative abundance , density , composition and putative annotations of di- , tri- , tetra and penta-nucleotide repeats have been compared and SSR containing ESTs ( SSR-ESTs ) have been clustered to give a non-redundant set of EST-SSRs , available in a database .
[ Sen. 2, subscore: 1.00 ]: In this paper , the SSR distributions within ESTs from the legumes soybean ( Glycine max , representing 135 . 86 Mb ) , medicago ( Medicago truncatula , 121 . 1 Mb ) and lotus ( Lotus japonicus , 45 . 4 Mb ) have been studied relative to the distributions in cereals such as sorghum ( Sorghum bicolor , 98 . 9 Mb ) , rice ( Oryza sativa , 143 . 9 Mb ) and maize ( Zea mays , 183 . 7 Mb ) .
[ Sen. 4, subscore: 1.00 ]: Further , a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible , stay-green drought tolerant mapping population parent E 36-1 and its Striga-resistant , non-stay-green counterpart N13 .
[ Sen. 5, subscore: 1.00 ]: Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines .
[ Sen. 7, subscore: 1.00 ]: This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding .
[ Sen. 8, subscore: 1.00 ]: The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database ( http : //intranet . icrisat . org/gt1/ssr/ssrdatabase . html ) .
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Score: 7.00
Title: Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes .
Author: Wang BB OToole M Brendel V Young ND
Journal: BMC Plant Biol Citation: V : 8 P : 17 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18282305 Accession (PMID): 18282305
Abstract: BACKGROUND : Although originally thought to be less frequent in plants than in animals , alternative splicing ( AS ) is now known to be widespread in plants . Here we report the characteristics of AS in legumes , one of the largest and most important plant families , based on EST alignments to the genome sequences of Medicago truncatula ( Mt ) and Lotus japonicus ( Lj ) . RESULTS : Based on cognate EST alignments alone , the observed frequency of alternatively spliced genes is lower in Mt ( approximately 10% , 1 , 107 genes ) and Lj ( approximately 3% , 92 genes ) than in Arabidopsis and rice ( both around 20% ) . However , AS frequencies are comparable in all four species if EST levels are normalized . Intron retention is the most common form of AS in all four plant species ( 50% ) , with slightly lower frequency in legumes compared to Arabidopsis and rice . This differs notably from vertebrates , where exon skipping is most common . To uncover additional AS events , we aligned ESTs from other legume species against the Mt genome sequence . In this way , 248 additional Mt genes were predicted to be alternatively spliced . We also identified 22 AS events completely conserved in two or more plant species . CONCLUSION : This study extends the range of plant taxa shown to have high levels of AS , confirms the importance of intron retention in plants , and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events . The results also indicate that the frequency of AS in plants is comparable to that observed in mammals . Finally , our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing .
Matching Sentences:
[ Sen. 12, subscore: 2.00 ]: Finally , our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing .
[ Sen. 2, subscore: 1.00 ]: Here we report the characteristics of AS in legumes , one of the largest and most important plant families , based on EST alignments to the genome sequences of Medicago truncatula ( Mt ) and Lotus japonicus ( Lj ) .
[ Sen. 3, subscore: 1.00 ]: RESULTS : Based on cognate EST alignments alone , the observed frequency of alternatively spliced genes is lower in Mt ( approximately 10% , 1 , 107 genes ) and Lj ( approximately 3% , 92 genes ) than in Arabidopsis and rice ( both around 20% ) .
[ Sen. 4, subscore: 1.00 ]: However , AS frequencies are comparable in all four species if EST levels are normalized .
[ Sen. 7, subscore: 1.00 ]: To uncover additional AS events , we aligned ESTs from other legume species against the Mt genome sequence .
[ Sen. 10, subscore: 1.00 ]: CONCLUSION : This study extends the range of plant taxa shown to have high levels of AS , confirms the importance of intron retention in plants , and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events .
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Score: 7.00
Title: Annotated ESTs from various it issues of the brown planthopper Nilaparvata lugens : a genomic resource for studying agricultural pests .
Author: Noda H Kawai S Koizumi Y Matsui K Zhang Q Furukawa S Shimomura M Mita K
Journal: BMC Genomics Citation: V : 9 P : 117 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18315884 Accession (PMID): 18315884
Abstract: BACKGROUND : The brown planthopper ( BPH ) , Nilaparvata lugens ( Hemiptera , Delphacidae ) , is a serious insect pests of rice plants . Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties . Nevertheless , BPH strains that are resistant to agricultural chemicals have developed , and BPH strains have appeared that are virulent against the resistant rice varieties . Expressed sequence tag ( EST ) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect , with its poorly understood genetic background . RESULTS : More than 37 , 000 high-quality ESTs , excluding sequences of mitochondrial genome , microbial genomes , and rDNA , have been produced from 18 libraries of various BPH it issues and stages . About 10 , 200 clusters have been made from whole EST sequences , with average EST size of 627 bp . Among the top ten most abundantly expressed genes , three are unique and show no homology in BLAST searches . The actin gene was highly expressed in BPH , especially in the thorax . Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries . An EST database is available at our web site . CONCLUSION : The EST library will provide useful information for transcriptional analyses , proteomic analyses , and gene functional analyses of BPH . Moreover , specific genes for hemimetabolous insects will be identified . The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: About 10 , 200 clusters have been made from whole EST sequences , with average EST size of 627 bp .
[ Sen. 4, subscore: 1.00 ]: Expressed sequence tag ( EST ) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect , with its poorly understood genetic background .
[ Sen. 5, subscore: 1.00 ]: RESULTS : More than 37 , 000 high-quality ESTs , excluding sequences of mitochondrial genome , microbial genomes , and rDNA , have been produced from 18 libraries of various BPH it issues and stages .
[ Sen. 10, subscore: 1.00 ]: An EST database is available at our web site .
[ Sen. 11, subscore: 1.00 ]: CONCLUSION : The EST library will provide useful information for transcriptional analyses , proteomic analyses , and gene functional analyses of BPH .
[ Sen. 13, subscore: 1.00 ]: The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest
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Score: 7.00
Title: TriMEDB : a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae .
Author: Mochida K Saisho D Yoshida T Sakurai T Shinozaki K
Journal: BMC Plant Biol Citation: V : 8 P : 72 Year: 2008 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub18590523 Accession (PMID): 18590523
Abstract: BACKGROUND : The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach , including quantitative trait loci ( QTL ) analysis as well as the holistic population analysis and association mapping of natural variations . Because the tribe Triticeae includes important cereals such as wheat and barley , integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity , which can contribute to sustainable food production . Therefore , informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species . DESCRIPTION : The Triticeae mapped expressed sequence tag ( EST ) database ( TriMEDB ) provides information , along with various annotations , regarding mapped cDNA markers that are related to barley and their homologues in wheat . The current version of TriMEDB provides map-location data for barley and wheat ESTs that were retrieved from 3 published barley linkage maps ( the barley single nucleotide polymorphism database of the Scottish Crop Research Institute , the barley transcript map of Leibniz Institute of Plant Genetics and Crop Plant Research , and HarvEST barley ver . 1 . 63 ) and 1 diploid wheat map . These data were imported to CMap to allow the visualization of the map positions of the ESTs and interrelationships of these ESTs with public gene models and representative cDNA sequences . The retrieved cDNA sequences corresponding to each EST marker were assigned to the rice genome to predict an exon-intron structure . Furthermore , to generate a unique set of EST markers in Triticeae plants among the public domain , 3472 markers were assembled to form 2737 unique marker groups as contigs . These contigs were applied for pairwise comparison among linkage maps obtained from different EST map resources . CONCLUSION : TriMEDB provides information regarding transcribed genetic markers and functions as a semantic knowledgebase offering an informatics facility for the acceleration of QTL analysis and for population genetics studies of Triticeae .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: These data were imported to CMap to allow the visualization of the map positions of the ESTs and interrelationships of these ESTs with public gene models and representative cDNA sequences .
[ Sen. 4, subscore: 1.00 ]: DESCRIPTION : The Triticeae mapped expressed sequence tag ( EST ) database ( TriMEDB ) provides information , along with various annotations , regarding mapped cDNA markers that are related to barley and their homologues in wheat .
[ Sen. 5, subscore: 1.00 ]: The current version of TriMEDB provides map-location data for barley and wheat ESTs that were retrieved from 3 published barley linkage maps ( the barley single nucleotide polymorphism database of the Scottish Crop Research Institute , the barley transcript map of Leibniz Institute of Plant Genetics and Crop Plant Research , and HarvEST barley ver .
[ Sen. 8, subscore: 1.00 ]: The retrieved cDNA sequences corresponding to each EST marker were assigned to the rice genome to predict an exon-intron structure .
[ Sen. 9, subscore: 1.00 ]: Furthermore , to generate a unique set of EST markers in Triticeae plants among the public domain , 3472 markers were assembled to form 2737 unique marker groups as contigs .
[ Sen. 10, subscore: 1.00 ]: These contigs were applied for pairwise comparison among linkage maps obtained from different EST map resources .
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Score: 7.00
Title: [ Study on hyperspectral estimation model of crop vegetation cover percentage ]
Author: Zhu L Xu JF Huang JF Wang FM Liu ZY Wang Y
Journal: Guang Pu Xue Yu Guang Pu Fen Xi Citation: V : 28 P : 1827-31 Year: 2008 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub18975813 Accession (PMID): 18975813
Abstract: In order to boost the study and application of hyperspectral remote sensing for the estimation of crop vegetation coverage percentage , an ASD FieldSpec Pro FRTM spectroradiometer was used for canopy spectral measurements of rape , corn and rice at different vegetation cover levels and photos of individual plants were taken simultaneously in order to calculate the vegetation cover percentage in computer . Firstly , data of three crops respectively and the mixed data of them were used to make correlation analysis between vegetation coverage percentage and reflectance spectra There was a high correlation between them and no obvious difference in correlation coefficient among different types of crop in the region of blue , red and near-infrared band . This indicated that it was feasible to make correlation analysis and build estimation model using mixed data Secondly , mixed data were used as unique analytical data to calculate red edge variables and pair combination of bands in the region of blue , red and near-infrared band was used to calculate normal difference vegetation index ( NDVI ) . Hyperspectral estimation models with NDVI and red edge variable as independent variable were built individually . The correlation coefficient of the former was larger than the latter , which indicated that NDVI was most effective for the estimation of vegetation coverage percentage . Effective wavelength combinations of NDVI for vegetation cover percentage estimation were determined based on the principle of higher correlation coefficient . NDVI combined with bands in the regions from 350 to 590 nm and from 710 to 1150 nm or bands in the regions from 590 to 710 nm and from 710 to 1300 nm are most effective for vegetation coverage percentage estimation . The best estimation model is simple quadratic equation using NDVI ( 696-921 ) as independent variable . The correlation coefficient matrix shows that most of the correlation coefficients of vegetation coverage percentage and NDVI combined with bands in the regions from 630 to 690 nm and from 760 to 900 nm are larger than 0 . 8 . These two band regions correspond to TM3 and TM4 of landsat 4 , 5 , 7 . It proves that NDVI ( TM3-TM4 ) can be used to and has been used to simulate vegetation coverage percentage . In order to further the study , TM3 and TM4 of Landsat5 was modeled according to spectral response function to calculate NDVI . Correlation analysis was made with NDVI and corresponding vegetation coverage percentage . The correlation coefficient of them was 0 . 80 and the regression equation was verified by experimental data . This is exploratory research for the calculation of vegetation coverage percentage using TM data in large area .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: In order to boost the study and application of hyperspectral remote sensing for the estimation of crop vegetation coverage percentage , an ASD FieldSpec Pro FRTM spectroradiometer was used for canopy spectral measurements of rape , corn and rice at different vegetation cover levels and photos of individual plants were taken simultaneously in order to calculate the vegetation cover percentage in computer .
[ Sen. 3, subscore: 1.00 ]: This indicated that it was feasible to make correlation analysis and build estimation model using mixed data Secondly , mixed data were used as unique analytical data to calculate red edge variables and pair combination of bands in the region of blue , red and near-infrared band was used to calculate normal difference vegetation index ( NDVI ) .
[ Sen. 4, subscore: 1.00 ]: Hyperspectral estimation models with NDVI and red edge variable as independent variable were built individually .
[ Sen. 5, subscore: 1.00 ]: The correlation coefficient of the former was larger than the latter , which indicated that NDVI was most effective for the estimation of vegetation coverage percentage .
[ Sen. 6, subscore: 1.00 ]: Effective wavelength combinations of NDVI for vegetation cover percentage estimation were determined based on the principle of higher correlation coefficient .
[ Sen. 7, subscore: 1.00 ]: NDVI combined with bands in the regions from 350 to 590 nm and from 710 to 1150 nm or bands in the regions from 590 to 710 nm and from 710 to 1300 nm are most effective for vegetation coverage percentage estimation .
[ Sen. 8, subscore: 1.00 ]: The best estimation model is simple quadratic equation using NDVI ( 696-921 ) as independent variable .
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Score: 7.00
Title: Prevalence and molecular diversity of Listeria monocytogenes in retail establishments .
Author: Sauders BD Sanchez MD Rice DH Corby J Stich S Fortes ED Roof SE Wiedmann M
Journal: J Food Prot Citation: V : 72 P : 2337-49 Year: 2009 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub19903398 Accession (PMID): 19903398
Abstract: As our understanding of Listeria monocytogenes transmission in retail and deli operations is limited , we conducted a cross-sectional study of L monocytogenes contamination patterns in 121 retail establishments , using testing of food and environmental samples and subtype analysis ( ribotyping ) of L monocytogenes isolates . Seventy-three ( 60% ) establishments had at least one sample that tested positive for L monocytogenes ; 5 ( 2 . 7% ) of the 183 food and 151 ( 13 . 0% ) of the 1 , 161 environmental samples tested positive for L monocytogenes , including 125 ( 16 . 7% ) and 26 ( 6 . 3% ) of non-food contact and food contact surface samples , respectively . Thirty-two EcoRI ribotypes were identified among the 156 L monocytogenes isolated . Twenty-seven establishments had two or more L monocytogenes with the same ribotype within a given establishment , including 9 establishments where isolates from 3 to 5 samples had the same ribotype . In 5 of 7 establishments where follow-up sampling was conducted 8 to 19 months after the initial sampling , isolates with the same ribotype were obtained in both samplings ; persistence of a given strain was also confirmed by pulsed-field gel electrophoresis . Our data indicate that ( i ) L monocytogenes is regularly found in some retail environments ; ( ii ) L monocytogenes strains are often widely distributed in retail , indicating cross-contamination and dispersal ; ( iii ) L monocytogenes can persist in retail environments for more than 1 year ; and ( iv ) a number of L monocytogenes subtypes isolated at retail are common among human listeriosis cases . We also identified specific contamination patterns in retail establishments , providing critical information for the development of L monocytogenes control strategies .
Matching Sentences:
[ Sen. 4, subscore: 3.00 ]: Twenty-seven establishments had two or more L monocytogenes with the same ribotype within a given establishment , including 9 establishments where isolates from 3 to 5 samples had the same ribotype .
[ Sen. 1, subscore: 1.00 ]: As our understanding of Listeria monocytogenes transmission in retail and deli operations is limited , we conducted a cross-sectional study of L monocytogenes contamination patterns in 121 retail establishments , using testing of food and environmental samples and subtype analysis ( ribotyping ) of L monocytogenes isolates .
[ Sen. 2, subscore: 1.00 ]: Seventy-three ( 60% ) establishments had at least one sample that tested positive for L monocytogenes ; 5 ( 2 . 7% ) of the 183 food and 151 ( 13 . 0% ) of the 1 , 161 environmental samples tested positive for L monocytogenes , including 125 ( 16 . 7% ) and 26 ( 6 . 3% ) of non-food contact and food contact surface samples , respectively .
[ Sen. 5, subscore: 1.00 ]: In 5 of 7 establishments where follow-up sampling was conducted 8 to 19 months after the initial sampling , isolates with the same ribotype were obtained in both samplings ; persistence of a given strain was also confirmed by pulsed-field gel electrophoresis .
[ Sen. 7, subscore: 1.00 ]: We also identified specific contamination patterns in retail establishments , providing critical information for the development of L monocytogenes control strategies .
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Score: 7.00
Title: Genome-wide characterization of simple sequence repeats in cucumber ( Cucumis sativus L ) .
Author: Cavagnaro PF Senalik DA Yang L Simon PW Harkins TT Kodira CD Huang S Weng Y
Journal: BMC Genomics Citation: V : 11 P : 569 Year: 2010 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub20950470 Accession (PMID): 20950470
Abstract: BACKGROUND : Cucumber , Cucumis sativus L is an important vegetable crop worldwide . Until very recently , cucumber genetic and genomic resources , especially molecular markers , have been very limited , impeding progress of cucumber breeding efforts . Microsatellites are short tandemly repeated DNA sequences , which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance . Data from previously characterized genomes has shown that these repeats vary in frequency , motif sequence , and genomic location across taxa . During the last year , the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line 9930 and the North American pickling type inbred line Gy14 . These sequences provide a powerful tool for developing markers in a large scale . In this study , we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences , representing 55% of its nuclear genome , and in cucumber EST sequences . Similar analyses were performed in genomic and EST data from seven other plant species , and the results were compared with those of cucumber . RESULTS : A total of 112 , 073 perfect repeats were detected in the Gy14 cucumber genome sequence , accounting for 0 . 9% of the assembled Gy14 genome , with an overall density of 551 . 9 SSRs/Mbp . While tetranucleotides were the most frequent microsatellites in genomic DNA sequence , dinucleotide repeats , which had more repeat units than any other SSR type , had the highest cumulative sequence length . Coding regions ( ESTs ) of the cucumber genome had fewer microsatellites compared to its genomic sequence , with trinucleotides predominating in EST sequences . AAG was the most frequent repeat in cucumber ESTs . Overall , AT-rich motifs prevailed in both genomic and EST data . Compared to the other species examined , cucumber genomic sequence had the highest density of SSRs ( although comparable to the density of poplar , grapevine and rice ) , and was richest in AT dinucleotides . Using an electronic PCR strategy , we investigated the polymorphism between 9930 and Gy14 at 1 , 006 SSR loci , and found unexpectedly high degree of polymorphism ( 48 . 3% ) between the two genotypes . The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite . The in silico PCR results were validated empirically in 660 of the 1 , 006 SSR loci . In addition , primer sequences for more than 83 , 000 newly-discovered cucumber microsatellites , and their exact positions in the Gy14 genome assembly were made publicly available . CONCLUSIONS : The cucumber genome is rich in microsatellites ; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber , respectively . Considering all the species investigated , some commonalities were noted , especially within the monocot and dicot groups , although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined . The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community .
Matching Sentences:
[ Sen. 11, subscore: 2.00 ]: Coding regions ( ESTs ) of the cucumber genome had fewer microsatellites compared to its genomic sequence , with trinucleotides predominating in EST sequences .
[ Sen. 7, subscore: 1.00 ]: In this study , we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences , representing 55% of its nuclear genome , and in cucumber EST sequences .
[ Sen. 8, subscore: 1.00 ]: Similar analyses were performed in genomic and EST data from seven other plant species , and the results were compared with those of cucumber .
[ Sen. 12, subscore: 1.00 ]: AAG was the most frequent repeat in cucumber ESTs .
[ Sen. 13, subscore: 1.00 ]: Overall , AT-rich motifs prevailed in both genomic and EST data .
[ Sen. 19, subscore: 1.00 ]: CONCLUSIONS : The cucumber genome is rich in microsatellites ; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber , respectively .
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Score: 7.00
Title: Production of ferulic acid from lignocellulolytic agricultural biomass by Thermobifida fusca thermostable esterase produced in Yarrowia lipolytica transformant .
Author: Huang YC Chen YF Chen CY Chen WL Ciou YP Liu WH Yang CH
Journal: Bioresour Technol Citation: V : 102 P : 8117-22 Year: 2011 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub21683590 Accession (PMID): 21683590
Abstract: A gene ( axe ) encoding the AXE thermostable esterase in Thermobifida fusca NTU22 was cloned into a Yarrowia lipolytica P01g host strain . Recombinant expression resulted in extracellular esterase production at levels as high as 70 . 94 U/ml in Hinton flask culture broth , approximately 140 times higher than observed in a Pichia pastoris expression system . After 72 h of fermentation by the Y lipolytica transformant in the fed-batch fermentor , the fermentation broth accumulated 41 . 11 U/ml esterase activity . Rice bran , wheat bran , bagasse and corncob were used as hydrolysis substrates for the esterase , with corncob giving the best ferulic acid yield . The corncob was incubated with T fusca xylanase ( Tfx ) for 12h and then with the AXE esterase for an additional 12h . Ferulic acid accumulated to 396 muM in the culture broth , a higher concentration than with esterase alone or with Tfx and esterase together for 24 h .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: Ferulic acid accumulated to 396 muM in the culture broth , a higher concentration than with esterase alone or with Tfx and esterase together for 24 h .
[ Sen. 1, subscore: 1.00 ]: A gene ( axe ) encoding the AXE thermostable esterase in Thermobifida fusca NTU22 was cloned into a Yarrowia lipolytica P01g host strain .
[ Sen. 2, subscore: 1.00 ]: Recombinant expression resulted in extracellular esterase production at levels as high as 70 . 94 U/ml in Hinton flask culture broth , approximately 140 times higher than observed in a Pichia pastoris expression system .
[ Sen. 3, subscore: 1.00 ]: After 72 h of fermentation by the Y lipolytica transformant in the fed-batch fermentor , the fermentation broth accumulated 41 . 11 U/ml esterase activity .
[ Sen. 4, subscore: 1.00 ]: Rice bran , wheat bran , bagasse and corncob were used as hydrolysis substrates for the esterase , with corncob giving the best ferulic acid yield .
[ Sen. 5, subscore: 1.00 ]: The corncob was incubated with T fusca xylanase ( Tfx ) for 12h and then with the AXE esterase for an additional 12h .
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Score: 7.00
Title: Exploring the switchgrass transcriptome using second-generation sequencing technology .
Author: Wang Y Zeng X Iyer NJ Bryant DW Mockler TC Mahalingam R
Journal: PLoS One Citation: V : 7 P : e34225 Year: 2012 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub22479570 Accession (PMID): 22479570
Abstract: BACKGROUND : Switchgrass ( Panicum virgatum L ) is a C4 perennial grass and widely popular as an important bioenergy crop . To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches , the generation of genomic resources for this plant is necessary . The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies . Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass . PRINCIPAL FINDINGS : Switchgrass cDNA libraries from germinating seedlings , emerging tillers , flowers , and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology , generating 980 , 000 reads with an average read length of 367 bp . De novo assembly generated 243 , 600 contigs with an average length of 535 bp . Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs . Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium , sorghum , rice and maize indicated a 70-80% overlap . RPKM analysis demonstrated unique transcriptional signatures of the four it issues analyzed in this study . More than 24 , 000 ESTs were identified in the dormant seed library . In silico analysis indicated that there are more than 2000 EST-SSRs in this collection . Expression of several orphan ESTs was confirmed by RT-PCR . SIGNIFICANCE : We estimate that about 90% of the switchgrass gene space has been covered in this analysis . This study nearly doubles the amount of EST information for switchgrass currently in the public domain . The celerity and economical nature of second-generation sequencing technologies provide an in-depth view of the gene space of complex genomes like switchgrass . Sequence analysis of closely related members of the NAD ( + ) -malic enzyme type C4 grasses such as the model system Setaria viridis can serve as a viable proxy for the switchgrass genome .
Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs .
[ Sen. 8, subscore: 1.00 ]: Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium , sorghum , rice and maize indicated a 70-80% overlap .
[ Sen. 10, subscore: 1.00 ]: More than 24 , 000 ESTs were identified in the dormant seed library .
[ Sen. 11, subscore: 1.00 ]: In silico analysis indicated that there are more than 2000 EST-SSRs in this collection .
[ Sen. 12, subscore: 1.00 ]: Expression of several orphan ESTs was confirmed by RT-PCR .
[ Sen. 13, subscore: 1.00 ]: SIGNIFICANCE : We estimate that about 90% of the switchgrass gene space has been covered in this analysis .
[ Sen. 14, subscore: 1.00 ]: This study nearly doubles the amount of EST information for switchgrass currently in the public domain .
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Score: 7.00
Title: A new method to assign country of HIV infection among heterosexuals born abroad and diagnosed with HIV in the UK .
Author: Rice BD Elford J Yin Z Delpech VC
Journal: AIDS Citation: V : P : Year: 2012 Type: Publisher
Literature: oryza Field: abstract Doc ID: pub22781226 Accession (PMID): 22781226
Abstract: OBJECTIVE : : To apply a new method to ascertain likely place of HIV infection among persons born abroad and diagnosed with HIV in the United Kingdom ( UK ) . DESIGN : : Analyses of heterosexual adults born abroad , diagnosed with HIV in the UK between 2004 and 2010 , and reported to the national HIV diagnoses database . METHODS : : Year of infection was ascertained by applying an estimated rate of CD4-cell count decline between an individuals CD4-cell count at diagnosis and estimates of CD4-cell count at infection . A person was classified as having probably acquired HIV while living in the UK if estimated year of infection was later than reported year of arrival in the UK . RESULTS : : Of 10 , 612 heterosexual adults born abroad included in the analyses , 85% ( 9065 ) were of black-African ethnicity . We estimate that 33% ( 26%-39% ) of persons acquired HIV whilst living in the UK . This percentage increased from 24% ( 16%-39% ) in 2004 to 46% ( 31%-50% ) in 2010 ( p < 0 . 01 ) . The estimate of 33% is three times higher than national estimates of HIV acquired in the UK based on clinic reports ( 11% ) ( p < 0 . 01 ) . CONCLUSIONS : : Assigning place of HIV infection using routinely available clinical and demographic data and estimated rates of CD4-cell decline is feasible . We report a high and increasing proportion of persons born abroad who appear to have acquired their HIV infection whilst living in the UK These findings highlight the need for continued targeted HIV prevention efforts , particularly among black-African communities .
Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: METHODS : : Year of infection was ascertained by applying an estimated rate of CD4-cell count decline between an individuals CD4-cell count at diagnosis and estimates of CD4-cell count at infection .
[ Sen. 8, subscore: 2.00 ]: The estimate of 33% is three times higher than national estimates of HIV acquired in the UK based on clinic reports ( 11% ) ( p < 0 . 01 ) .
[ Sen. 4, subscore: 1.00 ]: A person was classified as having probably acquired HIV while living in the UK if estimated year of infection was later than reported year of arrival in the UK .
[ Sen. 6, subscore: 1.00 ]: We estimate that 33% ( 26%-39% ) of persons acquired HIV whilst living in the UK .
[ Sen. 9, subscore: 1.00 ]: CONCLUSIONS : : Assigning place of HIV infection using routinely available clinical and demographic data and estimated rates of CD4-cell decline is feasible .
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Score: 7.00
Title: Quantitation of steryl ferulate and p-coumarate esters from corn and rice .
Author: Norton RA .
Journal: Lipids Citation: V : 30 ( 3 ) P : 269-74 Year: 1995 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7791537 Accession (PMID): 7791537
Abstract: The principal steryl ferulate and p-coumarate esters of different fractions from processed corn brans and corn oils , unrefined and refined , and from rice bran and rice bran oil were quantified by high-performance liquid chromatography . The results show that hexane-extracted corn oils yield more than five times the amount of esters compared to expeller processed oils . The yields of esters from bran and related products ranged from 0 . 07 to 0 . 54 mg/g of bran . Unrefined corn oils had levels from 0 . 18 to 8 . 6 mg/g for oil from hexane-extracted bran . By comparison , rice bran had ester levels of 3 . 4 mg/g of bran , and rice bran oil had levels of 15 . 7 mg/g of oil . The predominant esters from corn were sitostanyl and campestanyl ferulate , and sitostanyl and campestanyl p-coumarate . The principal esters from rice bran were cycloartenyl , 24-methylenecycloartanyl , and campesteryl ferulate . Rice bran oils had low levels of 24-methylenecycloartanyl but high levels of cyclobranol esters . The data presented provide a direct comparison of steryl ferulate and p-coumarate levels in the two cereals , and will aid in selecting the most suitable sources for the isolation of these compounds from corn products .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The principal steryl ferulate and p-coumarate esters of different fractions from processed corn brans and corn oils , unrefined and refined , and from rice bran and rice bran oil were quantified by high-performance liquid chromatography .
[ Sen. 2, subscore: 1.00 ]: The results show that hexane-extracted corn oils yield more than five times the amount of esters compared to expeller processed oils .
[ Sen. 3, subscore: 1.00 ]: The yields of esters from bran and related products ranged from 0 . 07 to 0 . 54 mg/g of bran .
[ Sen. 5, subscore: 1.00 ]: By comparison , rice bran had ester levels of 3 . 4 mg/g of bran , and rice bran oil had levels of 15 . 7 mg/g of oil .
[ Sen. 6, subscore: 1.00 ]: The predominant esters from corn were sitostanyl and campestanyl ferulate , and sitostanyl and campestanyl p-coumarate .
[ Sen. 7, subscore: 1.00 ]: The principal esters from rice bran were cycloartenyl , 24-methylenecycloartanyl , and campesteryl ferulate .
[ Sen. 8, subscore: 1.00 ]: Rice bran oils had low levels of 24-methylenecycloartanyl but high levels of cyclobranol esters .
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