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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 .
Matching Sentences:
[ 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 .
Matching Sentences:
[ 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 ( Functional categorization of the annotated unigenes sequences showed that 153 ( 3 . 3% ) genes were assigned to cellular component category , 132 ( 2 . 8% ) to biological process , and 132 ( 2 . 8% ) in molecular function . Further , 19 genes were identified differentially expressed between FW responsive genotypes and 20 between SMD responsive genotypes . 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 . 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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