About Textpresso Categories/Ontology Copyright Downloads Feedback Home Query Language Search User Guide
Enter keyword(s) and/or category/ies. Selecting categories for a query makes a search more specific. For example, you can retrieve sentences that contain the word HSN and a Oryza sativa gene name by typing the keyword 'SPW1' and choosing the category 'gene (Oryza sativa)'. A category hit occurs when a particular word or phrase in the sentence is defined as a member of a particular category. Categories will be concatenated by a Boolean 'and' operation to other categories and keyword(s) if present. To search for terms in categories, click on the Categories/Ontology link above.
Keywords
Separate multiple, required keywords by white spaces (Boolean 'and').
Separate multiple, alternative keywords by a comma with no white spaces (Boolean 'or').
Enter phrases in double quotes, and put a '-' sign in front of words which are to be excluded.
Keyword Specification
AND/OR
Categories
Fields
Search Scope
Search Mode
Sort by
 
Narrow your search results with filter:
Put a '+' sign in front of words which have to be included, a '-' sign in front of words which have to be excluded. Enter the field of the word, viz author, title, year, journal, abstract, type or sentence in square brackets. Enter phrases in double quotes.
For example, to find all the papers in the search result that have Jack as author, but not John, enter +Jack-John[author]. To exclude all papers that have the phrase double mutant in title, enter -"double mutant"[title]. You can combine several filters and enter something like +Jack-John[author] -"double mutant"[title] +1994[year] -review[type].
Click on Filter! button to activate the filter.

Goto:
of 184
Display options:
author: on | off accession: on | off type: on | off abstract: on | off title: on | off
citation: on | off journal: on | off year: on | off supplementals: on | off textlinks: on | off
searchterm-highlighting: on | off matching sentences: none 1 5 10 entries/page: 5 10 20 50
5176 matches found in 3667 documents. Search time: 0.094 seconds.
Global links/files: all results in endnote all results in print version
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Goto:

Textpresso Wed Apr 1 04:19:47 2020 .