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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 .
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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 .
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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 .
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Score: 13.00
Title: Prevalence of autism spectrum disorders--Autism and Developmental Disabilities Monitoring Network , 14 sites , United States , 2008 .
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 .
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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 .
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