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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 | 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 .
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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 | 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 .
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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 | 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 .
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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 | 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 .
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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 | 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 .
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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 | Matching Sentences: [ Sen. 1, subscore: 2.00 ]: A total of 944 expressed sequence tags ( ESTs ) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat ( Triticum aestivum L ) . [ Sen. 2, subscore: 2.00 ]: EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution . [ Sen. 5, subscore: 2.00 ]: The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms . [ Sen. 3, subscore: 1.00 ]: EST loci were unevenly distributed among chromosomes 1A , 1B , and 1D with 660 , 826 , and 726 , respectively . [ Sen. 4, subscore: 1.00 ]: The number of EST loci was greater on the long arms than on the short arms for all three chromosomes . [ Sen. 6, subscore: 1.00 ]: Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35 . 5% . [ Sen. 7, subscore: 1.00 ]: Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences ( E < or = e ( -10 ) ) , where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10 . [ Sen. 8, subscore: 1.00 ]: Only 9 . 5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences .
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Score: 11.00 | Title: Estimation of the nuclear DNA content of gossypium species .
| Author: Hendrix B Stewart JM .
| Journal: Ann . Bot . Citation: V : 95 ( 5 ) P : 789-97 Year: 2005 Type: ARTICLE | Literature: oryza Field: abstract Doc ID: pub15701660 Accession (PMID): 15701660 | Matching Sentences: [ Sen. 2, subscore: 1.00 ]: DNA content estimates from about half of the species indicate over a 3-fold variation exists . [ Sen. 3, subscore: 1.00 ]: However , the nine DNA content estimates for G hirsutum reveal over a 2-fold difference for this species alone . [ Sen. 4, subscore: 1.00 ]: Recent reports have shown that several plant compounds can bias DNA content estimates obtained by commonly used methods . [ Sen. 5, subscore: 1.00 ]: The purpose of this research was to examine the standardization procedures used for DNA content determinations with flow cytometry as applied to Gossypium , and generate revised DNA content estimates for all available Gossypium species using best-standard practices . [ Sen. 7, subscore: 1.00 ]: Fluorescence values were converted to DNA content estimates based on the nuclear fluorescence of standard genotypes of barley , corn and rice . [ Sen. 8, subscore: 1.00 ]: Various combinations of nuclei preparations relative to the standards were evaluated for their influence on the estimates . [ Sen. 9, subscore: 1.00 ]: KEY RESULTS : Both external standardization and internal standardization with Oryza sativa IR36 yielded statistically similar DNA content estimates for Gossypium . [ Sen. 10, subscore: 1.00 ]: Internal standardization with Hordeum vulgare Sultan resulted in a high estimate of DNA content . [ Sen. 11, subscore: 1.00 ]: Nuclear DNA content estimates were generated for 37 Gossypium species using external standardization . [ Sen. 12, subscore: 1.00 ]: Estimates of ancestral genome sizes reveal that both increases and decreases in nuclear DNA content have occurred . [ Sen. 15, subscore: 1.00 ]: The current DNA content estimates support accepted cytogenetic divisions of the genus .
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Score: 11.00 | Title: Structural and functional analyses of the wheat genomes based on expressed sequence tags ( ESTs ) related to abiotic stresses .
| Author: Ramalingam J Pathan MS Feril O Ross K Ma XF Mahmoud AA Layton J Rodriguez-Milla MA Chikmawati T Valliyodan B Skinner R Matthews DE Gustafson JP Nguyen HT .
| Journal: Genome Citation: V : 49 ( 10 ) P : 1324-40 Year: 2006 Type: ARTICLE | Literature: oryza Field: abstract Doc ID: pub17218960 Accession (PMID): 17218960 | Matching Sentences: [ Sen. 8, subscore: 3.00 ]: Similarly , considering homoeologous group-specific ESTs , group 2 showed the highest number with 16 unique ESTs ( 58 loci ) , followed by group 4 with 9 unique ESTs ( 33 loci ) . [ Sen. 1, subscore: 2.00 ]: To gain insights into the structure and function of the wheat ( Triticum aestivum L ) genomes , we identified 278 ESTs related to abiotic stress ( cold , heat , drought , salinity , and aluminum ) from 7671 ESTs previously mapped to wheat chromosomes . [ Sen. 7, subscore: 2.00 ]: When considering the genome-specific ESTs , the B genome showed the highest number of unique ESTs ( 7 loci ) , while none were found in the D genome . [ Sen. 2, subscore: 1.00 ]: Of the 278 abiotic stress related ESTs , 259 ( 811 loci ) were assigned to chromosome deletion bins and analyzed for their distribution pattern among the 7 homoeologous chromosome groups . [ Sen. 3, subscore: 1.00 ]: Distribution of abiotic stress related EST loci were not uniform throughout the different regions of the chromosomes of the 3 wheat genomes . [ Sen. 10, subscore: 1.00 ]: Most of the mapped ESTs fell into the category of enzyme activity ( 28% ) , followed by binding activity ( 27% ) . [ Sen. 12, subscore: 1.00 ]: The comparison of stress-responsive ESTs with genomic sequences of rice ( Oryza sativa L ) chromosomes revealed the complexities of colinearity .
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Score: 11.00 | Title: Estradiol and SERM Treatments Influence Estrogen Receptor Coregulator Gene Expression in Human Skeletal Muscle Cells .
| Author: Dieli-Conwright CM Spektor TM Rice JC Todd Schroeder E | Journal: Acta Physiol ( Oxf ) Citation: V : P : Year: 2009 Type: Publisher | Literature: oryza Field: abstract Doc ID: pub19432593 Accession (PMID): 19432593 | Matching Sentences: [ Sen. 2, subscore: 3.00 ]: We investigated the influence of estradiol and selective estrogen receptor modulators ( tamoxifen , raloxifene ) on estrogen receptor coregulator mRNA expression in human skeletal muscle cells . [ Sen. 6, subscore: 2.00 ]: Importantly , mRNA expression of MyoD increased with estradiol and decreased with tamoxifen and raloxifene in human skeletal muscle cells ( p < 0 . 05 ) . mRNA expression of GLUT4 increased with estradiol and raloxifene and decreased with tamoxifen in human skeletal muscle cells ( p < 0 . 05 ) . [ Sen. 7, subscore: 2.00 ]: Conclusions : These findings are novel in that they provide the first evidence that estradiol and selective estrogen receptor modulators influence ER-alpha function in human skeletal muscle . [ Sen. 1, subscore: 1.00 ]: Aim : Estrogen receptors are present in human skeletal muscle ; however , the function of the receptor is currently unknown . [ Sen. 3, subscore: 1.00 ]: Methods : Human skeletal muscle cells were treated with the following conditions over a 24-hour period : 10 nM estradiol ; 5 muM of tamoxifen ; and 10muM raloxifene . [ Sen. 5, subscore: 1.00 ]: Results : ER-alpha mRNA expression increased with all 3 drug treatments ( p< 0 . 05 ) while there was no change in mRNA expression of ER-beta in human skeletal muscle cells . mRNA expression of SRC increased and SMRT decreased with estradiol , tamoxifen , and raloxifene in human skeletal muscle cells ( p< 0 . 05 ) . [ Sen. 8, subscore: 1.00 ]: This demonstrates the importance of the estrogen receptor and alterations in its coregulators , to potentially prevent sarcopenia and promote muscle growth in postmenopausal women using these forms of hormone replacement therapy .
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Score: 10.00 | Title: A comprehensive rice transcript map containing 6591 expressed sequence tag sites .
| Author: Wu J Maehara T Shimokawa T Yamamoto S Harada C Takazaki Y Ono N Mukai Y Koike K Yazaki J Fujii F Shomura A Ando T Kono I Waki K Yamamoto K Yano M Matsumoto T Sasaki T | Journal: Plant Cell Citation: V : 14 ( 3 ) P : 525-35 Year: 2002 Type: ARTICLE | Literature: oryza Field: abstract Doc ID: pub11910001 Accession (PMID): 11910001 | Matching Sentences: [ Sen. 3, subscore: 2.00 ]: Here , we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80 . 8% of the rice genome . [ Sen. 4, subscore: 2.00 ]: Chromosomes 1 , 2 , and 3 have relatively high EST densities , approximately twice those of chromosomes 11 and 12 , and contain 41% of the total EST sites on the map . [ Sen. 8, subscore: 2.00 ]: Our EST mapping also shows that 40% of the assigned ESTs occupy only approximately 21% of the entire genome . [ Sen. 1, subscore: 1.00 ]: To determine the chromosomal positions of expressed rice genes , we have performed an expressed sequence tag ( EST ) mapping project by polymerase chain reaction-based yeast artificial chromosome ( YAC ) screening . [ Sen. 2, subscore: 1.00 ]: Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis . [ Sen. 5, subscore: 1.00 ]: Most of the EST-dense regions are distributed on the distal regions of each chromosome arm . [ Sen. 6, subscore: 1.00 ]: Genomic regions flanking the centromeres for most of the chromosomes have lower EST density .
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