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| 1 | Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome显示文摘AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species.Candidate primers evaluated were from the European rRNA database.To assess the effect of sequence length on accuracy of classification,16S rRNA genes of various lengths were created by trimming the full length sequences.Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs.The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP).The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes,represented by 36 phyla.RESULTS:Truncation to 100 nucleotides(nt)downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87(39.7%)of the 219 sequences,compared with misclassification of only 29(13.2%)sequences with truncation to 350 nt.Among 350-nt sequence reads within various regions of the 16S rRNA gene,the reverse read of an amplicon generated using the 343F/798R primers had the least(8.2%)effect on classification.In comparison,truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0%of the 219 sequences.The 343F/798R amplicon accurately assigned 91.8%of the 219 sequences at the species level.Weighted by abundance of the species in the esophageal dataset,the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage(92%).Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species.Assuming that a typicalpolymerase chain reaction can tolerate 2 mismatches between a primer and a template,the modified 347F and 803R primers should be able to anneal 98%and 99.6%of all 16S rRNA genes in the RDP database.CONCLUSION:347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes. | Carlos W Nossa William E Oberdorf Jφrn A Aas Bruce J Paster Todd Z DeSantis Eoin L Brodie Daniel Malamud Michael A Poles Zhiheng Pei | 2010 | World Journal of Gastroenterology2010，16，33： | 16 |
| 2 | Ron receptor-dependent gene regulation in a mouse model of endotoxin-induced acute liver failure显示文摘BACKGROUND:Prior experimentation has shown that loss of the tyrosine kinase(TK) signaling domain of the Ron receptor leads to marked hepatocyte protection in a model of lipopolysaccharideinduced acute liver failure(ALF) in D-galactosamine(GalN)sensitized mice.The aim of this study was to identify the role of Ron in the regulation of hepatic gene expression.METHODS:Microarray analyses were performed on liver RNA isolated sequentially from wild-type(WT) and TK-/mice during the progression of ALF.Gene array data were validated using Western and immunohistochemistry analyses as well as with ex vivo culture systems.RESULTS:At baseline,101 genes were differentially expressed between WT and TK-/-livers,which regulate processes involved in hypoxia,proliferation,apoptosis and metabolism.One hour after ALF induction,WT livers exhibited increased cytokine expression compared to TK-/-livers,and after 4 hours,an induction of suppressor of cytokine signaling(SOCS) genes as well as JAK-STAT pathway activation were prominent in TK-/livers compared to controls.CONCLUSION:Our studies suggest a novel hepato-protective mechanism in Ron TK-/-mice wherein increased and sustained SOCS production and JAK-STAT activation in the hepatocyte may inhibit the destructive proinflammatory milieu and promote survival factors which blunt hepatic death and the ensuing development of ALF. | Rishikesh M Kulkarni Louis W Kutcher William D Stuart Daniel J Carson Mike A Leonis Susan E Waltz | 2012 | Hepatobiliary & Pancreatic Diseases International2012，11，4： | 3 |
| 3 | Label-retaining liver cancer cells are relatively resistant to sorafenib显示文摘 | Hong-Wu Xin Chenwi M Ambe Danielle M Hari Gordon W Wiegand Tyler C Miller Jin-Qiu Chen Andrew J Anderson Satyajit Ray John E Mullinax Tomotake Koizumi Russell C Langan Douglas Burka Michelle A Herrmann Paul K Goldsmith Alexander Stojadinovic Udo Rudloff S | 2013 | Gut2013，，12： | 2 |
| 4 | Absorption Spectra of Para-substituted Tetraphenylporphines显示文摘 | Arthur E Martell | 1956 | J Am Chem Soc1956，78，7： | 1 |
| 5 | Catalytic combustion of methane on Co/MgO:characterisation of active cobalt sites显示文摘 | Ulla M A Spretz R Lombardo E Daniell W Knozinger H | | 0，，： | 1 |
| 6 | Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013显示文摘 | Meijer A Rebelo-de-Andrade H Correia V Besselaar T Drager-Dayal R Fry A Gregory V Gubareva L Kageyama T Laekenby A Lo J Odagiri T Pere- yaslov D Siqueira M M Takashita E Tashiro M Wang D Wong S Zhang W Daniels R S Hurt A C | 2014 | An- tiviral Research2014，110，： | 1 |
| 7 | N-acyl homoserine lactone binding to the CarR receptor determines quorumsensing specificity in Erwinia 显示文摘 | Martin W Daniel E T Neil A | 2000 | EMBO J2000，1999，4： | 1 |
| 8 | Peak discharge estimates of glacia-lake outburst floods and 'normal' climatic floods in the Mount Everest region,Nepal显示文摘 | DANIEL A C ELLEN E W | 2001 | Geomorphology2001，，1： | 1 |
| 9 | Scale development and construct clarification of servant leadership 显示文摘 | JOHN E BARBUTO JR DANIEL W WHEELER | 2006 | Group&Organization Management2006，，31： | 1 |
| 10 | Interactive inverse design op-timization of fuselage shape for low boom supersonic con-cepts显示文摘 | Li W Shieds E Daniel L | 2008 | Journal of Aircraft2008，45，9： | 1 |
| 11 | Effects of freezing on hydraulic conductivity of compacted clay显示文摘 | Kim W H Daniel D E | 1992 | Journal of Geotechnical Engineering1992，118，7： | 1 |
| 12 | Cloning and sequencing of a full length cDNA encoding ovine lipoprotein lipase 显示文摘 | EDWARDS W D DANIELS S E PAGE R A | 1993 | Biochim Biophys Acta1993，1172，12： | 1 |
| 13 | Bt toxin resistance from loss of a putative carbohydrate2 modifying enzyme 显示文摘 | Joel S G Johanna L W Daniel E S | 2001 | Science2001，293，3： | 1 |
| 14 | A computerized method of visual acuity testing显示文摘 | Roy W Beck Pamela S Moke Andrew H Turpin Frederick L Ferris John Paul SanGiovanni Chris A Johnson Eileen E Birch Danielle L Chandler Terry A Cox R.Clifford Blair Raymond T Kraker | 2003 | American Journal of Ophthalmology2003，，2： | 1 |
| 15 | Evolving morphotropic phase boundary in lead-free ( Bil/2 Nal/2 )TiO3 - BaTiO3 pi- ezoceramics 显示文摘 | JO W DANIELS J E JONES J L | 2011 | Journal of Applied Physics2011，109，01： | 1 |
| 16 | 显示文摘 | STEVEN E W DANIEL H E HOUK K N | 2008 | J Phys Chem A2008，112，： | 1 |
| 17 | Tillage effects on soil properties and crop production in the sub-humid and semiarid Argentinean Pampas 显示文摘 | Daniel E B Jose L P Paul W U | 1998 | Soil & Tillage Res1998，49，： | 1 |
| 18 | Improved finite element modelling of a cable-stayed bridge through systematic manual tuning显示文摘 | Daniell W E Macdonald J H | 2007 | Engineering Structures2007，29，3： | 1 |
| 19 | Preparation of ABS (aerylonitrile/butadiene/styrene) latexes using hydroperoxide redox initiators显示文摘 | Daniels E S Dimonie V L Vanderhoff J W | 1990 | J Appl Polym Sci1990，41，9： | 1 |
| 20 | Foot strike patterns and collision forces in habitually barefoot versus shod runners 显示文摘 | Daniel E L Madhusudhan V William A W | 2010 | Nature2010，463，28： | 1 |
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