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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 | Efficacy of human papillomavirus testing for the detection of invasive cervical cancers and cervical intraepithelial neoplasia: a randomised controlled trial显示文摘 | Guglielmo Ronco Paolo Giorgi-Rossi Francesca Carozzi Massimo Confortini Paolo Dalla Palma Annarosa Del Mistro Bruno Ghiringhello Salvatore Girlando Anna Gillio-Tos Laura De Marco Carlo Naldoni Paola Pierotti Raffaella Rizzolo Patrizia Schincaglia Manuel Z | 2010 | Lancet Oncology2010，，3： | 3 |
| 3 | Immunohistochemical Characterization of Pancreatic Tumors Induced by Dimethylbenzanthracene in Rats显示文摘 | Ramon E. Jimenez Kaspar Z’graggen Werner Hartwig Fiona Graeme-Cook Andrew L. Warshaw Carlos Fernandez-del Castillo | 1999 | The American Journal of Pathology1999，，4： | 2 |
| 4 | Fragile histidine triad gene and skin cancer显示文摘 | Nicola Z Carlo MC | 2001 | Euro J Dermatol2001，11，5： | 1 |
| 5 | Changes in soil enzyme activities following additions of cyanobaeterial biomass and exopolysaccharide 显示文摘 | De Caire G Z De Carlo M S Palma R M | 2000 | Soil Biology & Biochemistry2000，32，： | 1 |
| 6 | STIM1 converts TRPC1 from a receptor-operated to a store-operated channel: moving TRPC1 in and out of lipid rafts 显示文摘 | Alicia S Angelica Z Carlos S | 2008 | Cell Calcium2008，44，5： | 1 |
| 7 | Results of a laboratory experiment relating spectral reflectance to total suspended solids显示文摘 | Carlos A S Evlyn M L Claudia Z F B | 1991 | Remote Sensing of Environment1991，36，： | 1 |
| 8 | Cortical excitability and rest activity properties in patients with depression 显示文摘 | Carlo S Franca T Filippo Z | 2007 | J Psychiatry Neurosci2007，32，： | 1 |
| 9 | Determination of the behaviour factor of steel moment-resisting (MR) frames by a damage accumulation approach 显示文摘 | Carlo A C Alessandra Z | 2010 | Journal of Constructional Steel Research2010，66，5： | 1 |
| 10 | Effect of interferon gamma-1b on survival in patients with idiopathic pulmonary fibrosis (INSPIRE): a multicentre, randomised, placebo-controlled trial显示文摘 | Talmadge E King Carlo Albera Williamson Z Bradford Ulrich Costabel Phil Hormel Lisa Lancaster Paul W Noble Steven A Sahn Javier Szwarcberg Michiel Thomeer Dominique Valeyre Roland M du Bois | 2009 | The Lancet . 2009 (9685)2009，，： | 1 |
| 11 | Biological implications of tumor cells in blood and bone marrow of pancreatic cancer patients显示文摘 | Kaspar Z’graggen Barbara A. Centeno Carlos Fernandez-del Castillo Ramon E. Jimenez Jens Werner Andrew L. Warshaw | 2001 | Surgery2001，，5： | 1 |
| 12 | Effective Fresnel-number concept for evaluating the relative focal shift in focused beams 显示文摘 | MANUEL M CARLOS J Z PEDRO A | 1998 | J O S A1998，15，2： | 1 |
| 13 | Stent - graft treatment of pseudoaneurysms and arteriovenous fistulae in the carotid artery 显示文摘 | Schonholz C Krajcer Z Carlos Parodi J | 2006 | Vasc2006，14，3： | 1 |
| 14 | Application of Mechanism Design to Electric Power Markets显示文摘 | Carlos Silva Bruce F Zheng C Z | 2001 | IEEE Trans on Power Systems2001，16，1： | 1 |
| 15 | Home care and short-run nursing homes:organizational aspects of their integration with oncological organizations显示文摘 | Carlo Z | 2001 | Critical Reviews in Ontology/Hematology2001，39，： | 1 |
| 16 | Stent graft treatment of pseudoaneurysms and arteriovenous fistulae in the carotid artery显示文摘 | Schonholz C Krajcer Z Carlos Parodi J | 2006 | Vascular2006，14，3： | 1 |
| 17 | fl-glucan enchancement of T cell IFN-r response in swine显示文摘 | Xiao Z G Carlos A T Murtaugh M P | 2004 | Vet lmmunol hnnmnopathol2004，102，： | 1 |
| 18 | Optimal design of gating systems by gradient search methods 显示文摘 | Carlos E Esparza Martha P Guerrero-Mata Roger Z Rios-Mercado | 2006 | Computational Materials Science2006，36，： | 1 |
| 19 | Efficacy of human papillomavirus testing for the detection of invasive cervical cancers and cervical intraepithelial neoplasia: a randomised controlled trial显示文摘 | Guglielmo Ronco Paolo Giorgi-Rossi Francesca Carozzi Massimo Confortini Paolo Dalla Palma Annarosa Del Mistro Bruno Ghiringhello Salvatore Girlando Anna Gillio-Tos Laura De Marco Carlo Naldoni Paola Pierotti Raffaella Rizzolo Patrizia Schincaglia Manuel Z | 2010 | Lancet Oncology2010，，3： | 1 |
| 20 | Global Robust Disturbance Attenuation and Almost Disturbance Decoupling for Uncertain Cascaded Nonlinear Systems显示文摘 | Su W Z Xie L H Carlos E de Souza | 1999 | Automatica1999，35，4： | 1 |
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