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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 | Dysfunctional stem and progenitor cells impair fracture healing with age显示文摘Successful fracture healing requires the simultaneous regeneration of both the bone and vasculature;mesenchymal stem cells (MSCs) are directed to replace the bone tissue, while endothelial progenitor cells (EPCs) form the new vasculature that supplies blood to the fracture site. In the elderly, the healing process is slowed, partly due to decreased regenerative function of these stem and progenitor cells. MSCs from older individuals are impaired with regard to cell number, proliferative capacity, ability to migrate, and osteochondrogenic differentiation potential. The proliferation, migration and function of EPCs are also compromised with advanced age. Although the reasons for cellular dysfunction with age are complex and multidimensional, reduced expression of growth factors, accumulation of oxidative damage from reactive oxygen species, and altered signaling of the Sirtuin-1 pathway are contributing factors to aging at the cellular level of both MSCs and EPCs. Because of these geriatric-specific issues, effective treatment for fracture repair may require new therapeutic techniques to restore cellular function. Some suggested directions for potential treatments include cellular therapies, pharmacological agents, treatments targeting age-related molecular mechanisms, and physical therapeutics. Advanced age is the primary risk factor for a fracture, due to the low bone mass and inferior bone quality associated with aging;a better understanding of the dysfunctional behavior of the aging cell will provide a foundation for new treatments to decrease healing time and reduce the development of complications during the extended recovery from fracture healing in the elderly. | Diane R Wagner Sonali Karnik Zachary J Gunderson Jeffery J Nielsen Alanna Fennimore Hunter J Promer Jonathan W Lowery M Terry Loghmani Philip S Low Todd O McKinley Melissa A Kacena Matthias Clauss Jiliang Li | 2019 | World Journal of Stem Cells2019，11，6： | 3 |
| 3 | Identification of chicken enterovirus-like viruses, duck hepatitis virus (DHV) type 2 and DHV type 3 as astroviruses 显示文摘 | TODD D SMYTH V J BALL N W | 2009 | Avian Pathol2009，38，： | 1 |
| 4 | Selective electrodeposition of metal from simulated waste solutions 显示文摘 | Armstrong R D Todd M Atkinson J W | 1996 | Applied Electrochem1996，26，： | 1 |
| 5 | Tin-transition metal-carbon systems for lithium-ion battery negative electrodes显示文摘 | Todd A D W Mar R E Dahn J R | 2007 | Journal of the Electrochemical Society2007，154，6： | 1 |
| 6 | The development, testing, and application of a numerical simulator for predicting miscible flood performance显示文摘 | Todd M R Longstaff W J | 1972 | Journal of Petroleum Technology1972，24，7： | 1 |
| 7 | Fascioloides magna in white tailed deer ( Odocoileus virginianus ) : observations on thepairing tendency显示文摘 | Foreyt W J Samuel W M Todd A C | 1977 | J Parasitol1977，63，： | 1 |
| 8 | Environmental aspects of corrosion in MSF and RO desalination plants 显示文摘 | J W Oldfield B Todd | 1996 | Desalination1996，108，： | 1 |
| 9 | Landsat Wildland Mapping Accuracy显示文摘 | Todd W J Gehring D G | 1980 | Photogrammetric Engineering & Remote Sensing1980，46，4： | 1 |
| 10 | Using the Monte Carlo-Library Least-Squares (MCLLS) approach for the invivo XRF measurement of lead in bone显示文摘 | Guo W J Gardner R P Todd A C | 2004 | Nuclear Instruments and Methods in Physics Research A2004，516，23： | 1 |
| 11 | Evaluation of candidate vaccine approaches for mers-cov显示文摘 | Wang L Shi W Joyce M G Modjarrad K Zhang Y Leung K Lees C R Zhou T Yassine H M KanekiyoM Yang Z Y Chen X Becker M M Freeman M Vogel L Johnson J C Olinger G Todd J P Bagci U Solomon J Mollura D J Hensley L Jahrling P Deni- son M R Rao S S Subbarao K Kwong P D Mascola J R Kong W P Graham B S | 2015 | Nat Commun2015，6，： | 1 |
| 12 | Combinatorial study of tin-transition metal alloys as negative electrodes for lithiumion batteries显示文摘 | Todd A D W Mar R E Dahn J R | 2006 | J Electrochem Soc2006，153，10： | 1 |
| 13 | Development of the large American liver fluke Fascioloides magna in white-tailed deer, cattle and sheep 显示文摘 | Foreyt W J Todd A C | 1976 | J Parasitol1976，62，： | 1 |
| 14 | Comparison of mechanically alloyed and sputtered tin-cobalt-carbon as an anode material for lithium-ion batteries 显示文摘 | FERGUSON P P TODD A D W DAHN J R | 2008 | Electrochemistry Communications2008，10，： | 1 |
| 15 | The Fur-like protein Mur of Rhizobium leguminosarum is a Mn(2+)-responsive transcriptional regulator显示文摘 | Diaz-Mireles E Wexler M Sawers G Bellini D Todd J D Johnston A W | 2004 | Microbiology2004，150，5： | 1 |
| 16 | Mild intra operative hypothermia during surgery for intracranial aneurysm显示文摘 | TODD M M HINDMAN B J CLARKE W R | 2005 | N England J Med2005，352，： | 1 |
| 17 | Direct chill casting of CLAD ingot显示文摘 | Robert B W David J L Todd F B | 2006 | Materials Science Forum2006，，： | 1 |
| 18 | Tin-transition met- al-carbon systems for lithium-ion battery negative elec- trode 显示文摘 | Todd A D W Mar R E Dahn J R | 2007 | J Electrochem Soc2007，154，6： | 1 |
| 19 | Urbanization effects on tree growth in the vicinity of New York City显示文摘 | GREGG J W JONES C G TODD E | 2003 | Nature2003，424，： | 1 |
| 20 | Space and vacuum tribology显示文摘 | Roberts E W Todd M J | 1990 | Wear1990，136，： | 1 |
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