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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 | Laser patterning for the study of MSC cardiogenic differentiation at the single-cell level显示文摘Mesenchymal stem cells(MSCs)have been cited as contributors to heart repair through cardiogenic differentiation and multiple cellular interactions,including the paracrine effect,cell fusion,and mechanical and electrical couplings.Due to heart–muscle complexity,progress in the development of knowledge concerning the role of MSCs in cardiac repair is heavily based on MSC–cardiomyocyte coculture.In conventional coculture systems,however,the in vivo cardiac muscle structure,in which rod-shaped cells are connected end-to-end,is not sustained;instead,irregularly shaped cells spread randomly,resulting in randomly distributed cell junctions.Consequently,contact-mediated cell–cell interactions(e.g.,the electrical triggering signal and the mechanical contraction wave that propagate through MSC–cardiomyocyte junctions)occur randomly.Thus,the data generated on the beneficial effects of MSCs may be irrelevant to in vivo biological processes.In this study,we explored whether cardiomyocyte alignment,the most important phenotype,is relevant to stem cell cardiogenic differentiation.Here,we report(i)the construction of a laser-patterned,biochip-based,stem cell–cardiomyocyte coculture model with controlled cell alignment;and(ii)single-cell-level data on stem cell cardiogenic differentiation under in vivo-like cardiomyocyte alignment conditions. | Zhen Ma Qiuying Liu Huaxiao Yang Raymond B Runyan Carol A Eisenberg Meifeng Xu Thomas K Borg Roger Markwald Yifei Wang Bruce Z Gao | 2013 | Light(Science & Applications)2013，2，1： | 2 |
| 3 | Signaling mechanisms in growthfactor-stimu- lated cell motility 显示文摘 | Bela Bruce Z | 1997 | Stem Cells1997，15，： | 1 |
| 4 | Breeding oilseed rape for pod shattering resistance 显示文摘 | Morgan C L Ladbrooke Z L Bruce D M | 2000 | Journal of Agricultural Science2000，135，： | 1 |
| 5 | The INTERPHONE study: design, epidemiological methods, and description of the study population显示文摘 | Elisabeth Cardis Lesley Richardson Isabelle Deltour Bruce Armstrong Maria Feychting Christoffer Johansen Monique Kilkenny Patricia McKinney Baruch Modan Siegal Sadetzki Joachim Schüz Anthony Swerdlow Martine Vrijheid Anssi Auvinen Gabriele Berg Maria Blet | 2007 | European Journal of Epidemiology2007，，9： | 1 |
| 6 | Lysozyme enhancement of tumor cell immunoprotection in a murine fibrosarcoma显示文摘 | Jeffrey S W John J R Bruce S Z | 1981 | Cancer Research1981，41，5： | 1 |
| 7 | Hydroxyl radical formation in aqueous reactions (pH 3-8) of iron(11) with hydrogen peroxide: the photo-Fenton reaction 显示文摘 | Richard G Z Bruce C F Juerg H | 1992 | Environmental Science and Technology1992，26，2： | 1 |
| 8 | Detection of differentially expressed genes in healing mouse corneas using cDNA microarrays显示文摘 | Cao Z Wu HK Bruce A | | 0，，： | 1 |
| 9 | SCR deactiva- tion in a full-scale confired utility boiler显示文摘 | Oshua R S Christopher J Z Bruce C F | 2008 | Fuel2008，87，： | 1 |
| 10 | Li-O2 battery with a dimethylforrnamide electrolyte 显示文摘 | CHEN Y H FREUNBEGER S A PENG Z Q BARDE F BRUCE P G | 2012 | Journal of the American Chemical Society2012，134，： | 1 |
| 11 | Application of mechanism design to electric power markets显示文摘 | Silva C Bruce F Zheng C Z | 2001 | IEEE Transactions on Power Systems2001，16，4： | 1 |
| 12 | Tumor Vascularity:Evaluation in a Murine Model with Contrast-Enhanced Color Doppler US Effect of Angiogenesis Inhibitors显示文摘 | Irina I Christian B Bruce Z | 2002 | Radiology2002，222，2： | 1 |
| 13 | 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 |
| 14 | Hoechst 33342 induces apoptosis in HL-60 cells and inhibitstopoisomerase Ⅰin vivo显示文摘 | Jenn C Bruce D | 1999 | Arch Pathol Lab Med1999，123，： | 1 |
| 15 | Breeding oilseed rape for shattering resistance 显示文摘 | Morgan C L Ladbrooke Z L Bruce D M | 2000 | Journal of Agricultural Sciences2000，135，： | 1 |
| 16 | Ionic conductivity in the crystalline polymer electrolytes PEO6: LiXF6, X=P, As, Sb显示文摘 | Stoeva Z Martin-Litas I Bruce P G | 2003 | J Am Chem Soc2003，125，15： | 1 |
| 17 | Meta-Analysis of Raloxifene for the Prevention and Treatment of Postmenopausal Osteoporosis显示文摘 | Ann C Peter T Nicole Z Vivian R Bruce W Jonathan A George W Beverley S Gordon G | 2002 | Endocrine Reviews2002，23，4： | 1 |
| 18 | HOX genes and their role in the devel- opment of human cancers 显示文摘 | Seema B Jeremy Z Bruce M | 2014 | J Mol Med2014，92，8： | 1 |
| 19 | Meta-Analysis of the Efficacy of Vitamin D Treatment in Preventing Osteoporosis in Postmenopausal Women显示文摘 | Emmanuel P George W Beverley S William G Bruce W Nicole Z Ann C Jonathan A Peter T Robert J Carol G Gordon G | 2002 | Endocrine Reviews2002，23，4： | 1 |
| 20 | Moisture migration in starch molding operations as observed by magnetic resonance imaging 显示文摘 | Gregory R Z Bryce M Bruce J B | 2003 | Food Research International2003，36，： | 1 |
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