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| 1 | The role of gut microbiota(commensal bacteria)and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer:contribution of germ-free and gnotobiotic animal models of human diseases显示文摘Metagenomic approaches are currently being used to decipher the genome of the microbiota(microbiome),and,in parallel,functional studies are being performed to analyze the effects of the microbiota on the host.Gnotobiological methods are an indispensable tool for studying the consequences of bacterial colonization.Animals used as models of human diseases can be maintained in sterile conditions(isolators used for germ-free rearing)and specifically colonized with defined microbes(including non-cultivable commensal bacteria).The effects of the germ-free state or the effects of colonization on disease initiation and maintenance can be observed in these models.Using this approach we demonstrated direct involvement of components of the microbiota in chronic intestinal inflammation and development of colonic neoplasia(i.e.,using models of human inflammatory bowel disease and colorectal carcinoma).In contrast,a protective effect of microbiota colonization was demonstrated for the development of autoimmune diabetes in non-obese diabetic(NOD)mice.Interestingly,the development of atherosclerosis in germ-free apolipoprotein E(ApoE)-deficient mice fed by a standard low-cholesterol diet is accelerated compared with conventionally reared animals.Mucosal induction of tolerance to allergen Bet v1 was not influenced by the presence or absence of microbiota.Identification of components of the microbiota and elucidation of the molecular mechanisms of their action in inducing pathological changes or exerting beneficial,disease-protective activities could aid in our ability to influence the composition of the microbiota and to find bacterial strains and components(e.g.,probiotics and prebiotics)whose administration may aid in disease prevention and treatment. | Helena Tlaskalova-Hogenova Renata Stepankova Hana Kozakova Tomas Hudcovic Luca Vannucci Ludmila Tuckova Pavel Rossmann TomasHrncır Miloslav Kverka Zuzana Zakostelska Klara Klimesova Jaroslava Pribylova Jirina Bartova Daniel Sanchez Petra Fundova Dana Borovska Dagmar Sru˚tkova Zdenek Zıdek Martin Schwarzer Pavel Drastich David P Funda | 2011 | Cellular & Molecular Immunology2011，8，2： | 47 |
| 2 | 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 |
| 3 | Adenosquamous carcinoma of the pancreas: Molecular characterization of 23 patients along with a literature review显示文摘Adenosquamous carcinoma of the pancreas(ASCP)is a rare entity. Like adenocarcinoma of the pancreas,overall survival is poor. Characteristics of ASCP include central tumor necrosis, along with osteoclasts and hypercalcemia. Various theories exist as to why this histological subtype exists, as normal pancreas tissue has no benign squamous epithelium. Due to the rarity of this disease, limited molecular analysis has been performed, and those reports indicate unique molecular features of ASCP. In this paper, we characterize 23 patients diagnosed with ASCP through molecular profiling using immunohistochemistry staining, fluorescent in situ hybridization, chromogenic in situ hybridization, and gene sequencing, Additionally, we provide a comprehensive literature review of what is known to date of ASCP.Molecular characterization revealed overexpression in MRP1(80%), MGMT(79%), TOP2A(75), RRM1(42%),TOPO1(42%), PTEN(45%), CMET(40%), and C-KIT(10%) among others. One hundred percent of samples tested were positive for KRAS mutations. This analysis shows heretofore unsuspected leads to be considered for treatments of this rare type of exocrine pancreas cancer. Molecular profiling may be appropriate to provide maximum information regarding the patient's tumor. Further work should be pursued to better characterize this disease. | Erkut Borazanci Sherri Z Millis Ron Korn Haiyong Han Clifford J Whatcott Zoran Gatalica Michael T Barrett Derek Cridebring Daniel D Von Hoff | 2015 | World Journal of Gastrointestinal Oncology2015，7，9： | 6 |
| 4 | The influence of cobalt on the electrochemical cycling stability of LaNi5-based hydride forming alloys 显示文摘 | Daniel Chartouni Felix Meli Andreas Zü ttel | 1996 | J Alloys Comp1996，241，： | 2 |
| 5 | The Shifting Bottleneck Proce- dure for Job Shop Scheduling 显示文摘 | Joseph A Egon B Daniel Z | 1988 | Management Science1988，34，3： | 1 |
| 6 | Adult attachment,social self-efficiency,self-disclosure,loneliness,and subsequent depression for freshman college student:a longitudinal study显示文摘 | Daniel W R Robyn A Z | 2005 | Journal of Counseling Psychology2005，52，4： | 1 |
| 7 | Oxidative DNA damage in the parkinsonian brain:an apparent selective increase in 8-hydroxyguanine levels in substantia nigra显示文摘 | ALAM Z I JENNER A DANIEL S E | 1997 | Neurochem1997，69，3： | 1 |
| 8 | A generalised increase in protein carbonyls in the brain in Parkinson's but not incidental Lewy body disease 显示文摘 | ALAM Z I DANIEL S E LEES A J | 1997 | J Neurochem1997，69，3： | 1 |
| 9 | Robust H∞ filtering for stochastic time-delay systems with missing measurements 显示文摘 | WANG Z D YANG F W DANIEL W C H | 2006 | IEEE Transactions on Signal Processing2006，54，7： | 1 |
| 10 | Electrostatic deflections and electronmechanical resonance of carbon nanotubes显示文摘 | PHILIPPE P WANG Z L DANIEL U | 1999 | Science1999，283，： | 1 |
| 11 | Nurturing Interpersonal Trust in Knowledge-sharing Networks显示文摘 | Lisa C Abrams Rob Cross Eric Lesser Daniel Z Levin | 2003 | Academy of Management Executive2003，，17： | 1 |
| 12 | Parametric process opti-mization to improve the accuracy of rapid prototyped stere-o lithography parts显示文摘 | Jack G Z Daniel H Calvin C C | 2000 | International Journal of Machine Tools & Manufacture2000，40，： | 1 |
| 13 | Collecting the Internet AS-Level Topology 显示文摘 | BEICHUAN Z RAYMOND L DANIEL M | 2005 | SIGCOMM Computer Commun Rev2005，35，1： | 1 |
| 14 | A systematic study of the kinetics of lignin pyrolysis 显示文摘 | Jiang G Z Daniel J N Anthony V B | 2010 | Thermochimica Acta2010，498，： | 1 |
| 15 | High grade carcino ma of the proximal ureter with negative nephroureteroseopy detected by a positive fish test: a rare case report 显示文摘 | Guoxian Z Daniel S Miezcyslaw G | 2015 | Urology Case Reports2015，6，9： | 1 |
| 16 | Molecular cloning and expression analysis of multiple polyphenol oxidase genes in developing wheat (Triticum aestivum) kernels显示文摘 | Brian B Daniel Z S | 2011 | Journal of Cereal Science2011，，： | 1 |
| 17 | Modeling the dynamtic of landscape structure in Asia, semerging desakota region显示文摘 | Daniel S Zeng Z | 2001 | Landscape and urban planning2001，21，1： | 1 |
| 18 | Antifun- gal and antimycobacterial activity of 1-( 3,5-diaryl- 4,5-dihydro-1H-pyrazol-4-y1 ) -1H-imidazole deriva- tives显示文摘 | DANIELE Z MARIA G M ERIK L | 2008 | Bioorg Med Chem2008，16，8： | 1 |
| 19 | Monoacylglycerol lipase regulates a fatty acid network that promotes cancer pathogenesis显示文摘 | Nomura Daniel K Long Jonathan Z Niessen Sherry | 2010 | Cell2010，140，1： | 1 |
| 20 | Abscisic acid induces CBF gene transcription and subsequent induction of cold-regulated genes via the CRT promoter element显示文摘 | Knight H Daniel G Z | 2004 | Plant Physiology2004，135，： | 1 |
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