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| 1 | 2019新型冠状病毒基因组特征和流行病学:病毒起源和受体结合的意义显示文摘研究者对来自9例新型冠状病毒肺炎住院患者的支气管肺泡灌洗液样本和培养的分离株进行了下一代测序。从这些个体中获得了严重急性呼吸综合征-冠状病毒2(severe acute respiratory syndrome-coronavirus 2,SARS-CoV-2)的完整和部分基因组序列。利用Sanger测序连接病毒重叠群以获得全长基因组,cDNA末端快速扩增确定终端区。对这些SARSCoV-2基因组和其他冠状病毒基因组进行了系统进化分析,以确定该病毒的进化史并有助于推断其可能的起源。 | 刘青(译) 刘莉(审校) Lu R Zhao X Li J Niu P Yang B Wu H Wang W Song H Huang B Zhu N Bi Y Ma X Zhan F Wang L Hu T Zhou H Hu Z Zhou W Zhao L Chen J Meng Y Wang J Lin Y Yuan J Xie Z Ma J Liu WJ Wang D Xu W Holmes EC Gao GF Wu G Chen W Shi W Tan W | 2020 | 中华高血压杂志2020，28，3： | 516 |
| 2 | 帕博利珠单抗单用或与放疗联用治疗转移性非小细胞肺癌:两个随机试验的汇总分析显示文摘背景放疗可以提高整个机体对免疫治疗的应答。在Ⅱ期PEMBRO-RT研究和Ⅰ/Ⅱ期MDACC研究中,患有转移性非小细胞肺癌(NSCLC)的患者被随机分配入组,接受免疫治疗(帕博利珠单抗)+放疗联合疗法,或免疫治疗单一疗法。当上述2个研究单独分析时,联合疗法组显示出潜在获益。由于每个研究的样本量较小,缓解率和结局并未显示出统计学意义,然而却有显著的临床获益。因此,本研究进行汇总分析,来判断放疗是否会改善转移性NSCLC患者的免疫治疗应答。方法PEMBRO-RT和MDACC研究纳入标准:患者年龄≥18岁,患有转移性NSCLC,且有≥1处未经放疗照射的病灶,以便进行射野外应答监测。PEMBRO-RT研究纳入曾接受过化疗患者,MDACC研究纳入曾接受过治疗或新诊断患者。2个研究中的患者均未接受过免疫治疗。在PEMBRO-RT研究中患者被等比例随机分配入组,并根据吸烟状态进行分层(分为<10年组和≥10年组)。MDACC研究的患者根据放疗计划可行性被等比例随机分配入2个受试组。由于联合治疗组的干预本质,每个研究中的放疗均不适用盲法。在2个研究中,不论是否进行放疗,均静脉滴入帕博利珠单抗(每3周200 mg)。在PEMBRO-RT研究中,在放疗(24 Gy 3次分割照射)结束后1周给予第1剂帕博利珠单抗。在MDACC研究中,在第1次放疗(50 Gy 4次分割照射或45 Gy 15次分割照射)同时给予帕博利珠单抗。仅检测未经照射病灶的应答。本研究的终点为最佳射野外(远隔)应答率(ARR)、最佳射野外疾病控制率(ACR)、12周时ARR、12周时ACR、无进展生存期(PFS)和总生存期(OS)。2个研究的意向治疗(ITT)人群均纳入分析。PEMBRO-RT研究(NCT02492568)和MDACC研究(NCT02444741)均在ClinicalTrials.gov上注册。发现纳入148例患者,76例接受帕博利珠单抗治疗,72例接受帕博利珠单抗+放疗治疗。所有患者随访时间中位数为33个月[四分位距(IQR):32.4~33.6]。148例患者中124例(84%)组织学特征为非鳞癌,111例(75%)患者曾经接受过化疗。组间没有基线特征差异,包括PD-L1表达状态和转移灶体积。最常见的照射部位为肺转移灶(39%,28/72)、胸腔内淋巴结(21%,15/72)和非原发灶(17%,12/72)。帕博利珠单抗组和联合治疗组的最佳ARR分别为19.7%(15/76)和41.7%(30/72),OR=2.96,95%CI:1.42~6.20,P=0.0039;最佳ACR分别为43.4%(33/76)和65.3%(47/72),OR=2.51,95%CI:1.28~4.91,P=0.0071;PFS中位数分别为4.4(IQR:2.9~5.9)和9.0个月(IQR:6.8~11.2),HR=0.67,95%CI:0.45~0.99,P=0.045;OS中位数分别为8.7(IQR:6.4~11.0)和19.2个月(IQR:14.6~23.8),OR=0.67,95%CI:0.54~0.84,P=0.0004。在汇总分析中没有发现新的安全问题。解读帕博利珠单抗免疫疗法+放疗显著提高转移性NSCLC患者的应答和改善治疗结局。这些结果需要在三期临床试验中进行验证。 | 陈大卫(翻译) 于金明(校对) Willemijn S M E Theelen Vivek Verma Brian P Hobbs Heike M U Peulen Joachim G J V Aerts Idris Bahce Anna Larissa N Niemeijer Joe Y Chang Patricia M de Groot Quynh-Nhu Nguyen Nathan I Comeaux George R Simon Ferdinandos Skoulidis Steven H Lin Kewen He Roshal Patel John Heymach Paul Baas James W Welsh | 2021 | 中华肿瘤防治杂志2021，28，24： | 49 |
| 3 | Abnormal activation of the synuclein-gamma gene in hepatocellular carcinomas by epigenetic alteration.显示文摘 | Zhao W Liu H Liu W Wu Y Chen W Jiang B Zhou Y Xue R Luo C Wang L Jiang JD Liu J | 2006 | 中国生物学文摘2006，20，4： | 31 |
| 4 | Molecular and cellular characterization during chondrogenic differentiation of adipose tissue-derived stromal cells in vitro and cartilage formation in vivo显示文摘 | Lin Y Luo E Chen X Liu L Qiao J Yan Z Li Z Tang W Zheng X Tian W | 2006 | 中国生物学文摘2006，20，5： | 31 |
| 5 | Ellagic acid induces apoptosis through inhibition of nuclear factor κB in pancreatic cancer cells显示文摘AIM:To determine the effect of ellagic acid on apop-tosis and proliferation in pancreatic cancer cells and to determine the mechanism of the pro-survival effects of ellagic acid. METHODS:The effect of ellagic acid on apoptosis was assessed by measuring Phosphatidylserine externalization,caspase activity,mitochondrial membrane potential and DNA fragmentation;and proliferation by measuring DNA thymidine incorporation. Mitochondrial membrane potential was measured in permeabilized cells,and in isolated mitochondria. Nuclear factor kB(NF-kB) activity was measured by electromobility shift assay(EMSA) . RESULTS:We show that ellagic acid,a polyphenolic compound in fruits and berries,at concentrations 10 to 50 mmol/L stimulates apoptosis in human pancreatic adenocarcinoma cells. Further,ellagic acid decreases proliferation by up to 20-fold at 50 mmol/L. Ellagic acid stimulates the mitochondrial pathway of apoptosis associated with mitochondrial depolarization,cytochrome C release,and the downstream caspaseactivation. Ellagic acid does not directly affect mitochondria. Ellagic acid dose-dependently decreased NF-kB binding activity. Furthermore,inhibition of NF-kB activity using IkB wild type plasmid prevented the effect of ellagic acid on apoptosis. CONCLUSION:Our data indicate that ellagic acid stimulates apoptosis through inhibition of the prosu-rvival transcription factor NF-kB. | Mouad Edderkaoui Irina Odinokova Izumi Ohno Ilya Gukovsky Vay Liang W Go Stephen J Pandol Anna S Gukovskaya | 2008 | World Journal of Gastroenterology2008，14，23： | 30 |
| 6 | 成人、儿童及孕妇特发性血小板减少性紫癜诊治指南显示文摘特发性血小板减少性紫癜(ITP)是一种自体免疫性疾病,以持续性血小板减少为特征(血小板<150×109/L).其发病机理是自身抗体与血小板抗原结合导致它们在未成熟时即被网状内皮系统,特别是在脾脏中被破坏引起血小板减少. | Provan D Newland A Norfolk D Bolton-Maggs P Lilleyman J Greer I May A Murphy M Ouwehand W Watson S 李振宇 徐开林 | 2004 | 国外医学(输血及血液学分册)2004，27，4： | 25 |
| 7 | 2018加拿大心境障碍与焦虑障碍治疗协作组/国际双相障碍学会指南:双相障碍的管理显示文摘加拿大心境障碍与焦虑障碍治疗协作组(Canadian Network for Mood and Anxiety Treatments,CANMAT)曾于2005年发布了第1版双相障碍管理指南,并分别于2007、2009和2013年对该指南进行了更新,其中最近的2次更新是与国际双相障碍学会(International Society for Bipolar Disorders,ISBD)合作完成。2018版CANMAT/ISBD双相障碍治疗指南(以下简称指南)反映了自2005年首版指南发表以来本领域取得的重大进展,包括疾病诊断与疾病管理的更新以及药物治疗与心理治疗的近期研究进展。这些前沿进展中综合考虑了循证证据的级别,并基于治疗疗效、临床实践经验、安全性、耐受性和药物导致的转相风险等,对一线、二线及三线治疗方案进行了简明而清晰的推荐。本指南中新增内容涵盖了双相Ⅰ型障碍(BD-Ⅰ)的躁狂发作急性期、抑郁发作急性期和双相障碍维持期的一线及二线治疗推荐等级划分。这种对治疗推荐等级的划分综合考虑了治疗方法对双相障碍不同时相的影响,将进一步帮助临床医生做出基于循证证据的治疗决策。锂盐、喹硫平、双丙戊酸盐、阿塞那平、阿立哌唑、帕利哌酮、利培酮和卡利拉嗪单药或联合使用被推荐为躁狂发作急性期的一线治疗选择。BD-Ⅰ抑郁期的一线治疗选择包括喹硫平、鲁拉西酮、锂盐、拉莫三嗪单药,鲁拉西酮联合锂盐或双丙戊酸盐或拉莫三嗪辅助治疗。尽管急性期治疗有效的药物通常应继续用于BD-Ⅰ的维持期治疗,但也存在一些特殊情况(例如抗抑郁药)。现有数据表明,锂盐、喹硫平、双丙戊酸盐、拉莫三嗪、阿塞那平和阿立哌唑单药或联合治疗应被视为维持治疗的初始或更换治疗方案时的一线选择。除了探讨BD-Ⅰ的相关问题外,本指南中还对双相Ⅱ型障碍(BD-Ⅱ)的临床管理进行了系统回顾并给予治疗推荐,同时针对特殊人群也有相关推荐,如处于各个生殖周期的女性、儿童、青少年和老年人。此外,本指南中还讨论了特定精神疾病及共病(如物质滥用、焦虑障碍和代谢性疾病)的影响。最后,本指南中概述了安全性和药物监测的相关问题。CANMAT/ISBD工作组希望本指南能够成为全球临床医生的实用工具。 | Lakshmi N Yatham Sidney H Kennedy Sagar V Parikh Ayal Sehaffer David J Bond Benicio N Frey Verinder Sharma Benjamin I Goldstein Soham Rej Serge Beaulieu Martin Alda Glenda MaeQueen Roumen V Milev Arun Ravindran Claire O'Donovan Diane Mclntosh Raymond W Lam Gustavo Vazquez Flavio Kapczinski Roger S Melntyre Jan Kozicky Shigenobu Kanba Beny Lafer Trisha Suppes Joseph R Calabrese Eduard Vieta Gin Malhi Robert M Post Michael Berk 胡晨(译) 王刚(译) | 2019 | 中华精神科杂志2019，52，1： | 25 |
| 8 | 关键基础设施及其安全管理显示文摘关键基础设施(CI)系统是复杂的、高度相互依存的、网络化的社会—技术系统,一旦系统被中断或者被破坏,将会对国民健康、国土安全、经济稳定以及政府的正常运转等产生重大的影响.主要研究关键基础设施及其安全管理过程中的若干问题,对CI的特点进行了分析和总结,建立了网络化CI系统的体系结构,并利用视图模型来描述系统,同时还给出了灾难处理的一般过程.最后,进一步探讨了如何使用系统工程的方法来分析和模拟网络化CI系统的运行方式、潜在的薄弱环节以及改进这些薄弱环节的实施方法. | 刘晓 张隆飙 Zhang W J Tu Y L | 2009 | 管理科学学报2009，12，6： | 22 |
| 9 | 血管周围脂肪组织中的Bmal1通过血管紧张素原转录调控管理静息期血压显示文摘血管周围脂肪组织(perivascular adipose tissue,PVAT)围绕血管,构成了在生理条件下保持血管张力所需的脉管系统的独特的功能整体层。然而,关于PVAT与血压调节之间的关系的资料很少,包括其对昼夜血压变化的潜在作用。 | Chang L Xiong W Zhao X Fan Y Guo Y Garcia-Barrio M Zhang J Jiang Z Lin JD Chen YE 刘青 叶鹏 | 2018 | 中华高血压杂志2018，26，2： | 23 |
| 10 | 《过敏性鼻炎及其对哮喘的影响(ARIA)》指南2019版过敏性鼻炎管理路径(中国版)显示文摘2018年12月3日,慢性疾病管理大会在巴黎召开,经过与会的过敏科学及气道疾病领域的专家和患者组织讨论,针对未来鼻炎和哮喘的管理,推荐采用真实世界综合管理路径评估系统,旨在实现数字化、综合化、以人为本的管理。本文是该文件的摘要版,其中也介绍了中国过敏性鼻炎和哮喘的流行状况以及《过敏性鼻炎及其对哮喘的影响》(ARIA)在中国应用的具体情况。 | Bachert C Fokkens WJ Haahtela T Hellings PH Klimek L Papadopoulos N Pham-Thi N PfaarO Valiulis A Ventura MT Onorato G Czarlewski W Bedbrook A Bousquet J 王向东(编译) 王成硕(编译) 郑铭(编译) 杜崑(编译) 张罗(编译) | 2019 | 中国耳鼻咽喉头颈外科2019，26，12： | 23 |
| 11 | 利用变形河流阶地限定帕米尔北缘木什背斜的缩短、隆升和侧向扩展显示文摘位于帕米尔前缘逆冲推覆体(Pamir Front Thrust,PFT)东端的木什滑脱背斜,是帕米尔弧形推覆构造带最前缘和最新的变形带。对地形横剖面、纵剖面和水系发育特征的分析表明,木什背斜总体上具有由西向东扩展生长的特征。在背斜核部及北翼发育数级开阔平坦的沿轴向展布的河流阶地,阶地可划分为4期。利用阶地堆积细颗粒石英光释光测年获得阶地面T2a、T3和T4的形成年龄分别为(15.8±2.40)ka、(55.1±10.3)ka、(131.4±23.9)ka。伴随背斜的生长扩展,河流阶地面发生了横向和纵向掀斜,并形成断层陡坎和褶皱陡坎。木什背斜晚第四纪的缩短和隆升主要是通过褶皱翼旋转机制进行的,估算其最小缩短速率为(1.6±0.3)mm/a,最小隆升速率为(1.9±0.3)mm/a。与此同时,沿轴向背斜发生了向东的侧向迁移和旋转。根据背斜垂直隆升与侧向扩展之间的关系,估算背斜在131~16ka期间向东的侧向迁移扩展速率较快,为(14.6±3.6)mm/a;自16ka至今,侧向迁移扩展速率迅速减小至(1.7±0.3)mm/a,背斜向东的迁移扩展可能已基本停止,而以侧向旋转为主。 | 李涛 陈杰 肖伟鹏 Burbank D W 黄明达 Thompson J | 2011 | 地震地质2011，33，2： | 21 |
| 12 | Observation of ocean current response to 1998 Hurricane Georges in the Gulf of Mexico显示文摘The ocean current response to a hurricane on the shelf-break is examined. The study area is the DeSoto Canyon in the northeast Gulf of Mexico, and the event is the passage of 1998 Hurricane Georges with a maximum wind speed of 49 m/s. The data sets used for analy- sis consist of the mooring data taken by the Field Program of the DeSoto Canyon Eddy Intrusion Study, and simultaneous winds ob- served by NOAA (National Oceanic and Atmospheric Administration) Moored Buoy 42040. Time-depth ocean current energy density images derived from the observed data show that the ocean currents respond almost immediately to the hurricane with important differ- ences on and off the shelf. On the shelf, in the shallow water of 100 m, the disturbance penetrates rapidly downward to the bottom and forms two energy peaks, the major peak is located in the mixed layer and the secondary one in the lower layer. The response dissipates quickly after external forcing disappears. Off the shelf, in the deep water, the major disturbance energy seems to be trapped in the mixed layer with a trailing oscillation; although the disturbance signals may still be observed at the depths of 500 and 1 290 m. Verti- cal dispersion analysis reveals that the near-initial wave packet generated off the shelf consists of two modes. One is a barotropic wave mode characterized by a fast decay rate of velocity amplitude of 0.020 s-1, and the other is baroclinic wave mode characterized by a slow decay rate of 0.006 9 s-1. The band-pass-filtering and empirical function techniques are employed to the frequency analysis. The results indicate that all frequencies shift above the local inertial frequency. On the shelf, the average frequency is 1.04f in the mixed layer, close to the diagnosed frequency of the first baroclinic mode, and the average frequency increases to 1.07f in the thermocline. Off the shelf, all frequencies are a little smaller than the diagnosed frequency of the first mode. The average frequency decreases from 1.035f in the mixed layer to 1.02f in the thermocline, implying a trend for the shift in frequency of the oscillations towards f with the depth. | ZHENG Quanan LAI Ronald J HUANG Nortlen E PAN Jiayi LIU W Timothy | 2006 | Acta Oceanologica Sinica2006，25，1： | 20 |
| 13 | Current status of laparoscopic and robotic ventral mesh rectopexy for external and internal rectal prolapse显示文摘External and internal rectal prolapse with their affiliated rectocele and enterocele, are associated with debilitating symptoms such as obstructed defecation, pelvic pain and faecal incontinence. Since perineal procedures are associated with a higher recurrence rate, an abdominal approach is commonly preferred. Despite the description of greater than three hundred different procedures, thus far no clear superiority of one surgical technique has been demonstrated. Ventral mesh rectopexy(VMR) is a relatively new and promising technique to correct rectal prolapse. In contrast to the abdominal procedures of past decades, VMR avoids posterolateral rectal mobilisation and thereby minimizes the risk of postoperative constipation. Because of a perceived acceptable recurrence rate, good functional results and low mesh-related morbidity in the short to medium term, VMR has been popularized in the past decade. Laparoscopic or robotic-assisted VMR is now being progressively performed internationally and several articles and guidelines propose the procedure as the treatment of choice for rectal prolapse. In this article, an outline of the current status of laparoscopic and robotic ventral mesh rectopexy for the treatment of internal and external rectal prolapse is presented. | Jan J van Iersel Tim JC Paulides Paul M Verheijen John W Lumley Ivo AMJ Broeders Esther CJ Consten | 2016 | World Journal of Gastroenterology2016，22，21： | 20 |
| 14 | Alcohol metabolites and lipopolysaccharide: Roles in the development and/or progression of alcoholic liver disease显示文摘The onset of alcoholic liver disease (ALD) is initiated by different cell types in the liver and a number of different factors including: products derived from ethanol-induced inflammation, ethanol metabolites, and the indirect reactions from those metabolites. Ethanol oxidation results in the production of metabolites that have been shown to bind and form protein adducts, and to increase inflammatory, fibrotic and cirrhotic responses. Lipopolysaccharide (LPS) has many deleterious effects and plays a significant role in a number of disease processes by increasing inflammatory cytokine release. In ALD, LPS is thought to be derived from a breakdown in the intestinal wall enabling LPS from resident gut bacterial cell walls to leak into the blood stream. The ability of adducts and LPS to independently stimulate the various cells of the liver provides for a two-hit mechanism by which various biological responses are induced and result in liver injury. Therefore, the purpose of this article is to evaluate the effects of a two-hit combination of ethanol metabolites and LPS on the cells of the liver to increase inflamma-tion and fi brosis, and play a role in the development and/or progression of ALD. | Courtney S Schaffert Michael J Duryee Carlos D Hunter Bartlett C Hamilton 3rd Amy L DeVeney Mary M Huerter Lynell W Klassen Geoffrey M Thiele | 2009 | World Journal of Gastroenterology2009，15，10： | 20 |
| 15 | Coordinated peak expression of MMP-26 and TIMP-4 in preinvasive human prostate tumor显示文摘因为早察觉和治疗为病人的医药管理是批评的,为早前列腺癌症诊断的新奇简历标记的鉴定是高度重要的。在基础房间层和地下室膜的连续性的混乱为高级职业人员静电干扰 intraepithelial 瘤形成(HGPIN ) 的前进是必要的到在人的前列腺的侵略腺癌。涉及变换到侵略显型的分子是强烈审查的题目。我们以前报导了矩阵 metalloproteinase-26 (MMP-26 ) 经由地下室膜蛋白质并且由激活 MMP-9 的酶原形式的劈开支持人的前列腺癌症房间的侵略。而且,我们发现了 metalloproteinases-4 (TIMP-4 ) 的那个织物禁止者是大多数有势力 MMP-26 的内长的禁止者。这里,我们更高示威(p<0.0001 ) 在 HGPIN 和癌症的 MMP-26 和 TIMP-4 表示,与非肿瘤的 acini 相比。他们的表示层次在 HGPIN 是最高的,但是在一样的纸巾在侵略癌症(为各个的 p<0.001 ) 衰退。连续前列腺癌症织物节染色的 Immunohistochemical 建议 MMP-26 和 TIMP-4 的 colocalization。现在的学习显示 MMP-26 和 TIMP-4 可以在 HGPIN 的变换期间起一个不可分的作用到侵略癌症并且可以也为早前列腺癌症诊断用作标记。房间研究(2006 ) 16:750-758。做 i:10.1038/sj .cr.7310089;出版联机 2006 年 8 月 29 日。 | Seakwoo Lee Kevin K Desai Kenneth A Iczkowski Robert G Newcomer Kevin J WU Yun-Ge Zhao Winston W Tan Mark D Roycik Qing-Xiang Amy Sang | 2006 | Cell Research2006，16，9： | 18 |
| 16 | Nicotine attenuates beta-amyloid-induced neurotoxicity by regulating metal homeostasis.显示文摘 | Zhang J Liu Q Chen Q Liu NQ Li FL Lu ZB Qin C Zhu H Huang YY He W Zhao BL | 2006 | 中国生物学文摘2006，20，9： | 17 |
| 17 | Feedback-feedfor- ward individual pitch control for wind turbine load reduction显示文摘 | Selvarn K Kanev S van Wingerden J W | 2009 | International Journal of Robust and Nonlinear Control2009，19，1： | 17 |
| 18 | Ⅰ期癌症患者切除淋巴结内隐匿性微小转移癌灶的检查及其临床病理意义显示文摘目的 检查癌症患者切除淋巴结内有无微小癌转移 ,具有临床、病理重要性。方法 350例 期癌症患者包括非小细胞肺癌 94例 ,乳腺癌 112例 ,食管癌 115例及外阴癌 2 9例病理报告无癌转移的淋巴结 3715枚。应用单克隆抗细胞角蛋白 ( AE1/ AE3)、抗上皮细胞膜 ( EMA) ,及多克隆抗角蛋白抗体进行免疫组化染色重新检查。结果 所有病例的 32 .3% ( 113/ 350 )、被检淋巴结的 5.5%( 2 0 3/ 3715)有淋巴结内隐匿性肿瘤转移。肺癌患者及被检淋巴结的阳性率均比其他肿瘤高。肺鳞癌58%、腺癌 53.8%的淋巴结为阳性 ,分别比食管鳞癌 2 2 .5%、外阴鳞癌 10 .3%及乳腺癌 2 7.7%高 ( P<0 .0 5)。部分乳腺癌患者术后随访显示 :淋巴结阳性患者比阴性者预后更差 ( P<0 .0 5)。结论 说明免疫组化技术可大大提高淋巴结微小癌转移的检出率 ,其阳性率的不同可能与患者的临床经过甚至癌患者的死亡率相关联。 | 陈朝伦 卢晓梅 黄绒 黎音 古丽娜尔 沈宝茵 A J Cochran D R Wen W F Coulson | 1997 | 中华肿瘤杂志1997，19，1： | 16 |
| 19 | Association of farnesyl diphosphate synthase polymorphisms and response to alendronate treatment in Chinese postmenopausal women with osteoporosis显示文摘 | Liu Y Li M Zhou PR Xing XP Xia WB Xu L Liu H J Zhang ZL LiaoEY Chen DC Liu J Tao TZ Wu W | 2014 | Chinese Medical Journal2014，，4： | 16 |
| 20 | 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 |
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