Insights from Comparative Genomics for the Treatment of Pneumococcal Infections

7.项目摘要 该提案包括1年的指导研究，以发展微生物领域的职业生涯 发病机制，因为它涉及中耳炎（OM），随后3年的独立研究，在同一 纪律首席研究员在哈佛大学获得了免疫学和微生物发病学博士学位。 在Kasturi Haldar博士的指导下，西北大学。作为她论文工作的一部分，她 在生物信息学上鉴定了一种与疟疾感染相关的新的真核分泌组， 扩大了潜在的抗疟疾药物靶点。她继续接受博士后研究员的培训 与加思埃利希博士，在那里她把重点转向原核病原体，专注于细菌- 诱发中耳炎和一套生物信息学工具的比较基因组学的发展，以确定 基因型-表型相关性她的工作揭示了在临床中非常广泛的基因组多样性， S. pneumoniae菌株，并已表明水平基因转移（HGT）是多样性的主要机制 在慢性多克隆S.肺炎感染。 现任提案中概述的行动计划将继续通过以下方式扩大她的科学技能 教育机会的独特整合;尖端的设施和资源;以及科学和 基因组科学中心（Center for Genomic Sciences，CGS）提供的专业指导。指导部分将进行 在加思埃利希医生的指导下埃利希博士是CGS的执行董事， 负责主要的范式转变，即培养阴性，耐药的慢性细菌 感染是由代谢变化引起的，代谢变化是从促细胞生长剂到生物膜形式。他也是作者， 分布式基因组假说，与生物膜概念相似的遗传学概念，是许多生物膜理论的先驱。 比较细菌基因组学的工具。他培养了许多研究生，博士后研究员， 和初级教员 科学和职业建议也将提供由CGS生物膜主任，博士J.威廉Costerton 他是皇家学会和美国微生物学会的会员。此外，Costerton博士 现代生物膜范例的创始人（1978年），以及微生物生物膜许多方面的先驱研究者。 生物膜、生态学和多微生物群落。科斯特顿博士曾接受过许多大师级的教师 获得世界各地学生团体的奖项，并被公认为开发和推进 与他一起工作的年轻科学家的职业生涯。 计算课程，生物信息学研讨会，科学会议，以及 最近多个合作项目的发展，其中一些已被纳入本项目的设计， 将进一步加强PI的培训经验。与外部科学家的合作包括：1）Darren博士 开普敦大学的马丁博士是检测重组及其在进化中作用的专家。 密歇根大学的生物化学合成专家大卫谢尔曼; 3）密歇根大学的埃尔韦泰特林博士。 马里兰州大学和诺华公司的克劳迪奥·多纳蒂，他们开发了许多数学工具， 比较基因组学，并领导了创建一个通用的肺炎球菌注释系统的努力; 洛克菲勒的亚历山大·托马兹和里斯本新大学的赫米尼亚·德·伦卡斯特博士 是肺炎球菌发病机理和流行病学方面的权威， 杰出的菌株库;和5）洛杉矶的加州大学的Wenyuan Shi博士， 开发了特异性靶向抗菌肽（STAMP）。 候选人致力于细菌致病机理的研究，旨在提高诊断和治疗水平。 治疗细菌诱导的OM。该提案的重点是临床上重要的子集， 肺炎链球菌菌株（SP-1）是大流行和耐药性。其目的是：1） 开发S。肺炎超基因组基因芯片，提供了一种高通量和成本效益的手段， 对大量临床分离株进行比较基因组杂交（CGH），并最终 作为一种分子诊断，以指导治疗OM; 2）研究的分子机制， 新的SP-1特异性限制修饰系统，并确定使用抑制剂的治疗潜力， 阻断甲基转移酶; 3）研究新的SP-1乳酸菌群的作用机制 传感基因座，以及使用该基因座内编码的肽将抗微生物剂靶向S. 肺炎和治疗感染。CGS为这项工作提供了一个理想的环境， 细菌生物膜，比较基因组学和中耳炎动物模型，具有最先进的设施， DNA测序、比较基因组杂交、计算生物学和共聚焦激光扫描 显微镜 总而言之，本项目，加上优秀的人员和设施资源， CGS将最大限度地发挥主要研究者的潜力，建立科学利基，启动多个 合作，在未来三年内申请NIH R 01资金，并开始独立的职业生涯， OM的微生物学和相关的慢性细菌感染。

7. Project Summary This proposal consists of 1 year of mentored research for the development of a career in microbial pathogenesis as it relates to otitis media (OM), followed by 3 years of independent research in the same discipline. The principal investigator completed a doctorate in Immunology and Microbial Pathogenesis at Northwestern University under the mentorship of Dr. Kasturi Haldar. As part of her dissertation work she identified bioinformatically a novel eukaryotic secretome associated with malarial infection that has vastly expanded the pool of potential anti-malarial drug targets. She continued her training as a post-doctoral fellow with Dr. Garth Ehrlich, where she switched her emphasis to prokaryotic pathogens focusing on bacterially- induced otitis media and the development of a suite of bioinformatic tools for comparative genomics to identify genotype-phenotype correlations. Her work has exposed the very extensive genomic diversity among clinical S. pneumoniae strains, and has shown that horizontal gene transfer (HGT) is the major mechanism of diversity generation during chronic polyclonal S. pneumoniae infections. The plan of action outlined in the incumbent proposal will continue to expand her scientific skills through a unique integration of educational opportunities; cutting-edge facilities and resources; and scientific and mentoring expertise available at the Center for Genomic Sciences (CGS). The mentored section will be carried out under the guidance of Dr. Garth Ehrlich. Dr. Ehrlich is the Executive Director of the CGS, and is responsible for the major paradigm shift that states that culture-negative, antibiotic-resistant chronic bacterial infections result from a metabolic change from a planktonic to a biofilm form. He is also the author of the Distributed Genome Hypothesis, a genetic parallel to the biofilm concept and is the pioneer of many of the tools of comparative bacterial genomics. He has trained numerous graduate students, postdoctoral fellows, and junior faculty. Scientific and career advice will also be provided by the CGS Biofilm Director, Dr. J. William Costerton who is a fellow of the Royal Society and of the American Society for Microbiology. Moreover, Dr. Costerton is the originator of the modern biofilm paradigm (1978), and a pioneer researcher in many aspects of microbial biofilms, ecology, and polymicrobial communities. Dr. Costerton has received numerous master teacher awards from student groups around the world and is recognized as an expert in developing and advancing the careers of junior scientists with whom he works. Computational coursework, a bioinformatic workshop, and scientific meetings, as well as the development of multiple recent collaborations, some of which have been incorporated into this project's design, will further enhance the PI's training experience. Collaborations with outside scientists include: 1) Dr. Darren Martin at Cape Town University, an expert in the detection of recombination and it's role in evolution; 2) Dr. David Sherman at the University of Michigan, a specialist in biochemical synthesis; 3) Drs. Herve Tettelin at the University of Maryland and Claudio Donati at Novartis who have developed many mathematical tools for comparative genomics and led the effort to create a universal pneumococcal annotation system; 4) Drs. Alexander Tomasz at the Rockefeller and Dr. Herminia de Lencastre at the Universidade Nova de Lisboa who are authorities on the pathogenesis and epidemiology of pneumococcus and who have collected an outstanding library of strains; and 5) Dr. Wenyuan Shi at University of California in Los Angeles who has developed specifically targeted anti-microbial peptides (STAMPs). The candidate is devoted to a career in bacterial pathogenesis designed to improve the diagnosis and treatment of bacterially-induced OM. The focus of this proposal is on a clinically important subset of Streptococcus pneumoniae strains (the SP-1) that are pandemic and drug resistant. The aims are to: 1) develop an S. pneumoniae supragenome gene chip to provide a high-throughput and cost-effective means to perform comparative genomic hybridizations (CGH) on large numbers of clinical isolates, and ultimately to function as a molecular diagnostic to guide treatment of OM; 2) investigate the molecular mechanism of a novel SP-1-specific restriction-modification system, and determine the treatment potential of using inhibitors to block the methyltransferase; and 3) investigate the mechanism of action of an novel SP-1 lantibiotic-quorum sensing locus, and the potential to use a peptide encoded within this locus to target anti-microbials to S. pneumoniae and treat infections. The CGS provides an ideal setting for this work by combining expertise in bacterial biofilms, comparative genomics, and otitis media animal models, with a state-of-the-art facilities for DNA sequencing, comparative genomic hybridization, computational biology, and confocal laser scanning microscopy. In summary, this project, combined with the outstanding personnel and facilities resources available at the CGS, will maximize the potential for the principal investigator to establish a scientific niche, initiate multiple collaborations, apply for NIH R01 funding within the next three years, and commence an independent career in the microbiology of OM and related chronic bacterial infections.