Feedback Control of Biological Polymers in a Nanopore

纳米孔中生物聚合物的反馈控制

• 批准号: 7281328
• 负责人: William Bruce Dunbar
• 金额: $ 12.85万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7281328
• 关键词: Affect; Algorithms; Base Sequence; Bioinformatics; Biological; Biology; Cell Count; Cell Differentiation process; Cells; Computer software; Cytosine; DNA Sequence; Data; Detection; Development; Devices; Disease; Electronics; Embryology; Event; Feedback; Frequencies; Genetic Variation; Genome; Genomics; Goals; Health; Hemolysin; Human; Lead; Learning; Machine Learning; Measurement; Measures; Membrane; Messenger RNA; Methods; Molecular; Molecular and Cellular Biology; Nucleotides; Other Genetics; Patients; Pharmacogenomics; Physics; Poly C; Poly U; Polymers; RNA; Rate; Reading; Recording of previous events; Research; Research Personnel; Resolution; Sampling; Scanning; Signal Transduction; Speed; Technology; Time; Training; Translating; Uracil; Vision; base; cell analyzer; copolymer; design; desire; improved; laptop; mammalian genome; nanopore; novel; programs; response; single molecule; success; technology development; tool; voltage

DESCRIPTION (provided by applicant): Electronic sequencing in nanopores shows great promise for inexpensive DNA sequencing at high speed and with minimal preparative steps. Such capability would lead to efficient reading of human SNPs or other genetic variations, which would in turn have a significant impact in pharmacogenomics and other disease treatments and preventions based on information from the patient's own genome. Recently, researchers identified the inability to regulate the speed of a molecule's translocation through the pore as the primary obstacle to realizing the sequencing potential of hemolysin nanopores. The proposed research will investigate the application of feedback control to substantially improve the ability to regulate molecule translocation speeds in a nanopore, thereby improving the ability to sequence with existing nanopore technology. In particular, the primary goal is to design novel hardware and software algorithms for feedback control of single polymers in a hemolysin nanopore on a microsecond time scale and with near angstrom precision. Such capability would contribute to the development of nanopore-based sequencing technologies, augment the efforts of the $1000/mammalian genome project, and be a revolutionary contribution to the realm of applied feedback control. The control algorithms would also leverage the long-term objective of the proposed effort: the development of a nanopore-based single cell analyzer. The device would enable one to efficiently determine the concentration of all mRNA in a single cell at an instant of time. This technology would improve the ability to accurately track molecular events that occur during cell differentiation, by reducing the number of cells required for event detection and increasing the time resolution of detection measurements. There are two primary aspects to the proposed research program that are necessary augmentations to my expertise in control. First, I will engage in a two-year intensive period of didactic training in relevant courses, including molecular and cellular biology, embryology, cell signaling, genomics and bioinformatics. The basic understanding gained is required for success in the application of control to problems in human health broadly, and in technology development for cell interrogation specifically. Second, I will participate in the $1000/mammalian genome project to learn about the physics and biology of the hemolysin nanopore. In parallel to the $1000 genome project, I will explore the controlled capabilities of the nanopore for efficient mRNA sequencing, using tools from bioinformatics and machine learning to translate the controlled response data into the identity of unknown nucleotides.

描述（由申请人提供）：纳米孔中的电子测序显示出以高速和最少的制备步骤进行廉价DNA测序的巨大前景。这种能力将导致人类SNP或其他遗传变异的有效阅读，这反过来将对基于来自患者自身基因组的信息的药物基因组学和其他疾病治疗和预防产生重大影响。最近，研究人员发现，无法调节分子通过孔的易位速度是实现溶血素纳米孔测序潜力的主要障碍。 拟议的研究将研究反馈控制的应用，以大幅提高调节纳米孔中分子移位速度的能力，从而提高利用现有纳米孔技术进行测序的能力。特别是，主要目标是设计新颖的硬件和软件算法，用于在微秒时间尺度上以近埃的精度反馈控制溶血素纳米孔中的单个聚合物。这种能力将有助于发展基于纳米孔的测序技术，增加1000美元/哺乳动物基因组计划的努力，并成为应用反馈控制领域的革命性贡献。控制算法还将利用拟议工作的长期目标：开发基于纳米孔的单细胞分析仪。该装置将使人们能够在一个瞬间有效地确定单个细胞中所有mRNA的浓度。该技术将通过减少事件检测所需的细胞数量和增加检测测量的时间分辨率来提高准确跟踪细胞分化期间发生的分子事件的能力。 有两个主要方面的拟议研究计划是必要的增强我的专业知识在控制。首先，我将参加为期两年的相关课程的密集教学培训，包括分子和细胞生物学，胚胎学，细胞信号，基因组学和生物信息学。所获得的基本理解是成功地将控制应用于广泛的人类健康问题，以及具体的细胞询问技术开发所必需的。其次，我将参加1000美元/哺乳动物基因组计划，了解溶血素纳米孔的物理学和生物学。在1000美元的基因组计划的同时，我将探索纳米孔用于高效mRNA测序的受控能力，使用生物信息学和机器学习的工具将受控响应数据转化为未知核苷酸的身份。