麻省理工学院“开放式课程网页” | 物理学 | 8.591J 2004秋季课程：系统生物学

本课程网页中含（M）标记的档案需由MATLAB®软件运行。
MATLAB® software is required to run the .m files in this section.

生物学建议阅读资料
Suggested Readings in Biology

以下Bruce Alberts等著，《细胞分子生物学》，第四版中的部分，New York: Garland Science, 2002.。
The following sections from Alberts, Bruce, et al. Molecular Biology of the Cell. 4th ed. New York: Garland Science, 2002. ISBN: 0815332181, are suggested:

RNA和蛋白质的合成
RNA and Protein Synthesis
基因调控概述
Overview of Gene Control
基因如何调控其工作
How Genetic Switches Work
细胞讯息传导的基本原理
General Principles of Cell Signaling

以下课程讲义由Alexander van Oudenaarden教授及其它下列所提及的作者提供。
Downloadable course notes are included courtesy of Prof. Alexander van Oudenaarden as well as any additional authors noted in the table below.
讲	课程单元	阅读资料
第一部分：系统微生物学－将细胞视成一个完全搅拌反应器 Part I: Systems Microbiology - 'The Cell as a Well-stirred Bioreactor'
1	简介 Introduction 酵素动力学 Michaelis-Menten Kinetics
2	平衡结合 Equilibrium Binding 合作现象 Cooperativity	酵素动力学 (PDF) Michaelis-Menten Kinetics (PDF) 相关MATLAB® 档案 (M) Associated MATLAB® code file (M)
3	嗜菌体 Lambda Phage 多稳定性 Multistability	嗜菌体的基因开关(PDF) A Genetic Switch in Lamba Phage (PDF) 相关MATLAB® 档案 (M) Associated MATLAB® code file (M) Hasty, Jeff, Joel Pradines, Milos Dolnik, and J. J. Collins. 〈基因的干扰基底开关和放大器〉，《美国国家科学学会公报》97, no. 5 (Feb 29, 2000): 2075-80. Hasty, Jeff, Joel Pradines, Milos Dolnik, and J. J. Collins. "Noise-based Switches and Amplifiers for Gene Expression." Proc. Natl. Acad. Sci. USA 97, no. 5 (Feb 29, 2000): 2075-80.
4	多稳定性（继续上次课程） Multistability (cont.)	Isaacs, Farren J., Jeff Hasty, Charles R. Cantor, and J. J. Collins.〈自我调节基因模块的预测及测量〉，《美国国家科学学会公报》 100, no. 13 (June 24, 2003): 7714-19. Isaacs, Farren J., Jeff Hasty, Charles R. Cantor, and J. J. Collins. "Prediction and Measurement of an Autoregulatory Genetic Module." PNAS 100, no. 13 (June 24, 2003): 7714-19.
5	合成基因开关 Synthetic Genetic Switches	合成基因开关(PDF) Synthetic Genetic Switches (PDF) Gardner, Timothy S., Charles R. Cantor, and James J. Collins. 〈在大肠杆菌中建构一个基因摇头开关〉，《自然》403, no. 6767 (January 20, 2000): 339-42. Gardner, Timothy S., Charles R. Cantor, and James J. Collins. "Construction of a Genetic Toggle Switch in Escherichia coli." Nature 403, no. 6767 (January 20, 2000): 339-42.
6	稳定性分析 Stability Analysis	稳定性分析(PDF) Stability Analysis (PDF)
7	大肠杆菌的趋化性介绍 Introduction E. coli Chemotaxis
8	格式化和稳健形趋化性模型的比较 Fine-tuned versus Robust Chemotaxis Models	大肠杆菌的趋化性建模(PDF) Modeling Escherichia coli chemotaxis (PDF) 相关MATLAB® 档案(M) Associated MATLAB® code file (M) Spiro, Peter A., John S. Parkinson, and Hans G. Othmer. 〈细菌趋化性中的刺激及适应模型〉，《美国国家科学学会公报》 94, no. 14 (July, 1997): 7263–68. Spiro, Peter A., John S. Parkinson, and Hans G. Othmer. "A Model of Excitation and Adaptation in Bacterial Chemotaxis." Proc. Natl. Acad. Sci. USA 94, no. 14 (July, 1997): 7263–68.
9	掩饰趋化性 Wrapping up Chemotaxis	生物震荡器(PDF) Biological Oscillators (PDF)
10	基因震荡器 Genetic Oscillators	生物震荡器(PDF) Biological Oscillators (PDF) 相关MATLAB® 档案(M) Associated MATLAB® code file (M) Elowitz, Michael B., and Stanislas Leibler.〈转路调控的合成震荡网络〉，《自然》403, no. 6767 (January 20, 2000): 335-8 Elowitz, Michael B., and Stanislas Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403, no. 6767 (January 20, 2000): 335-8.
11	基因震荡器（继续上次课程） Genetic Oscillators (cont.)	Routh-Hurwitz测试法(PDF) Routh-Hurwitz (PDF) 相关MATLAB®档案 (M) Associated MATLAB® code file (M) Myers, and Alexander J. Ninfa.〈大肠杆菌中基因线路展示摇头开关或震荡行为的发展〉，《细胞》 113, no. 5 (May 30, 2003): 597-607. Atkinson, Mariette R., Michael A. Savageau, Jesse T. Myers, and Alexander J. Ninfa. "Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli." Cell 113, no. 5 (May 30, 2003): 597-607.
12	随机化学动力学 Stochastic Chemical Kinetics	生化系统中干扰的来源和结果(PDF) The Origin and Consequences of Noise in Biochemical Systems (PDF) (Courtesy of Alexander van Oudenaarden and Mukund Thattai. Used with permission.)
13	随机化学动力学（继续上次课程） Stochastic Chemical Kinetics (cont.)
第二部分：细胞系统生物学－将细胞视成一个既有浓度梯度的分隔系统 Part II: Cell Systems Biology - 'The Importance of Diffusion and Gradients for Cellular Regulation'
14	细胞系统生物学简介 Introduction Cell Systems Biology Fick法则 Fick's Laws
15	局部刺激 Local Excitation 整体抑制理论 Global Inhibition Theory	局部刺激，整体抑制理论(PDF) Local Excitation, Global Inhibition Model (PDF)
16	局部刺激（继续上次课程） Local Excitation (cont.) 整体抑制理论（继续上次课程） Global Inhibition Theory (cont.)
17	大肠杆菌中快速极间震荡 Rapid Pole-to-pole Oscillations in E. coli	〈细菌的动力学隔间：大肠杆菌中正确的分隔〉，《物理评论通讯》 87, no. 27 (December 31, 2001). Howard, Martin, Andrew D. Rutenberg, and Simon de Vet. "Dynamic Compartmentalization of Bacteria: Accurate Division in E. Coli." Physical Review Letters 87, no. 27 (December 31, 2001).
18	大肠杆菌中快速极间震荡（继续上次课程） Rapid Pole-to-pole Oscillations in E. coli (cont.)
19	真核生物的梯度感应模型 Models for Eukaryotic Gradient Sensing	真核生物的梯度感应模型(PDF) Models for Eukaryotic Gradient Sensing (PDF) 相关MATLAB® 档案(M) Associated MATLAB® code file (M) Narang, Atul, K. K. Subramanian, and D. A. Lauffenburger.〈以受体调控的磷脂膜讯息传导动力学为基础的梯度感应趋化性数学模型〉，《生医工程年鉴》 29, no. 8 (2001): 677-91. Narang, Atul, K. K. Subramanian, and D. A. Lauffenburger. "A Mathematical Model for Chemoattractant Gradient Sensing based on Receptor-regulated Membrane Phospholipid Signaling Dynamics." Annals of Biomedical Engineering 29, no. 8 (2001): 677-91.
20	真核生物的梯度感应模型（继续上次课程） Models for Eukaryotic Gradient Sensing (cont.)	Postma, Marten, and Peter J. M. Van Haastert.〈趋化性细胞梯度感应的扩散易位模型〉，《生物物理期刊》81, no. 3 (September, 2001): 1314-23. Postma, Marten, and Peter J. M. Van Haastert. "A Diffusion–Translocation Model for Gradient Sensing by Chemotactic Cells." Biophysical Journal 81, no. 3 (September, 2001): 1314-23.
21	细胞骨架动力学建模 Modeling Cytoskeleton Dynamics	Dogterom, Marileen, and Stanislas Leibler.〈物理层面的微管结构生长与调控〉，《物理评论通讯》 70, no. 9 (March 1, 1993). Dogterom, Marileen, and Stanislas Leibler. "Physical Aspects of the Growth and Regulation of Microtubule Structures." Physical Review Letters 70, no. 9 (March 1, 1993).
22	细胞骨架动力学建模（继续上次课程） Modeling Cytoskeleton Dynamics (cont.)	Cytrynbaum, E. N., V. Rodionov, and A. Mogilner.〈动力蛋白依赖性自我组织微管星状体的数值模型〉，《细胞科学期刊》117, no. 8 (March 15, 2004): 1381-97. Cytrynbaum, E. N., V. Rodionov, and A. Mogilner. "Computational Model of Dynein-dependent Self-organization of Microtubule Asters." Journal of Cell Science 117, no. 8 (March 15, 2004): 1381-97.
第三部分：发育系统生物学－由单一细胞建构一个生物体 Part III: Developmental Systems Biology - 'Building an Organism Starting From a Single Cell'
23	数量感应 Quorum Sensing	You, Lingchong, Robert Sidney Cox III, Ron Weiss, and Frances H. Arnold.〈胞间讯息传递和调控性杀戮的计划形群体控制〉，《自然》 428, no. 6985 (April 22, 2004): 868-71. You, Lingchong, Robert Sidney Cox III, Ron Weiss, and Frances H. Arnold. "Programmed Population Control by Cell-Cell Communication and Regulated Killing." Nature 428, no. 6985 (April 22, 2004): 868-71.
24	期末习题集咨询时间 Final Problem Set Question Hour
25	果蝇发育学 Drosophila Development	Houchmandzadeh, Bahram, Eric Wieschaus, and Stanislas Leibler.〈早期果蝇胚胎发育精准度和比例的建立〉，《自然》 415, no. 6873 (February 14, 2002): 798-802. Houchmandzadeh, Bahram, Eric Wieschaus, and Stanislas Leibler. "Establishment of Developmental Precision and Proportions in the Early Drosophila embryo." Nature 415, no. 6873 (February 14, 2002): 798-802.