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Course
| Code: | 8.591J |
| Subject: | Biology |
| Views: | 26,432 |
Systems Biology
Video Lectures
Displaying all 24 video lectures.
Lecture 1 Play Video |
Introduction to the class and overview of topics In this lecture, Prof. Jeff Gore introduces the topics of the course, which broadly include gene networks and cellular decision-making, evolutionary systems biology, and ecological systems biology. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 2 Play Video |
Input function, Michaelis-Menten kinetics, and cooperativity Prof. Jeff Gore discusses the kinetics of gene expression. Simple input-output relationships and chemical/enzyme kinetics. Response time for stable proteins. Ultrasensitivity: cooperative binding or multimer molecular titration. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 3 Play Video |
Autoregulation, feedback and bistability Prof. Jeff Gore continues his discussion of gene expression, this time with a focus on autoregulation (when a gene regulates its own expression). He begins by discussing the network motif, then moves on to both negative and positive autoregulation. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 4 Play Video |
Synthetic biology and stability analysis in the toggle switch In this lecture, Prof. Jeff Gore discusses the toggle switch, or two genes that repress each other. He then moves on to dimensionless equations and stability analysis. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 5 Play Video |
Oscillatory genetic networks Prof. Jeff Gore introduces oscillatory genetic networks. He asks why oscillations are useful, and why might we want to design an oscillator. Central to the lecture is a Nature article: A synthetic oscillatory network of transcriptional regulators. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 6 Play Video |
Graph properties of transcription networks Prof. Jeff Gore continues the discussion of oscillators, including alternative designs for oscillators. He then discusses the article Emergence of scaling in random networks, by Barabási & Albert. The final topic is network motifs. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 7 Play Video |
Feed-forward loop network motif In this lecture, Prof. Jeff Gore discusses the feed-forward loop (FFL) network motif. He covers coherent type 1 (C1) and the incoherent type 1 (I1) FFL motifs. This discussion of network motifs is extended to larger structures. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 8 Play Video |
Introduction to stochastic gene expression This lecture by Prof. Jeff Gore centers on discussion of one of his favorite scientific papers: "Probing gene expression in live cells, one protein molecule at a time," by Yu et al. http://dx.doi.org/10.1126/science.1119623 License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 9 Play Video |
Causes and consequences of stochastic gene expression In this lecture, the class analyzes a simple model of gene expression, first to understand the deterministic behavior of the model, and then to look at the stochastic behavior of the model. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 10 Play Video |
Stochastic modeling Prof. Jeff Gore discusses modeling stochastic systems. The discussion of the master equation continues. Then he talks about the Gillespie algorithm, an exact way to simulate stochastic systems. He then moves on to the Fokker-Planck equation. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 11 Play Video |
Life at low Reynold’s number In this lecture, Prof. Jeff Gore asks, and answers, questions like how do bacteria find food? How do they know which direction to swim, and how do they swim? All of these questions relate to the low Reynold's number regime in which bacteria live. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 12 Play Video |
Robustness and bacterial chemotaxis In this lecture, Prof. Jeff Gore continues his discussion of bacterial chemotaxis, or how bacteria find food. The principle is a biased random walk of runs and tumbles, and is a shown to display perfect adaptation. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 13 Play Video |
Robustness in development and pattern formation This lecture by Prof. Jeff Gore is about the mechanisms of biological pattern formation. One mechanism discussed is diffusion. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 14 Play Video |
Microbial evolution experiments and optimal gene circuit design In this lecture, Prof. Jeff Gore discusses the Nature article "Optimality and evolutionary tuning of the expression level of a protein," with emphasis on the connection between theory, prediction, and experiment. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 15 Play Video |
Evolution in finite populations This lecture by Prof. Jeff Gore is on the topic of evolution in finite populations. Several aspects are covered, including the Moran process, neutral and non-neutral evolution, and stochastic extinction of beneficial mutants. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 16 Play Video |
Clonal interference and the distribution of beneficial mutations In this lecture, Prof. Jeff Gore covers the principles of the scientific article "An equivalence principle for the incorporation of favorable mutations in asexual populations." License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 17 Play Video |
Fitness landscapes and sequence spaces In this lecture, Prof. Jeff Gore continues his discussion of clonal interference (CI) and the equivalence principle. He discussed CI and the rate of evolution. And finally he thinks about evolution from the perspective of rugged fitness landscapes. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 18 Play Video |
Evolutionary games In this lecture, Prof. Jeff Gore begins with a review problem on rugged landscaped. He then moved on to the main subject: evolutionary game theory. This includes the Nash equilibrium, the prisoner's dilemma, and the hawk-dove game. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 19 Play Video |
Survival in fluctuating environments In this lecture, Prof. Jeff Gore discusses the regulation of genes in response to changing environments. He discusses a few theories for phenotypic heterogeneity and examples from biology. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 20 Play Video |
Parasites, the evolution of virulence and sex This lecture by Prof. Jeff Gore covers two topics. The first is the evolution of virulence, and how to model host-parasite interactions. The second is the evolutionary benefit of sex. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 21 Play Video |
Interspecies interactions This lecture by Prof. Jeff Gore covers models and experiments of predator-prey interactions and oscillations. He begins with the Lokta-Volterra model, which has been called both "bad" (mathematically speaking) and "profoundly important." License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 22 Play Video |
Ecosystem stability, critical transitions, and biodiversity In this lecture, Prof. Jeff Gore discusses the stability, resilience, and diversity of populations at a systems level. He begins by considering a single population, and then moves on to a simple model of interactions between species. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 23 Play Video |
Dynamics of populations in space In this lecture, Prof. Jeff Gore finishes the discussion of the Lotka-Volterra competition model. He then moves on to the topic of non-transitive interactions, what he calls rock-paper-scissor interactions. License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
Lecture 24 Play Video |
The neutral theory of ecology In this lecture, Prof. Jeff Gore asks why are some species abundant and others rare? Are there universal patterns at play? And what lead to these patterns? License: Creative Commons BY-NC-SA More information at http://ocw.mit.edu/terms More courses at http://ocw.mit.edu |
