Guest Seminars
Upcoming Seminars
February 18th 2008
Amy Schmid, Institute for Systems Biology (CV)
4:15pm, Monday, February 18, 2008.
French Family Science Center Room 2231
Title: Systems biology in archaea: anatomy of cell state transitions in response to oxygen.
Abstract: Adjustment of physiology in response to changes in oxygen availability is critical for the survival of all organisms. However, the chronology of events and the regulatory processes that determine how and when changes in environmental oxygen tension result in an appropriate cellular response is not well understood at a systems level. Therefore, transcriptome, proteome, ATP, and growth changes were analyzed in a halophilic archaeon to generate a temporal model that describes the cellular events that drive the transition between the organism’s two opposing cell states of anoxic quiescence and aerobic growth. According to this model, upon oxygen influx, an initial burst of protein synthesis precedes ATP and transcription induction, rapidly driving the cell out of anoxic quiescence, culminating in the resumption of growth. This model also suggests that quiescent cells appear to remain actively poised for energy production from a variety of different sources. Dynamic temporal analysis of relationships between transcription and translation of key genes suggests several important mechanisms for cellular sustenance under anoxia as well as specific instances of posttranscriptional regulation. In the future, research in my laboratory will be directed toward understanding the mechanisms behind these posttranscriptional regulatory processes in response to oxygen in an archaeal model organism.
February 20th, 2008
Ilya Nemenman,
Los Alamos National Laboratory (CV)
3:30 PM, February 20, 2008
Rm 128 PHYSICS
Title: Exploring dynamics and function of small biochemical networks.
Abstract: In a recent article in APS News, John Hopfield, one of the founders of what has now become quantitative and systems biology, has defined physics as "The idea ... that the world is understandable." As a physicist working on biological problems, I pursue this understanding as the ultimate goal. Unfortunately, even for the simplest cellular networks, understanding their function is often obscured behind long part lists of interaction partners, wiring diagrams, and differential equations. In this talk, I will describe how ideas of statistical physics and information theory allow us to make small steps towards formulation of and answers to questions like: What are the signal processing capabilities of stochastic biochemical networks? Which functions can they perform? How important is stochasticity? How can we understand network dynamics without microscopic simulations? While addressing these questions, I will also show examples of cross-fertilization between physics and systems biology: on the one hand, physics will suggest tools for faster simulation and deeper understanding of the networks dynamics, and, on the other, study of a biological problem will show an unexpected and illuminating connection between seemingly unrelated areas of theoretical physics.
Coffee and cookies before the presentation at 3:15 pm, and refreshments after the presentation will both be served in Room 128.
Previous Seminars
February 11th, 2008
Suzanne Gaudet, Harvard Medical School Monday
4:15pm February 11, 2008
French
Family Science Center Auditorium Room 2231
Title: Regulation of apoptosis by death-receptor ligands: a systems perspective
Abstract: The appropriate control of cell death in multicellular organisms is critical to homeostasis and health. While death receptor ligands promote cell death by activating caspases, these pro-death signals can be opposed by pro-survival signals in vivo. How do cells weigh these opposing signals to make a decision to die or to live? To tackle this question, two types of computational modeling approaches are combined with quantitative measurements from single cells and populations of cells. First, detailed mechanistic models of relevant signaling networks are used to investigate which factors control caspase activation dynamics. Second, descriptive, data-driven models have led to the exciting discovery of a TNF-induced autocrine cascade, providing evidence for the involvement of a network of extracellular signals in the cell death decision. These examples show how two different systems-level approaches have led to distinct types of insights in the cell death decision process.