Pizza Lunch tomorrow!

December 12, 2011 § Leave a comment

Ian Swinburne (Megason Lab)
Fusing for Morphogenesis
Tuesday, December 13, 12:30pm, Goldenson 122

Don’t miss your pizza…

Synthetic biology center at MIT: Kickoff meeting

December 9, 2011 § 1 Comment

MIT has a new Synthetic Biology Center and they’re celebrating its opening tomorrow, Dec 10, with a kick-off meeting that involves talks from Doug Lauffenburger, Ron Weiss, Chris Voigt, Timothy Lu, Domitilla del Vecchio, Eric Lander, Peter Carr and others, including a series of student talks.

The meeting starts at 8.30 am with coffee, first talk at 9.  500 Tech Square.  Register here.

Theory Lunch this week

December 7, 2011 § Leave a comment

A whole-cell computational model of Mycoplasma genitalium

Markus Covert
Stanford University

Friday, 9 December, 12-1.30 in WAB563

A major challenge in the field of systems biology is to build a computational model of all the cellular processes in a living cell. A whole cell model will provide a better understanding of cellular physiology as well as multifaceted behaviors such as complex disease states. It may also serve as a predictive tool to guide cellular engineering and synthetic biology. I will describe our efforts to build a comprehensive model of the lifecycle of a single living cell that simulates all known gene functions. Our model system is Mycoplasma genitalium, the bacterium with the smallest known self-replicating genome. The model incorporates the cross talk between all of the cellular processes including metabolism, transcription, translation, replication, and cell division among others. To integrate these diverse processes, we have created a novel modeling approach that represents different biological functions as separate modules, each implemented with different mathematical representations. I will end with some discussion of what this model has been teaching us as we compare our simulations with in-house experiments.

Current TL schedule here

Invasive frog species seen in downtown Boston

December 5, 2011 § Leave a comment

Our artist friend Brian Knep has been commissioned to create a mega-frog piece on the facade of a building in downtown Boston.

Rapture, 2011 from Brian Knep on Vimeo.

Brian does love to see those frogs struggle to be free… and this time there is more than one metamorphosis to watch out for.    Go and check it out if you can — the building is right behind the Boston Common movie theatre.

Theory Lunch this week

December 1, 2011 § Leave a comment

Selective constraints on bacterial signaling proteins
Michael Laub
Department of Biology, MIT

Friday, 2 Dec 2011, 12-2 pm
Warren Alpert 563 – HMS

Our lab is interested in the specificity and evolution of signaling pathways. We study two-component signal transduction systems, the predominant form of signaling in bacteria, which involve sensor histidine kinases and their cognate substrates. We have previously shown that the specificity of kinase-substrate interactions is dictated at the level of molecular recognition and relies on a relatively small set of residues. We can now probe the evolution of kinase-substrate specificity by focusing on changes that occur to these residues. We are probing the selective pressures that influence these residues and, in particular, trying to understand how gene duplication impacts specificity. For example, how are the proteins produced by duplication insulated from one another and from other existing pathways? Can we infer the mutational trajectories followed by duplicates and what, if anything, constrains these trajectories?

Current theory lunch schedule here.

Pizza tomorrow

November 28, 2011 § Leave a comment

Alexandra Zidovska (Mitchison Lab)

“Interphase Chromatin Dynamics or, An Introduction to Nuclear Physics”

Tomorrow, 11/29/2011, 12.30 p, Goldenson 122.

(Don’t miss your pizza!)

Theory Lunch this week

November 16, 2011 § Leave a comment

François Nédélec
Cell Biology and Biophysics
European Molecular Biology Laboratory (EMBL)

How to pattern molecular motors to control the motion of fibers
Friday, November 18th, 12:00-2pm
Warren Alpert 563

In a “gliding assay” cytoskeletal fibers are propelled by molecular motors immobilized on a substrate. When the motors are uniformly distributed on the substrate, the path of the fibers is usually tortuous, and they move equally in all directions. To use the motion of these fibers for example in a micro-device, it is however necessary to be able to direct the fibers in a particular direction. Different techniques have been proposed to achieve this, for instance using external forces or surrounding the fibers with ratchet-like walls. In this lecture, we will argue that sparsely positioning motors over a flat surface is sufficient to precisely control the direction of fiber motility. We will present different patterns on which the motion of the fibers is directed, and we will also brainstorm together to see if we can discover more patterns. We will also discuss ways to sort apart fibers of different length. The conclusion will be that the fibers can be controlled at will, provided that one is able to pattern motors with precision on the substrate.

Theory Lunch schedule here

PIzza Lunch TODAY

November 15, 2011 § Leave a comment

Michael Baym (Kishony Lab)

Microstructure in the Soil Resistome

Tuesday, November 15, 12:30pm

Goldenson 122

… don’t miss your pizza…

No Theory Lunch this week

November 10, 2011 § Leave a comment

… Friday is Veteran’s day, for those of you who haven’t noticed.

TL schedule here.

Theory lunch this week

November 1, 2011 § Leave a comment

Degeneracy in the brain and the maintenance of robust homeostasis

4 Nov 2011

James Schwaber
Daniel Baugh Institute for Functional Genomics & Computational Biology
Thomas Jefferson University, Philadelphia

12.00 — 1.30 pm, Warren Alpert Building (HMS) 563

How does the brain work? What is “the neural code”? How is the elegant structure of the brain used, is it an information processing machine? The complexity of the brain suggests that neuroscience offers rich opportunities for systems approaches. However, there is little interaction between systems biology and neuroscience, creating a need and opportunity to relate observed complexity to emergence of robust function.

I hope to provoke discussion of these issues using the specific example of the brain’s regulation of physiological homeostasis, in which there is a surprising disconnect between the robust, linear input-output regulatory behavior and highly conditional central neuronal measures, across all scales from genetic to neural circuit.

Brain data shows complexity and heterogeneous variability. It seems that robust controlled-system responses ride on top of variable and dynamic underlying mechanisms, suggesting that the interactions of the components provide robust control and that system responses are not particularly sensitive to the variability of any one component (or possibly many components).

TL schedule here

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