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CCMB Distinguished Lectures Series 2007-2008
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CCMB Distinguished Lecture Series
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Jim Collins
Center for BioDynamics
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Department of Biomedical Engineering
Boston University
Engineering Gene Networks:
Integrating Synthetic Biology & Systems Biology
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Abstract:
Many fundamental cellular processes are governed by genetic programs which employ
protein-DNA interactions in regulating function. Owing to recent technological advances,
it is now possible to design synthetic gene regulatory networks, and the stage is
set for the notion of engineered cellular control at the DNA level.
Theoretically, the biochemistry of the feedback loops associated with protein-DNA
interactions often leads to nonlinear equations, and the tools of nonlinear analysis
become invaluable. In this talk, we describe how techniques from nonlinear dynamics
and molecular biology can be utilized to model, design and construct synthetic gene
regulatory networks. We present examples in which we integrate the development of
a theoretical model with the construction of an experimental system. We also discuss
the implications of synthetic gene networks for biotechnology, biomedicine and biocomputing.
In addition, we present integrated computational-experimental approaches that enable
construction of first-order quantitative models of gene-protein regulatory networks
using only steady-state expression measurements and no prior information on the
network structure or function. We discuss how the reverse-engineered network models,
coupled to experiments, can be used: (1) to gain insight into the regulatory role
of individual genes and proteins in the network, (2) to identify the pathways and
gene products targeted by pharmaceutical compounds, and (3) to identify the genetic
mediators of different diseases.
Wednesday, November 7th, 2007
4:00pm
CIT Building, Room 227
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CCMB Distinguished Lecture Series
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James Yorke, Ph.D.
Distinguished University Professor of Mathematics and Physics
Institute for Physical Sciences and Technology (IPST)
University of Maryland
Determining the DNA sequence,
a billion dollar logic puzzle
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Abstract:
The genome of an individual is the collection of DNA in each of his/her/its cells.
It can be expressed as one or more sequences of the letters A, C, G, T. For mammals
the genome has about 3 billion letters while for a bacteria it has a couple million.
The dominant method used for determining the sequence is called whole genome shotgun
assembly. Using this method, The National Institutes of Health has spent about one
billion dollars determining genomes of many species in the past five years. Parts
of genome turn out to be easier to determine than other parts but overall each genome
becomes a giant jigsaw puzzle. At the University of Maryland, we try to find techniques
for solving as much of the puzzle as possible. The most difficult parts of puzzle
to assemble are often the parts that have been mutating the most in the recent millions
of years. We are also trying to determine the patterns of repeats.
Monday, October 15th, 2007
4:00 pm, CIT Building, Room 241 ~ SWIG Boardroom
Hosted by: Suzanne Sindi
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CCMB Distinguished Lecture Series
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Nancy Amato, Ph.D
Parasol Lab, Department of Computer Science
Texas A&M University
Using Motion Planning to Study Molecular Motions
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Abstract:
Protein motions, ranging from molecular flexibility to large-scale conformational
change, play an essential role in many biochemical processes. For example, some
devastating diseases such as Alzheimer's and bovine spongiform encephalopathy (Mad
Cow) are associated with the misfolding of proteins. Despite the explosion in our
knowledge of structural and functional data, our understanding of protein movement
is still very limited because it is difficult to measure experimentally and computationally
expensive to simulate.
In this talk we describe a method we have developed for modeling protein motions
that is based on probabilistic roadmap methods (PRM) for motion planning. Our technique
yields an approximate map of a protein's potential energy landscape and can be used
to generate transitional motions of a protein to the native state from unstructured
conformations or between specified conformations. We describe a method based on
rigidity theory that allows us to sample conformation space more efficiently than
our initial sampling strategy and enables us to study a broader range of motions
for larger proteins and new analysis tools that enable us to extract kinetics information,
such as folding rates. For example, we show that rigidity-based sampling results
in maps that capture subtle folding differences between protein G and its mutations,
NuG1 and NuG2, and we illustrate how our technique can be used to study large-scale
conformational changes in calmodulin, a 148 residue signaling protein known to undergo
conformational changes when binding. More information regarding our work, including
an archive of protein motions generated with our technique, are available from our
protein folding server:
http://parasol.tamu.edu/foldingserver/.
Wednesday, October 10th, 2007
4:00pm, CIT Bldg, Room 241 ~ SWIG Boardroom
Hosted by: Franco P. Preparata
Refreshments will be served at 3:45pm
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