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February 2007


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=?iso-8859-1?Q?Frank_Doyle?= <[log in to unmask]>
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=?iso-8859-1?Q?Frank_Doyle?= <[log in to unmask]>
Tue, 27 Feb 2007 11:16:53 -0500
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Department of Chemical Engineering & Biomolecular Science and Engineering
Institute for Collaborative Biotechnologies
University of California, Santa Barbara, CA

Project 1: Network Inference and Properties of a Steroidogenesis Metabolic
This proposal seeks to understand complex systems by examining how a model
biological network responds to, compensates for, and fails when exposed to
different stressors. The susceptibility of a network to failure is
greatly dependent upon how the different elements are controlled and
connected, otherwise known as the network architecture. We propose to
study the architecture and modularity of the steroidogenesis metabolic
network for synthesis of estradiol from cholesterol in fish ovaries. To
understand the role of architecture in network fragility, we will
investigate how the transcriptional or gene regulatory layer of control is
integrated into the steroidogenesis network to create a robust
architecture. This project is a collaborative endeavor with Chemical
Engineers, Molecular Biologists and Ecologists.

Project 2: Signal Integration in Control of Coral Lifescycles as a Model
for Engineering Networks
We aim to build mathematical models that describe the phenomena of
reproduction in coral as well as larval metamorphosis, that account for
both the response to global signals (solar and lunar cues), as well as
local (chemical and neuronal signaling cues between individual corals in a
population and between individual polyps in a colony). This integrated
biological system exhibits striking parallels to the multi-scale networks
required for engineering applications. The resulting multi-scale model to
be derived from the proposed work will span from the molecular details of
intra-colony and inter-colony signaling and the corresponding regulation
of key genes and proteins to the coordinated yet disseminated interaction
between the network of individuals and the local- and global-scale
environment. This project is a collaborative endeavor with Chemical
Engineers, Marine Biologists and Ecologists.

Project 3: Systems Approach to the Neuronally Controlled Adaptive Optical
Output in Cephalopods
The nervous systems of cephalopods (octopi, squid and cuttlefish) are
capable of driving adaptive changes in the color, reflectance and optical
appearance of the skin within milliseconds. The nervous systems of these
animals already have provided highly tractable models for experimental
analyses of neuronal structure and mechanisms of action for more than 50
years; the mechanism of neuronal conduction and the action potential were
discovered in studies of the giant nerve cells of the squid. In a project
that bridges the established strengths of systems engineers and molecular
biologists, this project seeks to analyze the systems-level control of the
dynamic, neuronally mediated control of the optical patterns of the skin
in squid. In particular, we will develop a detailed signal transduction
network model that relates the cue to the cellular response. This project
is a collaborative endeavor with Chemical Engineers, Molecular Biologists
and Marine Biologists.

The project openings are in the laboratory of Prof. Frank Doyle, and would
entail, primarily, the computational modeling and systems analysis of the
respective organisms.

The ideal candidate(s) would have experience in mathematical
modeling of biological systems and would have sufficient background in the
biosciences to interact with molecular biologists, marine biologists
and/or ecologists. Interested candidates should send their CVs, including
contact information for references, to Professor Doyle
([log in to unmask]).