Spring 2004 BioMath PFUGs
Each
Undergrad will have a Graduate student mentor who will in turn
have a
Postdoctoral mentor who will in turn have a Faculty mentor.
Such a team will be referred to as a PFUG, pronounced like fugue:
a composition in which a subject is announced by one voice and then
developed contrapuntally by each of usually two or three other voices.
PFUGs
 Neuronal Calcium Signaling: Calcium is the second messenger
that leads to long term change in the brain. We will investigate the
seductive hypothesis of Berridge that the
endoplasmic reticulum (ER) constitutes a neuron within a neuron.
We will survey, assimilate and synthesize
(i) Sources of neuronal calcium: Calcium channels and NMDA receptors,
(ii) Models of buffering and propagation via calcium induced calcium release
and the roles played by IP3 and mGluRs.
(iii) The means by which intracelluar calcium is imaged and quantified.
(iv) The role calcium plays in modulating action potentials via, e.g., calcium
gated potassium channels.
(v) The role calcium plays in triggering the CREB gene circuit.
Members: Zack Kilpatrick, Jane Hartsfield, Brad Peercy, Megan Abadie,
Joanna Papakonstantinou, Steve Cox.
Meeting Time & Place: M 45, KH 101
 Oxygen sensing in E. Coli: Bacteria such as E. Coli have an
amazing ability to thrive in extreme environments. We shall investigate
the sensing mechanisms they employ for dioxygen and how these signals
regulate, and are regulated by, downstream metabolism.
Gunsalus
has produced alot of nice experimental work. Here is one of his survey papers.
We will survey, assimilate and synthesize
(i) Models of the twocomponent ArcAB sensor. Starting with 5 works by
Lin's group
1 and 2 and
3 and 4 and
5
(ii) Models of the FNR
sensor/reulator.
(iii) The role ArcAB and FNR in gene regulation.
(iv) Applications to anaerobic production of useful waste products.
Members: Jesse Turner, Brad Peercy, Kelly Benedict, Steve Cox,
Jay Raol, Megan Abadie, Kurt Icenogel and Joey Neggers
Software
Meeting Time & Place: Th 45 KH 105
 Phage Lambda:
The phage lambda gene network makes use of several basic gene
regulation
strategies common to many other more complicated gene networks. We wish to
accurately
model these basic strategies using such tools as boolean logic, ordinary
differential
equations, and timedelay differential equations in the hopes of being able to
apply
our phage lambda modeling techniques to more complicated networks.
Here is a glimpse of some of last year's
work. This semester, we
will focus on
(i) Modeling with
Probabilistic Boolean Nets or Bayesian nets
(ii) Modeling Positive and negative feedback loops
(iii) Modeling Cooperative binding
(iv) Modeling Antitermination
Members: Jay Raol, Blair Christian, Eddie Castillo,
Jordan Almes, Steve Cox.
Software
Meeting Time & Place: F 23 in DH 1044.
 Reverse Engineering:
VIGRE reverse engineers investigate methods for inferring network
structure
and kinetics from gene chip data. The challenge is to marry
descriptive models
of gene interaction with powerful numerical optimization algorithms.
Thus far, we have investigated three gene network paradigms:
(i) Nonlinear ODEs derived from the Law of Mass Action;
(ii) Boolean networks, which force genes to be either "on" or
"off";
(iii) Linearized ODEs with structured coefficient matrices.
With each model is associated the reverse engineering problem:
determine model parameters that agree with a given set of gene
expression data.
ODE models (i) yield difficult optimization problems that restrict
network size;
Boolean models (ii) are simpler to reverse engineer, but may be too
restrictive
to fully capture the data.
Structured matrices (iii) provide a middle ground where we can leverage
linear algebra ideas for efficient reverse engineering.
Members: Nick Henderon, Jordan Almes, Mark Embree,
Robert Mallery (abroad)
Software
Meeting Time & Place: T 12:101 DH 2014

Statistical Genomics:
Meeting Time & Place: Th 5:306:30 DH 1042.