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.


  1. 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 4-5, KH 101

  2. 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 two-component 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
    Meeting Time & Place: Th 4-5 KH 105

  3. 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 time-delay 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 Anti-termination
    Members: Jay Raol, Blair Christian, Eddie Castillo, Jordan Almes, Steve Cox.
    Meeting Time & Place: F 2-3 in DH 1044.

  4. 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)
    Meeting Time & Place: T 12:10-1 DH 2014

  5. Statistical Genomics:
    Meeting Time & Place: Th 5:30-6:30 DH 1042.