CAAM 499, Section 1, VIGRE Seminar, Fall 2004

Inverse Problems in Biology

When & Where: Everybody: Wednesdays 5-6 PM in HUM 117
Metabolic Engineering PFUG: Thursdays 1-2 PM in DH 1064
Computational Neuroscience PFUG: Thursdays 4-5 PM in KH 105

Instructors: Steve Cox, and Brad Peercy,

Content: 7 or 8 lectures (see below), after which 2 working groups, or PFUGs, will come together each week to share their findings and common interests. One PFUG will focus on Computational Neuroscience and the second on Metabolic Engineering.

Prereqs: CAAM 335 or MATH 211 or CoI.

1 credit: Participate in Wednesday seminar meetings and complete two writing assignments.
2 credits: Take an active role in a PFUG and complete two writing assignments.
3 credits: Take an active role in a PFUG and complete four writing assignments.
To complete a writing assignment is to submit (at least) two type written, 1-inch margin, double-spaced, 12pt font pages that review a relevant lecture, paper or text.

August 25: Adjoint Methods for Nonlinear Least Squares Problems with ODE constraints.
September 1: Continuation of last time. September 8: Applications to slug learning. Background. A single cell net and its code. The full report.
September 15: Adjoint Methods for Nonlinear Least Squares Problems with PDE constraints. Applications to channel localization.
September 22: Oxygen handling in E Coli.
September 29: AWOL
October 6: Carbon and Metabolite Stoichiometry. We will master this paper and exercise this code
October 13: LCMS, GCMS and NMR. Start with this nice Overview . Basic Mass Spectrometry . Gas Chromatography / Mass Spec The Movie
October 20: Flux determination
Nick Henderson.
October 27: Elementary Flux Modes
Fernando Acosta.
November 3: Progress in Neuronal Calcium Signaling
November 10: mGluRs and cerebellar LTD
Jane Hartsfield will serve up the highlights of this paper
November 17: Calcium and Metabolism
Steve Cox will fuse the 2 pfugitos by investigating the role of mitochondria in calcium signaling. We will follow this paper by Friel . Each (eukaryotic) cell has two organelles with distinct transition points in their handling of calcium, i.e., distinct concentrations at which they transition from sink to source. Friel studies these in isolation and then in tandem. These are simple cells. To get an idea of how things may depend on the distribution of mitochondria look here. Friel focuses on ryanodine receptors. To get an idea of how mitochondria interact with IP3 receptors look here.
November 24: No meeting.
December 1: Phil Baldwin of UTHSCH.
Some Issues in Image Reconstruction in CryoElectron Microscopy
The field of cryo-Electron microscopy provides interesting problems of signal processing. Images must be aligned, a transfer function must be accounted for, and reconstructions performed all at variable signal to noise ratios. I will give a very noncomprehensive survey of some of the work that I have been involved with and some of the problems that are on the drawing board. Included among these is image restoration of sets of two d-misaligned images, where one has knowledge of the amount of rotational and translational errors that characterize the set on average. Another problem is the use of cross-correlation functions to form preliminary models of the protein HRS. Some forward looking open problems will also be mentioned.

PFUG is pronounced fugue:
1. a composition in which a subject is announced by one voice and then developed contrapuntally by each of usually two or three other voices.
2. a pathological disturbance of consciousness during which the patient performs acts of which he appears to be conscious but of which on recovery he has no recollect ion.

  1. Computational Neuroscience: We will focus on 2 inverse problems in neuroscience (i) identifying conductances in networks of isopotential cells and (ii) identifying channel distribution in single cells. We shall also spend considerable time exploring 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.
    Meeting Time & Place: Th 4-5, KH 105

  2. Metabolic Engineering: 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.
    Meeting Time & Place: Th 1-2 DH 1064