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, firstname.lastname@example.org and Brad Peercy, email@example.com
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
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
September 1: Continuation of last time.
September 8: Applications to slug learning.
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
Basic Mass Spectrometry .
Gas Chromatography / Mass Spec
October 20: Flux determination
October 27: Elementary Flux Modes
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
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
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
of which he appears to be conscious but of which on recovery he has no recollect
- 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
- 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.
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
1 and 2 and
3 and 4 and
(ii) Models of the FNR
(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