ChE/BE 210 – Cellular Engineering

Spring 2004

30 March 2004

Instructor / Teaching assistant / Meetings
Prof. Anand Asthagiri
233 Spalding, x8130
/ Stephen Chapman
008 Fairchild, x8814
/ Lecture: 106 Spalding
Tu/Th: 9-10:30 a.m.
Office hrs: TBD based
on PS due dates

Catalog description. Quantitative analysis of molecular events governing mammalian cell behavior with emphasis given to derivation and interpretation of mechanistic mathematical models. Sample topics include receptor-ligand trafficking, models for cellular signaling networks, diffusion effects on intramembrane and intracellular events, biophysical models for cell adhesion and migration. Next offered in Spring 2006.

Grading

Problem sets (40%) – more in the beginning, ultimately giving way to…

Project (60%) – written and oral presentation. The purpose is to develop a mathematical model for an interesting biological phenomena (you choose), preferably one that we have some level of mechanistic understanding (need not be focused on molecular mechanism). In fact, it is preferable if mechanistic understanding is incomplete or even contentious, offering some modeler license to be creative about model design. The goal is to use this model to make quantitative predictions and to compare and contrast with what is known (either experimentally measured, or more likely, simply presumed) about system behavior. A one-paragraph draft summary will be required early on to make sure things are headed in the right direction.

No exams.

Reading material

  1. Receptors: models for binding, trafficking, and signaling. Lauffenburger and Linderman. Oxford University Press.
  2. Handouts and journal articles.

ChE/BE 210 – Cellular Engineering

Spring 2004

Syllabus

I. Sensing the Environment

  1. Soluble factors

Biology: soluble ligands and receptors, physiological significance

Quantitative models:interconverting receptor states, receptor aggregation, valency, diffusion and reaction; Experimental methods and data analysis

B. “Solid-state” ligands

Biology: cell-substratum and cell-cell adhesion, physiological significance

Quantitative models for adhesion – Biochemical and biophysical considerations; Experimental methods for studying adhesion.

II. Taking action – Cellular responses

  1. Cell spreading – biophysical model for expanding contact zone
  2. Cell migration, chemotaxis – mechanical model; biochemistry of sensing direction
  1. Cell proliferation – Phenomenological model; density-dependent growth

III. Opening up the Hood – Connecting detection to response: intracellular mechanisms

A. Oscillations and rhythms

Cell cycle biochemistry and oscillations; Circadian rhythms; Calcium

B. Receptor-ligand trafficking

C. Post-translational signaling networks:

MAP kinase signaling; Logic via biochemical cascades

  1. Transcriptional regulation networks