Lecture Notes

LEC # TOPICS
1

Course Introduction

Model networks involved in signaling - Signals that start outside of the cell (role of the ECM) and trigger cascades inside the cell, ultimately affecting gene expression
2

Information flow in the reverse direction - from DNA to RNA to protein (the central dogma)

Review of regulatory circuits and introduction to the concept of evolutionary genomics (PDF)

Key Issues: DNA replication and repair errors lead to mutations. Loss of mismatch repair leads to a hyper-Rec phenotype, which facilitates horizontal gene transfer (antibiotic resistance, etc.)
3 Decoding Information I (Transcription Regulation) (PDF)
4

Modeling Macromolecular Structure I

Individual Homework Assignments
5 Decoding Information II (Translation) (PDF)
6

Modeling Macromolecular Structure II

Students Present Homework
7 Roundtable Discussion
8 How to Write an NIH Grant Proposal
9 Analysis of the Interferon Network (The JAK/STAT system) (PDF)
10 Analysis of the Interferon Network (PDF)
11 Analysis of the Interferon Network (cont.)
12 Analysis of the Interferon Network (cont.) (PDF)
13 Roundtable 1: Students Present Model Projects on Apoptosis
14

Chemotaxis I - How Salvage Pathways Supplement Core Biochemical Pathways (PDF)

The Che System

Receptor Methylation as a Mechanism of Control of Chemotaxis
15

Chemotaxis II - How CheY(P) Signals to the Flagellar Motor

Chemiosmotic Coupling

Chemotaxis III - Proton Pumps
16 Introduction to the Extracellular Matrix
17 Epithelial Cell Morphogenesis Signaling Hierarchy I
18 Epithelial Cell Morphogenesis Signaling Hierarchy II
19 Round Table Discussion
20 Epithelial Cell Morphogenesis Signaling Hierarchy III
21 Roundtable 3
22 Changes in Lung Epithelium During Pathogenesis I
23 Changes in Lung Epithelium During Pathogenesis II
24 Network Example: Functional Glycomics