Revised outline

Introduction

Why H. influenzae and competence are important.

Background

Introductory background

• Gap 1:  Which proteins affect which steps in uptake?  [Here make the point that the steps themselves are not defined yet.]
• Gap. 2:  What is the real sequence specificity and how does it contribute to DNA uptake?
• Gap. 3: What proteins exert forces on the DNA?

Three-stage model of DNA uptake [here we define the steps of uptake].

Specific Aims: (5 questions, perhaps grouped into 'Aims')

• Q. 1, 
• Q. 2, 
• Q. 3, 
• Q. 4, 
• Q. 5

Preliminary Results

Methods

Q. 1:  Which genes affect which steps of DNA uptake?

Q. 2: Which genes cause the different uptake specificities of H. influenzae and A. pleuropneumoniae?*

Q. 3: What are the uptake specificities of  H.influenzae and A. pleuropneumoniae?*

Q. 4: What are the physical properties of the H. influenzae and A. pleuropneumoniae USSs?

Q. 5: What forces do cells exert on DNA during uptake, and which genes are needed for these forces?

* The reader will ask why Q. 3 comes after Q. 2 when Q. 3 should be answered before Q.2 can be answered. It depends on how/if the questions are organized into Aims.  (Otherwise we could just change the 'Specific Aims' heading to 'Specific Questions to be answered'.