In the context of the development of competence, there's the timing issue. How long should it take H. influenzae to assemble its DNA-uptake machinery once the genes have been turned on? We traditionally allow 100 minutes from transfer to starvation medium. The microarray analysis showed that under these conditions gene expression is higher at 30 minutes than at 10 minutes. Addition of cAMP to non-starved cells induced competence with a peak at 45 minutes. How much of this time is needed for assembling DNA uptake complexes in the membranes? What other factors might contribute to a lag? Should E. coli be faster?
Another issue Tom's interested in is energy sources for periplasmic and outer membrane processes. He might have some insight into the periplasmic ATP-dependent ligase that's co-induced with H. influenzae competence genes. Where might it get its energy and what might it be contributing to uptake.
He might also have ideas about the "getting stiff DNA across the outer membrane without a free end" problem. How flexible is the outer membrane to being pushed around? And what about the cell wall - is it an obstacle we should worry about?