A gene knockout experiment

In this section of the workshop you will be working with data from a gene knockout experiment where an E. coli UPEC isolate mutant lacking the etpD gene is made.

To establish that this gene makes a contribution to pathogen adherence, we need to satisfy Falkow’s molecular variant of Koch’s Postulates:

  1. The wild-type/control pathogen containing the gene must be able to adhere to human tissue/catheter material
  2. The mutant organism lacking only that gene must not adhere to human tissue/catheter material
  3. A complemented mutant, with the gene restored, must be able to adhere to human tissue/catheter material

A more complete account of this experiment is given on the next page.

A note about experimental data.

In real life experiments are not always β€œclean,” in the sense that we cannot always construct our experiments to exclude all events or factors that might influence the outcome.

In this part of the workshop you will work with real experimental data which, due to the need to spread the work over a period of months required parts of the experiment to be performed by different people at different times.

Caution

The situation we consider here, where more than one researcher carries out sections of the experiment months apart, is quite obvious. The scientists involved knew that there might be an infuence on the outcome and took it into account when recording their data.

However, many such interfering effects can creep into experimental data without our realising it. It is always good practice to investigate your experimental data to look for evidence of similar kinds of effects.

As you will see, it can be possible to account and correct for these effects when they arise.