2014-08-08 Progress Report

Experiment #1

I think I have finalized a simple design for my first experiment. The experiment has to be very simple since I will be attempting to outsource all of the steps.

• Design and synthesize an immunogenic protein (e.g., flagellin) that can be expressed in a plasmid (i.e., a DNA vaccine)
• Inject mice with the DNA vaccine using an immunostimulating method (probably skin tattooing)
• Draw blood from the mice (a) before DNA vaccine injection, (b) after 7 days, and (c) after 28 days. Sequence the VDJ region from immunoglobulin and T-cell receptors in peripheral blood.
• Determine which antibodies or TCRs have shown the greatest response to the expressed protein, and look for common patterns of immune response among the mice.

The ideal outcome of this experiment is that several mice injected with the same vaccine produce similar humoral (antibody) responses. Then I could say with some certainty that these antibodies are emerging in response to my vaccine.

My original depiction of a DNA vaccine experiment is below. The numbers are probably best ignored, since many caveats apply to each. Nevertheless, the general concept of an inexpensive iteration on DNA vaccine design still seems reasonable. This experiment also takes some inspiration and cues from the excellent Slovenian iGEM entry from 2008.