Thanks for the additional information. I must say this sounds a little OFATish. Why not study all factors in the same design? Agreed, it does not seem nested to me.
I'm still not sure I understand enough, but here are some ideas:
1. One factor (shift) 0 or 2º. At 1 hour intervals take samples and measure the antibodies (you might start at 0 and look for delta antibodies). If you want you can apply another treatment (either 0 or 2º) at those intervals.
2. Two factors: Temp (0, 2º) and Time (1, 2, 3). Factorial gives 6 treatment combinations. Measure antibodies at each hour as well.
"All models are wrong, some are useful" G.E.P. Box