I looked at Fig. 2, and understand your confusion.  There is a lot going on in this experiment for a beginner to understand.  It appears that the HCV core protein in this system is induced when tet is removed from the media (i.e. tet-repression system).  When HCV core protein is induced, which is a consequence of tet removal (see part B of figure), it interferes with IFN-alpha induced transcription factors to bind its target sequence in ISGF3 (EMSA assay on top).  You will note how the band goes away at later time points in the IFN-alpha + lanes.at later time points after tet removal.  I hope this helps.

Thank you , that helps a lot