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France Córdova, Purdue's 11th president, announced last July her intention to leave the office July 15 after five years in the post.
Daniels' second term as governor ends in January, and he is prohibited by Indiana term limits from running for a third consecutive term.
Daniels is reportedly the first sitting governor to be elected president of a university.
Purdue Provost Timothy Sands will serve in the interim as Daniels completes his term as governor.