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The old crypt of the Cathedral was re-modeled in 1985. In the crypt chapel, appropriately named the Emmanuel Chapel, daily Mass is celebrated, the Blessed Sacrament is reserved, and confessions are heard. The mortal remains of Bishop Paul Nussbaum, Bishop Emmanuel B. Ledvina, Bishop Mariano S. Garriga and Bishop Thomas J. Drury are buried there.
The Chapel was renovated under the guidance of the Reverend Monsignor Richard Shirley; Rector of the Cathedral at that time, and of Bishop Gracida. The design of the chapel makes it a place of artistic interest to visitors; because the former Bishops of Corpus Christi are buried there, it is a place of historical interest; and because sacred functions are regularly carried on there, it is a place of religious importance. The Emmanuel Chapel was dedicated by Bishop Gracida on November 21, 1985.
Work on the Blessed Sacrament Chapel, and work on the renovation of the sanctuary began in April of 1988. The dedication of the Blessed Sacrament Chapel took place January 1, 1989. His Eminence, Timothy Cardinal Manning celebrated the Mass, and the Most Reverend Archbishops and Bishops of Texas, Oklahoma, and Arkansas concelebrated on the notable occasion.