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Hundreds of extra troops have been brought in to join Federal forces already stationed in the nearby town of Oxford as the violence spread to its streets.
The protesters are angry at the admission of James Meredith, a black American, to the university.
Rioting erupted last night as President Kennedy addressed the nation in a televised broadcast urging a peaceful settlement to the dispute over racial segregation.
Earlier Mr Kennedy had 'federalised' the Mississippi National Guard to maintain law and order, and mobilised other regular infantrymen and military police across the state line in Tennessee.
The Federal Government had been expecting resistance from the Mississippi State police under the governorship of Ross Barnett, who has previously defied court orders requiring desegregation.
Despite Governor Barnett's assurances that his police would carry out their duties, there have been reports that they neglected to provide adequate security, and additional troops and marshals were called in.
US marshals, military police and National Guardsmen used teargas to take on rioters armed with rocks, lead pipes, petrol bombs and in some instances rifles and shotguns.
More than 100 people were arrested during the night. One US marshal was shot in the neck and critically wounded.
Cars and television trucks were smashed and burned and journalists and cameramen were beaten, as rioters turned on the media.
Mr Meredith remained under guard inside the campus in a university dormitory during the fighting.
After his enrolment this morning, Mr Meredith said: "This is not a happy occasion," but he is said to have remained calm throughout the ordeal.
He was then escorted to his first class - a seminar on American colonial history - through a crowd of several hundred jeering students.
Rioting has continued in the town of Oxford with further arrests made and more troops flown in.
In a broadcast Governor Barnett said that law and order must prevail "even though our state has been invaded by federal forces". He urged those who came from outside the Oxford area to go home.
The riots receded and over the coming days most troops were withdrawn from the town.
Mr Meredith said his enrolment was "more for America than it was for me". He faced continued hostility and required 24 hour protection but graduated in 1963 without incident.
Three years later he was shot and wounded on a lone civil rights march through Mississippi.
Soon after he dropped out of the civil rights movement to work as a stockbroker, and then in real estate. In 1967 he became an investor and entered Columbia University Law School in 1968.
That year he also became president of Meredith Enterprises and began to lecture on racial problems. In 1972 he stood unsuccessfully as a Republican candidate for the US House of Representatives.
The civil rights movement that began in the late 1950's won for black Americans basic rights long denied to them.
The landmark Civil Rights Act of 1964 and the Voting Rights Act of 1965 outlawed racial discrimination, removed obstacles to voting and furthered desegregation.
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