The arrest of Essam el-Erian, the deputy leader of the Brotherhood's political arm, the Freedom and Justice party, was the latest in a wide-ranging crackdown of both the Islamist group's leaders and its rank-and-file members since the ouster of President Mohammed Morsi, who also hails from the Brotherhood.
Morsi, himself in detention, has been held at an undisclosed military location since the July 3 coup. He is facing charges of inciting supporters to murder his opponents while in office. Morsi's trial is due to begin Nov. 4. It is not yet clear if the 62-year old ousted president will appear in court.
El-Erian is also one of the defendants in the Morsi trial. He is accused of inciting Brotherhood followers to break up anti-Morsi protesters gathered outside the presidential palace late last year.
In photographs broadcast on state television following his arrest, the 59-year-old el-Erian is wearing a white galabiya, the traditional male robe, and a skullcap, and flashes a smile to the cameras. He is the latest senior Brotherhood leader arrested on warrants from state prosecutors who accuse the group's key figures of crimes ranging from inciting violence to providing weapons to supporters and threatening public order.
The official state news agency MENA said el-Erian was arrested after a raid on an apartment in the eastern suburb of New Cairo, where he had been hiding. He was later transferred to the Torah prison complex in southern Cairo, where most of the group's arrested leaders are held.
The agency said he will be interrogated at Torah on accusations of inciting violence in a number of anti-government protests.
While Morsi was in power, el-Erian frequently spoke publicly, often causing a stir as he turned from a moderate to a hard-line member of the group.
During a large-anti-Morsi demonstration last December outside the presidential palace, el-Erian went on a Brotherhood-affiliate television channel to ask supporters "in the tens of thousands, to besiege those thugs." At least 10 people died in subsequent clashes outside the palace.
While in hiding, el-Erian distributed messages to followers, urging them to denounce the coup and demand Morsi's reinstatement. In a recent pre-recorded message aired on the Al-Jazeera satellite news network, el-Erian criticized the military and the interim authorities and called on supporters, including students, to keep up their protests.
Hours after el-Erian's arrest, pro-Muslim Brotherhood student protesters stormed the administrative building of Al-Azhar Islamic university. They smashed windows and equipment while besieging the office of university's chief and other administrators.
The assault prompted university officials to call the police to break up the rowdy protests. Riot police forces entered the campus and freed the officials, security officials said. The university, where the Brotherhood has a strong base, has been scene to near-daily protests. Wednesday's protest, however, was the first time students threatened the university president; although they had besieged the administrative building before.
Mahmoud Salah, one of the protesters, denied the violence was the work of the students. He accused authorities of planting troublemakers among them to stir the violence. "Our protests are peaceful," he told The Associated Press. "We are against the coup."
Salah said police forces stormed the campus with armored vehicles and arrested students.
Television footage of the university showed damage inside the offices. Graffiti covered building walls, including one message inside that read: "CC Killer," referring to Egypt's military chief Gen. Abdel-Fattah el-Sissi.
Following Morsi's ouster, the country's new, military-backed authorities cracked down on the group, arresting hundreds of Brotherhood figures and putting top leaders on trial. The authorities are seeking to show through the prosecutions that the Brotherhood fueled violence during Morsi's one-year presidency and after the coup.
Calls for reconciliation that would return the Brotherhood - which dominated elections after the 2011 fall of Hosni Mubarak - to the political system have gone nowhere, with neither side giving ground.
El-Erian's arrest came just hours after three judges presiding over a trial of nearly three dozen Brotherhood members, including its top spiritual leader and its chief financier, stepped down on Tuesday after security agencies refused to let the defendants attend the courtroom sessions.
The move was a sharp pushback from within the judiciary over the conduct of the trial amid criticism by the Brotherhood that wide-ranging prosecutions of its leaders, including Morsi and the group's spiritual guide, Mohammed Badie, are only vengeful show trials.
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