Raymond Clark III, a Yale animal lab technician, was arrested Thursday morning and charged with the murder of Annie Le GRD ’13, a 24-year-old doctoral student in pharmacology who authorities say was strangled to death at an on-campus research facility.

A warrant was issued for Clark’s arrest shortly after 8 a.m., New Haven Police Department Chief James Lewis said at a press conference. Clark, 24, was taken into custody without incident at the Super 8 motel in Cromwell, Conn., where he had been staying since Wednesday.

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Shortly after his arrest, Clark was taken to the New Haven Superior Court to face a judge, his legs shackled and his head down. At the three minute hearing, he only said two words — “yes, sir” — to affirm that he understood his rights. Surrounded by eight judicial marshals, Clark kept his eyes low, shifting his gaze between the judge and the public defenders representing him, Joseph Lopez and Beth Merkin.

Clark is being held on $3 million bond with a hearing slated for Oct. 6. Prosecutors have not yet announced whether they believe the crime was premeditated, nor whether they will seek the death penalty.

David Dworski, a Fairfield attorney who had been representing Clark, said Thursday that he is no longer Clark’s lawyer. Merkin, who said she and Lopez are “brand new” to the case, said Clark will plead not guilty and declined further comment.

In the meantime, Clark’s job at Yale has been suspended and he is barred from campus, University President Richard Levin said in an e-mail message to students and their parents.

“It is frightening that a member of our own community might have committed this terrible crime,” Levin said. “This incident could have happened in any city, in any university, or in any workplace. It says more about the dark side of the human soul than it does about the extent of security measures.”

Still, he added that the University would re-examine its security measures and re-emphasize its policy of zero tolerance for violent and threatening behavior. Levin added in an interview that Yale will continue to assist investigators and may now turn over personnel records if asked by prosecutors.

“Obviously if University records are subpoenaed, we’ll comply,” he said. “We did not and could not legally turn over our personnel records during the course of the investigation.”

At least six detectives from the NHPD narcotics unit had been following Clark at all times since Saturday, even before Le’s body was found, NHPD spokesman Joe Avery said. He was first detained late Tuesday night, when authorities called him a “person of interest,” served him with two search warrants and took a DNA sample. He was released at 3 a.m. Wednesday and served with two more search warrants.

In interviews, Clark’s neighbors and friends described him as personable and a “nice guy.” At Branford High School, Clark pitched for the baseball team, made the honor roll and, according to his yearbook, was a member of the Asian Awareness Club. Still, others added that he may have seemed distant and aloof to those who did not know him well.

A person familiar with the investigation said Wednesday that Clark’s DNA matched a piece of evidence taken from the Yale research facility at 10 Amistad St., where Le’s remains were found stuffed behind a basement wall Sunday, which was supposed to be her wedding day.

Lewis declined to confirm the DNA match, to identify a motive or to discuss anything else contained in the arrest warrant, which has been sealed by the court.

“It is important to note that this is not about urban crime, university crime, domestic crime, but an issue of workplace violence,” he said, adding that there is no evidence of a romantic relationship between Clark and Le.

Lewis declined to comment on reports that the murder is related to the lab animals that Clark cared for and Le studied. Levin, addressing a news report that Clark sent e-mails to Le before her death, said Wednesday, “To my knowledge there’s nothing that would be relevant to the case” in the correspondence between the two.

In his e-mail Thursday morning, Levin said that “nothing in the history of [Clark’s] employment at the University gave an indication that his involvement in such a crime might be possible.”

Clark, who has worked at Yale since Dec. 2004, is the only suspect, Lewis said. Police have seized 300 pieces of physical evidence, examined 700 hours of video footage and interviewed 150 people, sometimes more than once, as part of the investigation, Lewis said. While the police chief did not rule out whether the evidence would produce additional leads, Lewis said he does not anticipate identifying other suspects.

Unlike yesterday, when New Haven State’s Attorney Michael Dearington refused to name the judge who signed the search warrants, Lewis said the arrest warrant was signed by Superior Court Judge Brian Fischer. Fisher signed the warrant just 20 minutes before the arrest, after authorities spent all night preparing the documents, Lewis said.

Le was last seen entering the 10 Amistad St. building at 10 a.m. on Sept. 8, after leaving her keys, purse and phone in her office at the Sterling Hall of Medicine. She was considered a missing person until Sunday, when her body was found and the case became a homicide.

Described as sweet, outgoing and smart, the Placerville, Calif., native was dedicated to her research, colleagues at Le’s lab said. At Union Mine High School in El Dorado, Calif., Le was valedictorian and a member of the National Honor Society and the culture club.

Although she was small in stature, Le stood out among her classmates and was not afraid to speak up for herself. “She was a spunky little thing,” said one of her high school friends, Cierra Montes.

Le’s family has not spoken publicly but issued a statement Tuesday thanking the community for its support and sensitivity. The family of Le’s fiance, Jonathan Widawsky, issued a statement Thursday: “We share in the grief of the family of Annie Le and are, collectively, doing our best to deal with our tragic loss. Annie will live in our hearts forever.”

Isaac Arnsdorf and Paul Needham reported from New Haven, and Harrison Korn and Zeke Miller from Cromwell, Conn.