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KNOW IT ALL: Wednesday’s Top 7 Stories at NBC News

Good morning. Here are some of the stories we’re following today:

1. Man’s police-related death prompts fed probe

The death of Baltimore man Freddie Gray has led the Justice Department to open a civil rights investigation after his spine was allegedly severed while he was in police custody. Gray, 25, died Sunday, a week after he was arrested April 12 on a weapons charge. After the probe was announced, hundreds of protesters again gathered for a rally Tuesday at the site of Gray's arrest. Holding signs reading "Black Lives Matter" and "No Justice, No Peace," the protesters then marched to a nearby police station. Read more in NEWS.

Baltimore protests over Freddie Gray’s death grow 1:53

2. France says it foiled ‘imminent’ attack on church

An Islamic extremist with an arsenal of heavy weapons planned an imminent attack on one or more French churches, France's top security official said Wednesday, announcing the arrest of the man who is also accused in the death of a young woman. The nation has been on edge since the January attacks on the satirical newspaper Charlie Hebdo and a kosher supermarket left 20 people dead, including the three gunmen. Read more in NEWS.

3. Penalty phase opens in Boston bombing trial

A federal prosecutor told jurors on Tuesday that Dzhokhar Tsarnaev — "determined to be America's worst nightmare" and unrepentant to this day — deserves to die for the bombing of the Boston Marathon. Prosecutor Nicole Pellegrini opened the penalty phase of Tsarnaev's trial by focusing on photos of four victims — three killed at the marathon and a campus police officer gunned down three days later. Read more in NEWS.

4. Death toll in migrant boat disaster worst ever: U.N.

The United Nations refugee agency said Tuesday that more than 800 people are believed to have perished when a ship crammed with migrants capsized in the Mediterranean on Sunday, making it the worst maritime disaster the agency has ever recorded in the Mediterranean. The Tunisian captain of the boat, 27-year-old Mohammed Ali Malek, has been arrested and charged with manslaughter, Italian prosecutors said Tuesday. Read more in NEWS.

5. Blue Bell Listeria outbreak dates back to 2010: CDC

An outbreak of Listeria linked to the company's ice cream products has been going on quietly for as long as five years, federal health officials said Tuesday. The outbreak, which has killed three people and put seven others into the hospital, involves two distinct strains of the bacteria that have been making people sick from Kansas to South Carolina, the CDC says. The three exposed people who died all were in Kansas. Read more in HEALTH.

6. Senate trafficking deal clears way for Loretta Lynch vote

Republicans and Democrats in the Senate reached an agreement Tuesday on an anti-human-trafficking bill, clearing the way for a vote on President Barack Obama's nomination of Lynch for attorney general. The trafficking bill had been held up since February because it contained anti-abortion language opposed by Democrats. The bill and Lynch's nomination passed committee 54 days ago, an unusually long delay for a vote on the nomination of an attorney general. Read more in POLITICS.

7. Oklahoma reserve deputy pleads not guilty

Robert Bates, the reserve sheriff's deputy who says he mistook his gun for his Taser when he shot and killed a suspect earlier this month, pleaded not guilty on Tuesday to second-degree manslaughter. The judge, meanwhile, allowed Bates to take a previously planned vacation to the Bahamas. A lawyer for the family of the suspect said he was not surprised that Bates had pleaded not guilty — but allowing him to go on vacation shows "apathy." Read more in NEWS.

Nightly Spotlight

In an emotional interview, parents Travis Phillips and Michelle Honda-Phillips talk about why they decided to allow their 8-year-old son to transition to female. Malisa's story went viral when her grandfather — California Congressman Mike Honda — tweeted about her earlier this year.

Malisa’s Story: What It Means to Be a Transgender Child 5:16