Soon after he took up his post in El Salvador, U.S. Ambassador Ronald Johnson forged an unusually close relationship with the country’s president.

President Trump had nominated Mr. Johnson in 2019 as his ambassador to the country shortly after the White House declared war on El Salvador’s notoriously violent gangs, including MS-13.

The relationship between Mr. Johnson and the Salvadoran president, Nayib Bukele, was close enough that it worried some officials. The two posted photos on social media of their families spending weekends together and tweets highlighting their “personal friendship.”

That bond remained firm even in 2020 when the Salvadoran president was accused of secretly colluding with local gangs, seven current and former officials said. Mr. Johnson defended him and publicly dismissed a letter from U.S. Republican congressmen raising concerns about the claim.

Then, without clear reason, a U.S. Embassy staff member investigating the government’s potential ties to the gangs was sent home early.

The ambassador’s actions seemed to contradict the interests of the Trump administration, argued three current and former American officials who worked directly with Mr. Johnson. He appeared more focused on protecting a foreign leader, the officials said, than on dismantling the Salvadoran criminal organizations operating both there and within the United States.

Now Mr. Johnson has been tapped again by President Trump, this time to be the U.S. ambassador to Mexico. His nomination is expected to go to a Senate vote on Wednesday.

In an emailed response, Mr. Johnson described his relationship with Mr. Bukele as “cordial,” something short of the bond suggested by posts like one showing them eating crab together, wearing grins and giant bibs.

Mr. Johnson also said he was committed to dismantling Salvadoran gangs. “The dismantling of the vicious MS-13 gang, and other Salvadoran gangs, began during my tenure and it continues today under the leadership of President Trump,” he said.

The White House did not respond to a request for comment, but clearly Mr. Trump was supportive enough of Mr. Johnson’s performance in El Salvador to offer him a new — and more significant — post.

As a veteran military and C.I.A. officer, Mr. Johnson had a long career stretching from Latin America to Asia, but his stint in El Salvador, from September 2019 until January 2021, was his only diplomatic post.

Mexico is a much bigger assignment, a key U.S. trading partner, and Mr. Johnson will arrive there at one of the tensest chapters in the country’s relations with the United States.

Mr. Trump has threatened to send troops into Mexican territory to destroy the country’s drug cartels, which his administration recently designated as terrorist organizations. Mexico’s president warns that any unilateral American military action would be a violation of sovereignty.

Mr. Johnson’s experience with covert C.I.A. operations may be why he was picked for the ambassadorship, those close to him say, to defend a policy he knows well.

“His experience as a Green Beret and a seasoned C.I.A. officer in Latin America and elsewhere means he knows the issues, on defense security and especially counter terrorism,” said Mick Mulroy, a senior Pentagon official in the first Trump administration and a friend of Mr. Johnson.

Yet during his time in El Salvador, two U.S. Embassy staffers and two senior American diplomats said they warned Mr. Johnson that he and his wife were getting too close to Mr. Bukele, but that the ambassador brushed off those concerns. Mr. Johnson even told colleagues he was the godfather to Mr. Bukele’s oldest daughter, according to two former diplomats.

Mr. Johnson denied receiving such warnings and that he was the godfather of Mr. Bukele’s daughter.

Mr. Bukele created a national award for Mr. Johnson just before he departed as ambassador, which remains El Salvador’s highest honor and has only been given twice.

While cultivating relationships is part of the job for diplomats, they are typically discouraged from forging personal ties with politicians in the countries where they serve, out of a concern that those bonds could be used to manipulate them.

“We need our ambassadors to have a close relationship with heads of state, but we need to make sure they are serving the interest of the American people first,” said Eric L. Olson, an analyst on Central America.

Mr. Johnson also clashed with his staff over the involvement of his wife, Alina Johnson, in diplomatic affairs, according to three American officials.

The ambassador would sometimes introduce Ms. Johnson as his “co-ambassador” in official meetings, confusing Salvadoran officials, according to two U.S. Embassy officials and a local businessman who met with them. Mr. Johnson would also sometimes reject the embassy’s official translator to instead have his Cuban-born wife translate formal meetings for him, according to two embassy staffers. His wife also told embassy staffers that she weighed in on Salvadoran legislative affairs with Mr. Bukele, they added.

Mr. Johnson denied those claims and said his wife was “well aware of a spouses’ role” in his response to The New York Times.

In 2020, Mr. Bukele was accused by the Salvadoran media outlet El Faro of secretly colluding with the country’s gangs, agreeing to give perks and better treatment to imprisoned gang members, like visits from prostitutes and cellphones. In exchange, the report said, the gangs would reduce homicides and give their support to Mr. Bukele’s party in the coming election.

Such negotiations would violate Salvadoran laws, which classified the gangs as terrorist organizations and prohibited politicians from negotiating with them. When Mr. Bukele became president in 2019, he vowed he would go hard on the gangs, like no leader before.

The El Faro investigation challenged Mr. Bukele’s tough-on-crime message.

It also caught the attention of six Republican congressmen, who wrote a scathing letter to the Salvadoran president saying they were “troubled by reports that the government of El Salvador could be legitimizing MS-13.”

Mr. Bukele dismissed the letter on national television, saying the U.S. representatives who signed it “don’t represent 5 percent or 3 percent of Congress.” Mr. Johnson echoed Mr. Bukele, underscoring that the letter was signed by a “small portion” of Congress.

Shortly after, El Salvador’s attorney general raided the bureau of prisons, seizing hard drives, log books and CCTV footage, according to media reports at the time. Pressure was building on Mr. Bukele as it seemed Salvadoran and U.S. prosecutors were preparing separate indictments to prosecute his government, according to two American officials.

That is when an American diplomat investigating allegations of a secret deal with the gangs was abruptly sent back to the United States, according to U.S. and Salvadoran officials.

When he landed in Washington, the diplomat was told that both the Salvadoran government and his own boss, Mr. Johnson, had wanted him out of country, according to three people who debriefed the diplomat upon his return.

“Given what we know about the nature of the Bukele administration and its dealings with the gangs, to send someone home in the midst of their work on an investigation like that would be disruptive,” said Mark Feierstein who worked under several American administrations since the 1990s.

Last month in a Senate committee hearing, Mr. Johnson said the U.S. official investigating the administration’s relationship with the gangs was dismissed because he was having “unauthorized meetings” with journalists, but provided few details. Mr. Johnson denied having anything to do with the decision and said he had “deferred to his boss” on whether to send the diplomat home, without elaborating.

In his response to The Times, Mr. Johnson said he had “neither dismissed or professionally penalized U.S. Embassy staffers.”

But three of the diplomat’s superiors were upset that he was sent home early, according to people who spoke with them at the time.

The ousting of the American diplomat sent a chill through both the U.S. Embassy and the Salvadoran investigative unit probing allegations of government collusion with the gangs, American officials said.

After that, Mr. Bukele’s government seemed to hinder U.S. efforts aimed at dismantling Salvadoran gangs. In November 2021, the government secretly freed a top MS-13 leader from prison, despite a U.S. extradition request, according to a Justice Department detention order reviewed by The Times.

Mr. Bukele’s government did not respond to questions for this story but has previously denied links to the gangs.

Officials wonder why Mr. Johnson was such a defender of Mr. Bukele.

Some contend that Mr. Johnson’s judgment was skewed by friendship. Others point to Mr. Bukele’s success in lowering homicides across El Salvador, which had been dubbed the murder capital of the world before killings dropped 45 percent from 2019 to 2020.

Still others point to Mr. Bukele’s deal with the first Trump administration to require Central American migrants traveling through El Salvador to seek refuge there instead of the United States, signed weeks after Mr. Johnson arrived. According to two former American officials, the ambassador regularly told embassy staffers not to pursue any projects that may upset Mr. Bukele and jeopardize the agreement, which he said was an important bilateral achievement.

Mr. Johnson’s tenure as ambassador ended in January 2021, when President Biden was sworn in. The following month, Mr. Bukele’s party won a majority in Congress and swiftly dissolved the Salvadoran investigative unit looking into the gang negotiations. That affected a separate Justice Department investigation, according to two former American officials.

Still, in December of that year, the U.S. Treasury Department sanctioned two senior Salvadoran officials after its own investigations concluded they had orchestrated covert agreements with gang leaders.

A few months later, any agreement between the gangs and the government seemed to collapse, leading to a killing spree in the country’s capital that left dozens of people dead.

The government quickly imposed a state of emergency that remains in place today, mobilizing police and the military forces to carry out mass arrests.

Although no longer holding any public office, Mr. Johnson continued to advocate for Mr. Bukele, even as Mr. Bukele started referring to himself as the world’s “coolest dictator.”

Mr. Johnson ratcheted up support for him during his re-election last year, according to a friend of Mr. Johnson and an American official. This included enlisting notable Republicans like Donald Trump Jr. to attend the inauguration. (Legal scholars say Mr. Bukele violated his country’s constitution by running again).

Last month, the Trump administration sent migrants to El Salvador as part of a new deal to house suspected Venezuelan and Salvadoran gang members in El Salvador’s mega prison. As part of the agreement, Mr. Bukele has pressed Washington to return MS-13 leaders in U.S. custody to El Salvador, though only one has been sent back one so far.

“If the U.S. sends back MS-13 leaders to El Salvador, it would be a disaster for ongoing Justice Department investigations into the gangs and the deals they struck with Bukele’s government,” said Mr. Olson, the analyst. “Bukele has every interest in making sure that their information isn’t used in U.S. court cases or prosecutions and he will lock them up and throw away the key.”

Gabriel Labrador contributed reporting from San Salvador. Alain Delaquérière contributed research.

The human brain is so complex that scientific brains have a hard time making sense of it. A piece of neural tissue the size of a grain of sand might be packed with hundreds of thousands of cells linked together by miles of wiring. In 1979, Francis Crick, the Nobel-prize-winning scientist, concluded that the anatomy and activity in just a cubic millimeter of brain matter would forever exceed our understanding.

“It is no use asking for the impossible,” Dr. Crick wrote.

Forty-six years later, a team of more than 100 scientists has achieved that impossible, by recording the cellular activity and mapping the structure in a cubic millimeter of a mouse’s brain — less than one percent of its full volume. In accomplishing this feat, they amassed 1.6 petabytes of data — the equivalent of 22 years of nonstop high-definition video.

“This is a milestone,” said Davi Bock, a neuroscientist at the University of Vermont who was not involved in the study, which was published Wednesday in the journal Nature. Dr. Bock said that the advances that made it possible to chart a cubic millimeter of brain boded well for a new goal: mapping the wiring of the entire brain of a mouse.

“It’s totally doable, and I think it’s worth doing,” he said.

More than 130 years have passed since the Spanish neuroscientist Santiago Ramón y Cajal first spied individual neurons under a microscope, making out their peculiar branched shapes. Later generations of scientists worked out many of the details of how a neuron sends a spike of voltage down a long arm, called an axon. Each axon makes contact with tiny branches, or dendrites, of neighboring neurons. Some neurons excite their neighbors into firing voltage spikes of their own. Some quiet other neurons.

Human thought somehow emerges from this mix of excitation and inhibition. But how that happens has remained a tremendous mystery, largely because scientists have been able to study only a few neurons at a time.

In recent decades, technological advances have allowed scientists to start mapping brains in their entirety. In 1986, British researchers published the circuitry of a tiny worm, made up of 302 neurons. In subsequent years, researchers charted bigger brains, such as the 140,000 neurons in the brain of a fly.

Could Dr. Crick’s impossible dream be possible after all? In 2016, the American government began a $100 million effort to scan a cubic millimeter of a mouse brain. The project — called Machine Intelligence from Cortical Networks, or MICrONS — was led by scientists at the Allen Institute for Brain Science, Princeton University and Baylor College of Medicine.

The researchers zeroed in on a portion of the mouse brain that receives signals from the eyes and reconstructs what the animal sees. In the first stage of the research, the team recorded the activity of neurons in that region as it showed a mouse videos of different landscapes.

The researchers then dissected the mouse brain and doused the cubic millimeter with hardening chemicals. Then they shaved off 28,000 slices from the block of tissue, capturing an image of each one. Computers were trained to recognize the outlines of cells in each slice and link the slices together into three-dimensional shapes. All told, the team charted 200,000 neurons and other types of brain cells, along with 523 million neural connections.

For Nuno da Costa, a biologist at the Allen Institute and one of the leaders of the project, just watching the cells take shape on his computer screen was breathtaking. “These neurons are absolutely stunning — it gives me pleasure,” he said.

To understand how this mesh of neurons functioned, Dr. da Costa and his colleagues mapped the activity that had been recorded when the mouse looked at videos.

“Imagine that you come to a party that has 80,000 people, and you can be aware of every conversation, but you don’t know who is talking to whom,” Dr. da Costa said. “And now imagine that you have a way to know who is talking to whom, but you have no idea what they’re saying. If you have these two things, you can tell a better story about what’s happening at the party.”

Analyzing the data, the researchers discovered patterns in the wiring of the brain that had escaped notice until now. They identified distinct kinds of inhibitory neurons, for instance, that link only to certain other types of neurons.

“When you go into studying the brain, it seems kind of hopeless — there are just so many connections and so much complexity,” said Mariela Petkova, a biophysicist at Harvard who was not involved in the MICrONS project. “Finding wiring rules is a win. The brain is a lot less messy than people thought,” she said.

Many of the MICrONS researchers are now pitching in on a bigger project: mapping an entire mouse’s brain. With a volume of 500 cubic millimeters, a full brain would take decades or centuries to chart with current methods. The scientists will have to find additional tricks in order to finish the project in a decade.

“What they’ve already had to do to get here is heroic,” said Gregory Jefferis, a neuroscientist at the University of Cambridge who was not involved in the MICrONS project. “But we’ve still got a mountain to climb.”

Forrest Collman, a member of the MICrONS project at the Allen Institute, is optimistic. He and his colleagues recently discovered how to make microscopically thin sections from an entire mouse brain. “Some of these barriers are starting to fall,” Dr. Collman said.

But our own brain, which is about a thousand times bigger than a mouse’s, presents a much bigger challenge, he added. “The human brain right now feels like outside the range of what is possible,” he said. “We are not going there anytime soon.”

But Sebastian Seung, a neuroscientist at Princeton and a member of the MICrONS project, noted that mouse brains and human brains are similar enough that researchers might glean clues that could help them find medications to effectively treat psychological disorders without causing harmful side effects.

“Our current methods of manipulating the nervous system are incredibly blunt instruments,” Dr. Seung said. “You put in a drug, and it goes everywhere,” he added. “But being able to actually reach in and manipulate a cell type — that’s precision.”

The efforts to map a whole mouse brain are supported by funding from a long-running National Institutes of Health program called the BRAIN initiative. But the future of the endeavor is uncertain. Last year, Congress cut funding to the BRAIN initiative by 40 percent, and last month President Trump signed a bill cutting support by another 20 percent.

Dr. Bock noted that brain-mapping efforts like MICrONS take years, partly because they require the invention of new technologies and software along the way.

“We need consistency and predictability of science funding to realize these long-term goals,” Dr. Bock said.

Universal Studios will build its first European theme park in Bedfordshire, England, studio officials said Wednesday, previewing a sprawling resort that could combine iconic American brands like “Jurassic Park” with classic British characters like Paddington Bear, Dr. Who and Harry Potter.

Set to open in 2031, British officials said the yet-to-be-named theme park would be Britain’s largest single tourist attraction. Executives at Comcast, Universal’s parent company, said the 476-acre complex would include themed lands, rides, a 500-room hotel, shops and dining.

Keir Starmer, the British prime minister, hailed the announcement as a boost for his country’s sluggish economy and an example of his government’s attempt to cut through the red tape that has long made it costly and difficult to complete complex projects in Britain.

“Today we closed the deal on a multibillion-pound investment that will see Bedford home to one of the biggest entertainment parks in Europe,” Mr. Starmer said in a statement, adding that the project would create around 28,000 jobs.

The theme park, which Mr. Starmer said would generate nearly $64 billion (£50 billion) in revenue for the area by 2055, is a rare bright spot at a moment when the British economy has been barely growing.

But it will be years before the doors open to the public as the company transforms what is a bare piece of land about 35 minutes north of London by train. That delay creates the kind of uncertainty that has sometimes doomed previous theme park efforts.

In the late 1980s, London was considered, and ultimately rejected, as a location for the Euro Disneyland theme park that eventually was constructed outside of Paris. In 1994, Disney proposed a “Disney’s America” near the Manassas National Battlefield Park near Washington, D.C., but backed off amid intense public backlash from nearby residents and members of Congress.

And a theme park proposed in 2012 called The London Resort was never built after years of delays because of environmental concerns and permit issues.

Mr. Starmer and members of his government stressed on Wednesday the benefits of the new theme park for people in the area.

Lisa Nandy, Britain’s culture secretary, called it a “landmark investment” and told the BBC that “this is not just about bringing great American creations to Britain, this is also about showcasing great British creations to the world.”

“These are things like James Bond, Paddington Bear, these are things like Harry Potter,” she said. “We’ve got so much to be proud of.”

The success of the project will hinge on attracting millions of visitors. Studio and government officials were vague about what the theme park would look like.

An artist’s rendering of the park on the company’s website showed several roller coasters, shopping and other areas around a large lagoon. But officials declined to be more specific about what movie or television characters might be part of the development.

“It is still too early in the process to know the possibilities of featured attractions and experiences,” the company said in a statement. “Should we secure the necessary planning approvals, we would confirm the exact details at a later stage.”

Universal’s other theme parks include rides featuring characters from the studio’s own movie and TV library. There are “Jurassic Park” rides at parks in Singapore, Japan, China and the United States. Some of those parks also have rides featuring characters from “Shrek,” “E.T. the Extra-Terrestrial,” “Jaws” and “Back to the Future.”

But a theme park near London could also feature characters closer to the British imagination. Universal has licensed other companies’ characters, including those from Nintendo, Harry Potter and Sesame Street, to use in rides at its parks. It could do the same with other British brands like Paddington Bear or Dr. Who.

Germany’s centrist parties announced on Wednesday that they had formally reached a coalition agreement to allow Friedrich Merz, a conservative, to take the reins as chancellor at a tumultuous moment when Europe’s economic and security order is being upended.

Since Mr. Merz’s Christian Democrats came out on top in elections in February, he has been under tremendous pressure to get a government moving as the Trump administration batters Europe with tariffs, threatens the NATO alliance and cozies up to an aggressive and expansionist Russia.

Sensing the urgency, Mr. Merz took the exceptional step of using the interim period to push measures through Parliament to raise debt limits so that Germany could throw billions more at infrastructure and military spending. The coalition agreement announced on Wednesday was the fastest since 2009, when Angela Merkel won her second term.

Nonetheless, Germany, Europe’s largest economy, has been left virtually leaderless during the multiple overlapping global crises.

“We don’t yet know which direction the international situation will take, but that is why our message today is all the clearer: In this global change we want to — and we will — help shape Germany,” Mr. Merz told reporters as the coalition plan was presented.

The far-right Alternative for Germany, which finished second in the February election, has continued to rise in polls, but the mainstream parties had vowed not to partner with it because it is considered a threat to German democracy.

Instead, Mr. Merz’s conservatives will join with the center-left Social Democrats of the departing chancellor, Olaf Scholz, reconstituting the kind of centrist coalition that long dominated German politics. While the agreement still needs to be approved by each party, Mr. Merz is expected to be sworn in in early May.

Uwe Jun, a politics expert who teaches at the University of Trier, in western Germany, said that, because of the world political situation, the Christian Democrats and the Social Democrats “feel that Germany needs a government capable of action, and this has become even clearer from Trump’s actions in recent days.”

The coalition deal includes compromises on issues such as taxes, infrastructure spending, defense and migration. For Mr. Merz, who promised a political change during the campaign, it was important to show that his government would be substantially different from Mr. Scholz’s, which was hobbled by infighting that forced him to call elections more than half a year ahead of schedule.

Party leaders had spent the final hours negotiating tax brackets and pensions, with the Social Democrats insisting on higher taxes for top earners and the business-friendly conservatives demanding that a tax put in place to pay for reunification be struck down, according to reports.

The coalition partners agreed to stiffen measures to prevent illegal migration and to undo some recent changes that had made it easier to become a German citizenship. They will also reduce some taxes, including on overtime pay, and reduce unemployment benefits, hoping to push more Germans into the work force. The new government will also create a ministry focused on digitalization, Mr. Merz said.

Critics worry that the government, sometimes called a “black-red” coalition for the party colors, lacks the broad vision needed to lift Germany out of its economic funk and stop the rise of the AfD.

Polls show that Germans — deeply worried about the state of global affairs — have started losing trust in Mr. Merz even since the election, wary of his new spending measures and the appearance that he has conceded too much to his coalition partner.

Daniel Friedrich Sturm, writing in Der Tagesspiegel, Berlin’s largest daily newspaper, noted, “It is now really time for the black-red negotiators to finally get their act together — and for the citizens to be able to see six and a half weeks after the election what this potential government wants to tackle and how.”

Recent polls suggest that the AfD, which won 20.8 percent of the vote in February, and the conservatives, which took 28.6 percent, would be running neck and neck if an election were held now. On Wednesday, one poll put the AfD at the top with 25 percent, ahead of the conservatives, who got 24 percent. It’s the first poll showing a far-right party in the lead since the end of the Nazi era.

After some leaks about the coalition talks, members of Mr. Merz’s party criticized him for not being tough enough with the Social Democrats. Though that party received only 16.4 percent of the February vote, it is widely seen as having had the upper hand in coalition talks.

Some conservative party members were particularly irked by an expensive infrastructure commitment that Mr. Merz helped pass, despite frequent assurances during the campaign that he would not borrow before trying to find money in the regular budget.

“Where is the promised new direction in migration policy?” the Cologne chapter of the youth wing of Mr. Merz’s party challenged him in a letter cited by the German news media, adding, “Where is the economic turnaround we announced?”

An Israeli airstrike on a home in a neighborhood in Gaza City left a heavy death toll on Wednesday and others missing, with rescuers struggling to pull people out of the rubble with little equipment, Gaza’s civil defense service said.

The Israeli military said it had been targeting a Hamas operative who it said was responsible for planning attacks. It did not name the operative or give further details.

A spokesman for the Gazan civil defense service, Mahmoud Basal, said that rescuers had pulled 23 bodies from the destroyed buildings, including those of eight children, with about 20 people still missing. He said the strike had completely destroyed eight homes in Shajaiye, an already hard-hit neighborhood where Israel last week called for evacuations and which housed families who had been displaced from elsewhere in Gaza. Additional airstrikes had targeted other parts of the neighborhood on Wednesday, Mr. Basal said, but rescuers had not yet been able to respond to those strikes.

The service’s figures do not distinguish between civilians and combatants.

The Israeli military says Hamas operatives embed among civilians. On Wednesday, it said that it had taken “numerous steps” to reduce harm to civilians before striking, using aerial surveillance, “other intelligence” and precise weaponry. A New York Times investigation has found that the Israeli military has loosened its rules on how many civilians it can endanger with each airstrike, and experts on international law note that Israel still has an obligation to protect civilians.

The Gazan civil defense said that its crews were having difficulty pulling out survivors because they lacked heavy equipment to sift through the debris.

Israel has faced international condemnation for killing tens of thousands of people, including children, in Gaza during its pursuit of Hamas. Gaza health officials say that more than 50,000 Palestinians in Gaza have been killed since Israel began striking Gaza in October 2023 in response to the Hamas-led attack on Israel that killed more than 1,200 people. Both figures include combatants and civilians.

The Israeli military said on Friday that its forces had begun operating in Shajaiye to “expand the security zone,” referring to what the military has characterized as a buffer zone next to Israel’s border with Gaza.

The military had warned people to leave northern Gaza late last week as it expanded its ground campaign. But while many followed the evacuation orders, others chose to stay in their homes or in shelters, saying that they could not face more upheaval after enduring displacement after displacement earlier in the war. Israel is holding an increasing amount of territory, leaving Gazans even fewer places to go.

During the first 15 months of war, the fighting between the Israeli military and Hamas reduced much of Shajaiye to a wasteland. Buildings were demolished, roads torn apart and infrastructure destroyed.

A shaky cease-fire paused the fighting and allowed more humanitarian help than before to enter Gaza from January to March. But after cutting off aid in early March, Israel broke the cease-fire on March 18 with renewed airstrikes after the two sides failed to reach an agreement to extend the truce.

Since then, the Israeli military has bombed Gaza repeatedly and seized more territory, a strategy that Israeli officials say is intended to compel Hamas to release more hostages.