US Secretary of Education Betsy DeVos came into the Education Department with a bold vision: that parents should be able to send their kids to school wherever they wanted, by way of government-funded vouchers.

Nine months later, she’s made little progress on that goal. But her Education Department has made other, quieter changes that affect millions of students.

Many of those changes involve rolling back Obama-era regulations. It’s now harder for recent graduates of for-profit colleges to get their loans forgiven. Transgender students know the federal government isn’t backing them up as they fight to use the facilities that match their gender identity rather than the sex assigned to them at birth. And on college campuses, survivors of sexual assault wonder how seriously the Education Department is taking their claims.

So while Congress rejected DeVos’s proposed cuts of $9 billion to the Education Department, and with it, her strategy to implement school choice programs nationwide, it doesn’t mean she’s powerless. By rescinding Obama-era policies, DeVos has made an immediate mark.

A lack of protection for transgender students

M.S. is a 13-year-old girl from Virginia who loves makeup, hanging out with her friends, and keeping up her Snapchat streaks. She considers Jackie Kennedy and Hillary Clinton her role models, calling them “boss ladies,” and dreams of someday moving to California, going to UCLA, and becoming a makeup artist like her favorite YouTube and Instagram stars.

M.S., who is transgender and is identified by her initials to protect her privacy, has been living as a girl since she was in fourth grade. It’s never been an issue among her classmates or friends, she said: “They don’t see me as trans; they see me as their best friend.”

Some of the parents at her school feel differently. That started a local battle that echoed a bigger national debate, a debate in which the Obama administration sided with transgender kids like M.S. and the Trump administration with the parents of her classmates.

Since the fourth grade, M.S. has been advocating for the right to use the girls’ bathroom. For about three weeks after she transitioned, she was allowed to, until a group of parents found out.

What happened next was a school board meeting that her mother, Amy, still remembers vividly: Parents wearing “Save Our School” badges went up to the podium, calling her then-10-year-old daughter an abomination and a predator. One suggested that the school was opening the door for “bullying, rape ... and possibly death.”

“It was awful; it’s probably the most alone I ever felt, being in that room that night,” Amy said. Then the board hastily voted to keep her daughter from using the girls’ restroom.

As transgender kids gained more visibility nationwide, the Obama administration released federal guidance on this issue in May 2016. Obama’s Education Department declared that Title IX, which forbids sex discrimination in education, protects trans students, and told schools that trans students should be called by their preferred pronouns and names and be allowed to use the bathroom that corresponded to their gender identity.

But the guidance was short-lived — 11 states sued the administration, claiming the directive wasn’t lawful and would be too disruptive for school districts. A federal judge agreed in August 2016, halting it nationwide.

Then, about a month into Betsy DeVos’s tenure, the Education Department and Justice Department sent out a joint letter to school districts rolling back the guidelines, which they characterized as federal overreach. (DeVos herself reportedly opposed the move, but the department she leads still signed on to the letter.)

Neither the guidance nor its reversal really changed anything day to day in M.S.’s school. Her district is still waiting for a court decision in the case of another transgender student from Virginia, Gavin Grimm, who sued nearby Gloucester High School in 2015. His case is still ongoing. But for M.S., knowing President Obama was on her side made all the difference.

“When Obama was president, I knew I had someone that was rooting for me and supporting me,” M.S. said. “All Trump is going to do is nothing, or say no.”

Across the country, protections for trans students are growing at the local level; Harper Jean Tobin, director of policy for the National Center for Transgender Equality, estimates that just under half of US schools now have policies in place spelling out transgender students’ rights. But only 13 states and the District of Columbia have anti-discrimination laws on the books protecting transgender students.

Rescinding the Obama guidance isn’t going to take anything away from the schools and districts that have already implemented their own policies. But it makes things more difficult for students like M.S.

“What the Trump administration did I think was to send a message that discrimination against trans students might be okay,” said Tobin.

Those students’ best hope lies with the courts. A federal appeals court recently decided a transgender boy from Wisconsin should be permitted to use the boys’ restroom. Grimm, the transgender student from Gloucester, is still fighting his case in the lower courts, after the US Supreme Court said it would not hear the case this year.

That decision will matter a lot for M.S., who says she wants to advocate for the trans community when she grows up. For Amy, it’s heartbreaking, especially given how much M.S. has flourished since she transitioned. Amy had braced herself for the possibility that her daughter would be bullied by classmates after she transitioned, but the opposite happened. Initially, the kids had questions, but the teasing M.S. had endured stopped. And Amy noticed something else right away — M.S. was happy.

“As a mom, I can see it now,” she said. Looking back at old pictures, “she looks so unhappy. Now the smile takes over her entire face. It was like a puzzle piece shifted for her.”

At the Office for Civil Rights, goals have changed

The Education Department’s Office for Civil Rights is often associated with sexual harassment and transgender cases, but the scope of its work is much broader. It’s charged with enforcing the 1964 Civil Rights Act in public schools, which is supposed to make sure harassment doesn’t interfere with any student’s right to learn.

“It’s a beautiful mission; it’s a broad mandate,” said Catherine Lhamon, the chair of the US Commission on Civil Rights. Lhamon formerly served as the assistant secretary for civil rights in the Department of Education under Obama.

Officials at the Office for Civil Rights did not respond to a request for an interview.

One of OCR’s main duties is to investigate harassment complaints from students, faculty, or families. But the Obama administration had a two-pronged approach. It tried to look for patterns with harassment and target systemic problems, and issued guidance on how schools should treat students who were gay, transgender, disabled, or had experienced sexual assault and investigate allegations of sexual harassment and assault.

Under DeVos, OCR is closing out a backlog of more than 1,000 investigations at a record-setting pace. They have said they are focused less on systemic problems, to give individual cases a faster resolution. Students sometimes wait years to get their cases investigated, and staff cuts proposed by Trump could drag this out even further. Understaffing has always been an issue at the office; Lhamon said OCR investigators had about 26 cases per person under Obama, which could go up to 45 cases per person under Trump.

“I am still sick about the length of time that it took for us to solve cases,” Lhamon said. “The office was wildly understaffed the entire time I was there. Everybody was working as fast as they could.”

Critics, including conservatives and some legal experts, saw the approach from the Obama administration as heavy-handed. In rescinding it, DeVos said she was correcting federal overreach. But Lhamon said the guidance was supposed to provide schools with answers, after her department fielded many questions from schools about their responsibilities.

“Our view was that we needed to be responsive to the people that were asking questions,” Lhamon said. “The guidance is the job of the office because it tells people what the law is and how to satisfy it.”

Lhamon said she fears that by simultaneously rescinding guidance and closing out investigations, the Trump administration is sending a message to students that they won’t be taken seriously.

“The clearest message in this administration is that student civil rights will not be protected by the federal government,” she said.

Schools uncertain about professional development funding

At the Decatur City School District in Alabama, teachers and administrators are anxiously awaiting news about the fate of a federal program called Title II.

The district gets the vast majority of its teacher professional development funds from this program, about $347,000 in federal money each year, compared to $42,828 from the state. That money is used to keep teacher training current on everything from class planning to technology to helping English language learners.

School districts across the country get $2.1 billion in Title II grants that help pay for professional development and reduce class size. The Trump administration proposed eliminating the grants entirely, and the House Budget Committee also supports the cut.

The program isn’t dead yet, as the Senate appropriations subcommittee for education rejected the cuts. Title II’s fate won’t be decided until December, when Congress is set to vote on the budget. In the meantime, the uncertainty alone is making school districts nervous.

“Across our state, everyone’s just saying there’s no way to replace that,” said Melanie Maples, chief finance officer for the Decatur school district. “We would have to eliminate a lot of the teacher training we would provide. I think for most school districts, that has been their main source of professional development for their teachers.”

Added up, the proposed cut to Title II could impact the professional development of 2.4 million teachers. Cuts to the class size funding would result in more than 8,500 teachers across the nation losing their jobs, according to analysis from the National Education Association, the nation’s largest teachers union.

Title II has not been without criticism over the years; many people, including Obama Education Secretary Arne Duncan, have said the program needs more data to show that professional development benefits teachers.

“If you can’t answer that question in a clear and cogent way, you’ve got a problem,” said Mike Soules, president of Corwin, an education publishing company that provides professional development materials to many of the nation’s schools. “It’s an absolutely critical moment — it’s the moment of what do you believe in, where do you think dollars should be spent and why.”

National Education Association director of teacher quality Andrea Prejean said professional development programs help mentor young teachers struggling to adjust. The nation is experiencing a teacher shortage, especially in science and math, in part due to low pay and the high demands of the job.

If the proposed cuts go into effect, “we’re not going to be able to shift almost $2.1 billion from other pots in professional learning,” Prejean said. “Every state is going to lose significant amounts of money.”

School lunch nutrition standards are relaxed

Planning a weekly school lunch menu is like putting together a puzzle. School lunch directors and cafeteria workers have federal nutrition guidelines they must follow to make sure kids eat balanced meals, but they also want to make the food tasty enough for kid to eat it.

When it’s burrito day at the Cleveland Metropolitan School District in Ohio, the district’s executive director food and child nutrition services Chris Burkhardt has to plan things out carefully. The premade salsa has a lot of sodium, so his staff cut it with diced tomatoes and pair it with low-sodium taco meat, to make sure the burritos aren’t too salty. Then he has to make sure he’s not putting too much fat or sugar into a meal to compensate for the lack of salt.

“You could get one side correct, but you could get other side wrong,” he said. “A lot of times we hit the mark, and sometimes we don’t.”

Burkhardt and school lunch directors around the country have a lot of flexibility from the federal government to plan meals. That’s because in early May, new US Secretary of Agriculture Sonny Perdue announced that he would put a pause on school lunch standards passed by Congress in 2012 that lowered the amount of sodium and refined grains in school lunches.

Under regulations the Obama administration wrote to implement the Healthy, Hunger-Free Kids Act of 2010, public schools were required to make their school lunches more nutritious by getting rid of trans fats, setting limits on the amount of sodium, and making sure foods like pizza, bread, and pasta contained 50 percent or more whole grains. Schools were also asked to provide kids more fruit and vegetables.

Burkhardt said the whole-grain pasta was fine if it was served right after it was cooked, but “if you hold it for any length of time, it becomes a gelatinous mess. Whole grains tended to be more mealy; they had a different mouthfeel.”

When kids don’t like school lunches, districts lose money. For instance, in the Los Angeles Unified School District, the nation’s second-largest, students threw out at least $18 million worth of food per year, the district’s food service director told the LA Times in 2014.

The Obama administration started granting school district waivers to have the flexibility to use enriched pasta again. When Perdue became secretary, he also halted the standards to lower sodium before they went into full effect.

Many public health experts opposed the move. Doctors and nutritionists pointed to the fact that rates of childhood obesity have tripled since the 1970s, with about one in five schoolchildren considered obese, according to the Centers for Disease Control and Prevention. And public health advocates were optimistic that the new school lunch standards could help put a dent in the alarming trend; one study by researchers at Harvard, Columbia, and George Washington University estimated that the healthier school lunch standards could help prevent another 1.8 million children from becoming obese.

A friendlier climate for for-profit colleges

Enrollment at for-profit colleges exploded in the decade before Obama took office. So did the debt those students held — loans they often struggled to pay back. About one in every 10 federal student loans issued went to a student at a for-profit college. But among the loans that ended up in default, or with about nine months of missed payments, 44 percent had been taken out by for-profit college students.

So in 2009, Obama’s Education Department began an ambitious effort to try to close for-profit college programs, as well as vocational programs at all kinds of colleges, if their students didn’t earn enough after graduation to pay back their loans.

They ended up with a regulation known as the gainful employment rule. Vocational and for-profit college programs were judged on whether their students earned enough money to be able to repay their debts. Programs that couldn’t hit the federal government’s benchmarks would eventually be cut off from student loans.

After several court challenges, the final version of the regulation went into effect in July 2015. (In the meantime, the for-profit sector began to struggle, and several major colleges closed their doors.) DeVos plans to overhaul them, and is already dismantling key provisions — part of an overall shift in attitude at the department to be friendlier toward for-profit colleges.

In July, the department announced a one-year delay on the requirement that institutions disclose their graduates’ debt and earnings. On August 8, the department reported to Senate Democrats that it had “no timetable” for sending institutions data necessary to calculate those figures. More than 2,000 programs in trouble under the rule are also able to repeal their results.

Students in debt left in limbo

The new regulations the Obama administration wrote for for-profit colleges, though, didn’t do much for the students who had already attended them and were paying back their loans. Even if the college itself was in trouble, students were still saddled with their debt.

But after the collapse of two major for-profit college chains — Corinthian Colleges and ITT Technical Institutes — this started to change.

Former students turned to a little-known provision of federal law known as “defense to repayment.” It allows borrowers to apply for loan forgiveness if they were the victims of fraud or misrepresentation by their college or university. After former for-profit college students began using that provision to argue they shouldn’t have to repay their loans, the Obama administration wrote new rules, set to go into effect on July 1, 2017, that laid out exactly when students would be able to have their debts forgiven.

The regulations also required schools that might be at risk of closing to put up financial collateral and banned arbitration agreements, which have kept many students from suing schools they believe defrauded them.

But DeVos has begun efforts to roll back loan forgiveness policies by freezing the regulation, leaving thousands of students in limbo. In addition, the US Department of Education has not approved any borrower defense applications since the beginning of the Trump administration, leaving thousands of students uncertain about the status of their loans.

“They’re just sitting and the department isn’t processing them,” said Eileen Connor, the director of litigation for Harvard Law School’s Project on Predatory Student Lending.

Connor said that while the Trump administration has been noticeably warmer toward the for-profit college industry, predatory for-profit schools have been around for years, and many administrations have been slow to address the issue.

“I think it’s really far past time for the department to take seriously that students have rights, they’re in their loan contracts, and they can’t turn a blind eye to the fact the law has been broken,” Connor said. “It’s leaving the status quo in place, and the status quo is hurting students of for profit colleges.”

A step back on sexual assault guidelines

Last week, DeVos suddenly announced the Education Department would rescind the Obama-era guidelines that spelled out how universities should respond to allegations of campus sexual assault. The interim guidelines DeVos put in their place gives colleges the option to put a greater burden of proof on the accusers in such cases. It also gives colleges an indefinite amount of time to conduct their investigations and allows some cases to be resolved through mediation.

One of the impacts was confusion among students about what their rights were.

Elizabeth Boyle is a sophomore at Notre Dame University and a student representative for Know Your IX, an organization that advocates for survivors of sexual assault and harassment. After DeVos’s initial speech in early September, Boyle said many Notre Dame students were asking if this meant they were no longer protected under federal law.

“More confusion, more hysteria; it caused students to not know where to turn,” she said. “Knowing a lot of friends who had been assaulted themselves, it caused me great concern.”

In 2011, the Obama administration implemented strict guidelines for how schools should investigate and handle sexual assault allegations, when it sent out a “Dear Colleague letter” that urged universities to deal with allegations of sexual harassment and assault through the proper channels.

It wasn’t just a request; the Obama administration said sexual assault fell under the federal Title IX, which was passed in 1972 as part of a broader education law that prohibited discrimination in education based on sex. Though it mostly applied to women’s college athletics in the beginning, the Obama administration made Title IX the main line for tackling campus sexual assault; if schools didn’t comply with the guidelines, they risked losing their federal funding.

One of the most important and controversial parts of the letter established a new standard of evidence colleges were to use when finding students responsible for sexual assault. In a criminal court, someone accused of a crime has to be found guilty beyond a reasonable doubt. Many colleges, in sexual assault cases, had used a slightly lower standard of “clear and convincing evidence.” The Obama administration told colleges to instead use the “preponderance of the evidence” — a greater chance that someone is guilty than not — in their student justice systems, which is the standard of proof in a civil trial.

This lower standard of evidence and other changes prompted many in the legal and higher education communities to sound the alarm, saying the Obama administration was not giving accused parties due process and forcing schools to overreach with rules that were too broad. For instance, in 2014, a group of 28 Harvard Law School professors took the unprecedented step of writing a letter pushing back on the Obama guidance, saying it had caused Harvard’s administration to overcorrect to the extreme.

“I think they created an environment where schools felt in order to keep their federal funding, they had to change their policies to ones stacked against anybody accused,” said Elizabeth Bartholet, one of law professors who signed the letter and faculty director of Harvard Law School’s Child Advocacy Program.

But Obama’s initiative also won the support of many sexual assault victims and advocates, who believed they finally had a presidential administration taking them seriously and said the guidelines actually made it easier for schools to know the concrete rules they had to follow. That was reflected in the number of investigations into how schools were handling assault cases. Since 2011, a total of 439 investigations were opened into whether colleges were mishandling cases; 79 cases have been resolved, while another 360 remain open.