All this week we’ve been shining a light on juvenile justice in our series, Inside and Out. We’re asking what it would take to build a system that actually turns around troubled kids. Most of these young people come from hard circumstances – and everyone knows that’s a disadvantage. But now experts say going through trauma can alter a child’s brain. Violence at home or on the street, neglect, poverty – these things have profound effects on how a kid’s mind develops. We bring you more on this emerging brain science, and what it reveals about why, for so many kids, the justice system hasn’t worked.

So much of what Mario has become goes back to one day, when he was nine.

It was a chilly October night; Mario had just started fifth grade.

MARIO: Me and my little brother, we was like arguing and fighting, and my mother broke us up. And my stepfather was like, come on, I’m feeling to take y’all out for a ride.

They hopped in the van, and picked up his stepdad’s friend Duke.

They were going to drop him at the barbershop.

MARIO: Next thing I know I hear, like, loud noise. I felt the glass splattered all in my face. And my stepfather was like, anybody shot? Anybody shot?

Mario looked down at his side and saw the blood.

MARIO: The bullet traveled, it had came through the back and traveled inside of me, came out the side.

His step-dad hit the gas.

MARIO:And he got to yelling in my ear, please don’t die on me! Please don’t die on me!

They rushed to the E-R.

Mario dug one of the bullets out of his side with his fingers.

MARIO: Cutting open my shirt and everything. They even cut, like, my shoes!

His mother came, saw the blood, and fainted…his grandmother was so distraught she took a swing at a cop.

Later, a nurse rolled Mario to the operating room.

MARIO: I told her, can we stop real quick and you hold my hand and pray with me? And then they took me into surgery.

They opened up his abdomen and repaired his liver.

He drifted in and out of consciousness for days.

When he woke up, the nurse told him to take it slow.

MARIO: She was like, everything going to be alright, we’re gonna make sure you heal. I feel sorry for your face, too. And I was like, my face? What’s wrong with my face? And she, like, put the mirror on it, and I seen, like, all I seen was, meat and glass. I didn’t see no skin. And I was like, I’m never going outside again! Never!

This little boy had just taken two bullets and couldn’t recognize himself in the mirror.

What nine-year old has the emotional tools to deal with that?

Mario’s body would heal, but his mind was deeply wounded.

He started having nightmares.

It didn’t help that his stepdad terrorized and beat him … or that his real father was in prison.

MARIO: And it used to make me so mad. And I’d punch a hole in the wall or something because, there was adrenaline in my body that just felt like it had to be released. And when I fought, I felt calmer, a little bit.

Mario fought all the time.

He’d snap at tiny provocations. One time he assaulted his aunt with a screwdriver.

His behavior sounds shocking, but it’s no shock to Carl Bell.

BELL: It’s not surprising that children who come from that environment grow up to be violent. Hurt people hurt people.

Bell is a psychiatrist and directs the University of Illinois Chicago’s Institute for Juvenile Research.

He says trauma can warp the way a child develops.

BELL: Their brains are still growing. And if you overwhelm a child with trauma, their fight-flight-or-freeze mechanisms get distorted and broken. And it can impact their entire life’s course.

Research suggests growing up with chronic trauma can make the alarm center of a child’s brain hyperactive, maybe even larger.

The hippocampus – a brain structure that helps form memories – may wind up smaller and more sluggish.

The trauma response becomes embedded in the brain’s architecture: that fight-flight state, which is supposed to last a few minutes, becomes just the normal way to be.

BELL: You can be so jumpy and scared that if somebody even approaches you to ask a simple question, you immediately shift into fight, flight or freeze mode. And you don’t have any rest or relaxation or peace. These are brain pathways that get laid down as a result of a scar.

That scar means a traumatized kid may respond differently to authority and discipline.

Bell and others say the places these children often end up – foster care, mental hospitals, juvenile prisons – aren’t set up to deal with kids who are wired this way.

That was Mario’s experience at the special schools and hospitals where he spent much of his adolescence.

MARIO: When you snap or get out of control, they’ll throw you down, they put their knee, one knee in your back, one knee in the top of your neck. And then, it’ll be at least four dudes on you. And you stay like that until you’re calm. Me? It just made me madder.

GRIFFIN: If all you’re going to do is punish them, it’s just going to escalate and go on endlessly.

That’s Gene Griffin.

He’s a psychologist at Northwestern University, and he‘s working with the juvenile prisons to help them understand the effects of trauma better.

One study of kids in detention in Cook County found that nine of ten had experienced trauma.

More than 11 percent had full-blown post-traumatic stress disorder – by comparison, the rate for Iraq and Afghanistan veterans is thought to be about 14 percent.

Researchers say traumatized kids tend to have higher body temperatures and more muscle tone – it’s like they go through life on the balls of their feet.

Their bodies and brains are adapted to a world where they’re never safe.

GRIFFIN: These kids growing up in violent communities, they’re right – they’re not always safe. And so the more you can get them in a safe place with people who understand what they’re going through, all that helps them calm down. And then get back to them when they’re calm to do the learning about how the world is really different.

Griffin says that learning may be crucial to getting results.

Proven therapies based on that idea are emerging.

Take a kid like Mario: victimized, mixed up with the law, no father, tough neighborhood.

By the numbers, this young man should be locked up by the time he’s 20 – or dead.

MARIO: Um yeah, I have a lot of trophies…

Instead, Mario is a tall, lean college student, smiling as he shows off his tidy bedroom.

MARIO: One school I went to it was like hard to play sports ‘cause it was like basketball mixed with boxing. You’re doing a layup, gotta worry about getting a uppercut or something…

When he was 16, Mario got hooked up with the Chicago Child Trauma Center at La Rabida Children’s Hospital.

He started to understand why the care he got before wasn’t getting results.

MARIO: Some people was trying to help me, but they was trying to cure me. There’s like no cure, but there’s ways to deal with this.

The treatments at La Rabida focus on building those skills – how to calm himself down or cope with flashbacks.

And they capitalize on what psychologists call protective factors.

For Mario, strength came from a bond with his grandmother.

He had his intellect, and his talent with a pen and a basketball.

So by the time his brain was reaching maturity, he was ready to throw off some of his burden.

MARIO: If you think about the things that happened to you, and you stay there in that same position thinking about it, you’ll drown. I feel like in life we all are in the water, and we’re all trying to swim and make it. Sometimes it do take a light. Maybe you don’t see which way to go, maybe you think underneath is somewhere different, but for me, when people helped me out, that was that light above that had me kept swimming.

Mario wants to be that light for others.

His story has become a teaching tool for people in the juvenile justice system.

The coming months will tell us whether the kids there – and, maybe more importantly, the adults – are ready to hear it.