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Breathe in, breathe out

Speed read
  • Studying reptile lungs helps scientists discover links between bird and mammal lungs
  • Supercomputer models let scientists experiment with different lung structures and airflows
  • Evolution of lung structures illuminates where we came from and how the natural world works

What do a bird and an alligator have in common? There really is a similarity but it’s one you easily can’t see. The answer is: their lungs.

Breathing is a complex process, which seems to vary depending on the species. Biologists are learning that lungs in vertebrates seem to evolve and adapt to the environment. But there is still much to discover.

Airflow patterns. Robert Cieri studies lung structure and function in vertebrates by comparing bird lungs to mammal lungs. He uses the Blue Waters supercomputer to model structure and airflow patterns. Courtesy NCSA.

That’s why Robert Cieri, a PhD student at the University of Utah and Blue Waters Graduate Fellow, is studying the airflow patterns in monitor lizards.

“We’re trying to understand the evolution of the respiratory systems in higher vertebrates,” says Cieri. “On one side there’s mammals, like cows and sheep, and the other side is birds and reptiles.

“We have a good understanding of how the bird lung works - there’s a unidirectional flow pattern throughout much of the lung, so when the animal is breathing in or breathing out air takes the same pathway from the back of the lung to the front, which is different from how the human lung works. For a long time, biologists thought unidirectional flow was really about efficiency—it provided enough energy for birds to be endothermic and to fly.

<strong>Unidirectional flow in bird lungs.</strong> When a bird breathes in or out, the air takes the same pathway from the back of the lung to the front. Courtesy NCSA.“But about 10 years ago, my advisor (Professor CG Farmer at the University of Utah) discovered unidirectional flow patterns also in alligator lungs. So now we have the same trait in a cold-blooded reptile that is semi-aquatic and not flying.

“So we need to go into other reptiles and figure out what’s going on in their lungs to get at the root of where these traits came from. Do they have lungs that are functionally more similar to birds or similar to ours?”

Cieri says that monitor lizards, which are found in warm climates, greatly vary in body size, metabolic rate, and habitat. Lizards with the same general body and lung design have lung traits that might vary with habitat use and body size. That makes them “a good group to study because they might represent the lizard lung that’s been selected [evolved] most for high activity.”

Why is airflow pattern important?

<strong>Bidirectional flow in rabbit lungs.</strong> When a mammal breathes, air moves back and forth into and out of the lungs. As a result, air coming into a mammal’s lungs is mixed with ‘old’ air, so contains less oxygen. Courtesy NCSA.One reason airflow patterns are so important, says Cieri, is that there are fundamentally different lung designs in vertebrates. By contrast, if you look at the development of hearts in reptiles and amphibians, they have a very clear progression, he explains, from simpler fish hearts to birds and mammals with similar designs.

“It’s interesting,” he says, “that lung evolution took a different path, and made a switch in the vertebrate family tree, going one way in birds and reptiles and another in mammals. By understanding why that switch was made and what those choices mean in an evolutionary sense, you can get a sense of the shared evolutionary history of different animals, understand more about the selective pressures that led to each lineage.”

How Blue Waters changed his research

A Blue Waters graduate fellowship allows Cieri to focus solely on his research and provides access to the leadership-class Blue Waters supercomputer at the National Center for Supercomputing Applications (NCSA) in Illinois.

“This access has been transformative, as it has allowed me to run more models than I could do with just campus resources, and increase the number of hypotheses I can test.”

<strong>One million elements.</strong> Because monitor lizard lungs are very complex, modeling the expansion and contraction that causes airflow is computationally expensive. Courtesy Robert Cieri.“We’re trying to understand what direction the air is flowing through these lungs and how the structure determines the airflow patterns. The best way we’ve found to do that is to use computational fluid dynamics (CFD) simulations to simulate how air would flow through the lung and then validate those simulations on real lungs.

“This is better than trying to measure the airflow direction on a real lung because many reptile real lungs are really small, complicated, and very fragile structures.

“Once I have one of these models built, I can go in and change some stuff—what if we move this wall to that wall, what if we close off the main chamber, what if we make this hole three times bigger—and that’s allowing us to have a lot of experimental opportunities to ask questions about how these lungs are working.”

Cieri usually runs on 96 Blue Waters compute nodes at once, as he’s discovered that’s the most efficient size for his models. The simulations take anywhere from 24-100 hours.

“Nature didn’t make the lungs simple, the models are very complex,” explains Cieri. “Each model has roughly one million elements...In a lot of CFD simulations you just have air flowing through a solid or static structure, it’s not moving. But since the animals are breathing, we’re trying to have the meshes expand and contract. That expansion and contraction causes the flow and is part of the reason they’re so computationally expensive.”

Linking birds and mammals. CT scans of a monitor lizard’s airwaves, showing the one-way pattern of air coming into and out of its lungs. This pattern, once thought to be necessary only for high-altitude flight, may actually have evolved up to 100 million years before birds existed. Courtesy University of Utah.

Building biology fundamentals

The work Cieri is doing is fundamental research, although he says it could one day potentially be applied to develop better artificial lungs.

“Biologists have wanted to know how bird reptile lungs work for years. But we didn’t have a good methodology to answer the question because lungs are fragile. If you try to measure things they break, and if you try to put some type of recording device in there you can’t always trust your measurements.

“HPC has made this research possible, because without the simulation techniques that are accurately able to replicate the flow pattern from CT scan data or imaging data, my PhD wouldn’t be possible. My work represents how research can pull together techniques from multiple fields, and how interesting melding biology and engineering and physics can be.”

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