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Kui Zhang, Mathematical Sciences
Qiuying Sha, Mathematical Sciences

Decoding Genetics

It's all in the genes. But with an estimated 19,000 to 20,000 genes in the human body, and tens of thousands of variations for each, how do we figure out what our genes are trying to tell us? Statistical geneticists Qiuying Sha and Kui Zhang move closer to the answer every day.

Statistical genetics is the process of developing and applying statistical and computational methods to make inferences from genetic data. The goal is to develop a powerful method for finding the genes that cause disease.

Sha’s research centers on genetic epidemiology, which looks at the role genetic factors play in health and disease for families and populations. It also considers how genetic factors are influenced by environmental factors. Because common diseases are influenced by thousands of gene variations, and gene-to-gene and gene-to-environment interactions can influence how or whether a person develops a disease, the work is challenging.

"I want to find what causes disease so that we can find a cure," she says. "If we develop the right methodology, it can be applied to anything, as long as you have the data. The technology is improving. Now we need the right method."

Zhang's current research focuses on development of statistical methods for genotype calling and imputation for genes, especially for Human Leukocyte Antigen (HLA) genes, which help regulate the immune system. According to Zhang, variation in HLA genes is related to many complex human diseases. Understanding those variations is critical to developing therapies for immunological disorders and diseases.

"Obtaining accurate HLA genotypes from whole genome typing or sequencing is challenging and often cost prohibitive for large samples," Zhang says. Zhang and his team hope their research will result in more accurate genotype calling and imputation of HLA genes. They also plan to develop software for HLA genotype calling and imputation.

"Ultimately," Zhang says, "we hope our methods and improved accuracy for HLA genotypes will expedite our understanding of the genetic architecture of many human diseases."

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Tim Scarlett, Social Sciences

It wasn't a door to anything in particular anymore. Rusted, warped, with cracks repaired some time in the distant past, the old iron stove door was dug from the ground near the old settlement of Clifton on the Keweenaw Peninsula. For Tim Scarlett, behind this door is a story, one that connects physical objects to their environment. More than anything, however, objects like the stove door tell a uniquely human story. From this door Scarlett is able to pull details like the stove's expense, where it was probably installed, and how it came to have parts of it in a field.

The past they study physically and philosophically connects people with each other and their surroundings. Ultimately, that means the industrial archaeologist has to be a bit of an intellectual dilettante, bringing together knowledge from a variety of fields to build wisdom, but it also requires being aware of what there is to know, what knowledge there can be.

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Rudy Luck, Chemistry

When you join the military, there are certain risks you expect. Anything from enemy combatants to training accidents can strike in the blink of an eye.

What you don't expect is for the air you're breathing to spark an explosion.

Rudy Luck was presented with precisely this problem by the US military. The associate professor of chemistry at Michigan Tech was brought in when the military discovered R40—an unapproved coolant maintenance personnel were sold by local suppliers—in some of their armored vehicles. R40 reacts with aluminum to create the highly reactive gas trimethylaluminum, TMA. This is a problem in an environment like Iraq, where cooling is vital and continuous.

Making this more complicated is the fact that the impressively armored vehicles are not designed to open easily. With hydraulic doors that require additional time to open—preventing unwanted access from the outside—it's not like there's a margin of error when an explosive mix is washed in through the air vents.

"What they discovered was that vehicles would come back for refurbishing and the chloromethane (R40 coolant) could be reacting with the aluminum in the engine," says Luck. Chloromethane isn't supposed to be there. It's a cheap substitute that local suppliers use instead of the proper refrigerant, tetrafluoroethane.

The resulting mixture is explosive. "We brought two vehicles up here and demonstrated just how dangerous this can be," says Luck. "We shot a flask of this mixture at a test range to show what could happen. It was quite a bang."

The proper refrigerant, called R134a, works well, but the atmospheric effects are stark: more than 1300 times the warming effect as the greenhouse gas carbon dioxide. The European Union is now mandating a newer option referred to as HFO-1234yt. It's hard to make, however, and it may not work in the current generation of cooling systems.

Luck's team has devised a method to safely deactivate the TMA.  They are also finding ways to test for the unapproved coolant in both combat vehicles and Apache helicopters. So far they've found traces in a few, though not enough to produce the explosive TMA.

Still, even that small chance is enough for Luck to keep his focus.

"My neighbor's son went to Iraq three times," Luck explains. "I've seen pictures of him in these same vehicles. This is personal. This is important."

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Beth Reed, Mathemaatics
Stefaan de Winter, Mathemaatics

Long before we had smartphones and tablets, graphing calculators showed that a diverse collection of functions and applications could combine on one device. After a few basic math classes, all of those calculator buttons make sense, too. We've answered everything in math, right? Not quite; mathematicians have to discover new algorithms for new technology, all the while training the next generation of mathematicians to understand and apply their knowledge in new ways.

Trained as a forester, Beth Reed moved over to math to fulfill a lifelong teaching ambition. The problems she encountered with computing forestry research data came in handy when it was time to be in front of the classroom: it became a matter of giving students the tools they need to solve problems in science and technology.

Stefaan de Winter has a love for those tools as well; he sees the underlying beauty of mathematics, going so far as using a Sesame Street song to emphasize that while we all know the deceiving simplicity of 1-2-3-4, there is a massive forest of mathematics hidden among these numeric trees.

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Petra Huentemeyer, Physics

In the grand scheme of things, the twin Voyager spacecraft are close by. Petra Huentemeyer is looking beyond the wobbling radio signals from our interplanetary probes: she measures energy from our galaxy and throughout the universe with the help of a collection of giant water tanks. Near Puebla, in southern Mexico, the High-Altitude Cherenkov (HAWC) Gamma-Ray Observatory catches fleeting glimpses of that energy's strength. Part of a multi-national effort—with primary institutions in the United States and Mexico augmented with researchers from Europe—this instrument is the latest in the arsenal scientists like Petra—who was involved at CERN as a grad student—use to understand the most intense energy sources in the universe.

Gamma rays are energetic and elusive. When a particle resulting from the interaction of a cosmic or gamma ray with our atmosphere enters a water tank, it creates a cone of photons, a brief explosion of light that the very sensitive detectors of HAWC can measure. Software, written by Petra and her team, then records the results, determining the nature of the energy, and extrapolates the origin of the gamma ray in the sky. More detectors means more sensitivity and finer precision on the origin of the burst. HAWC Observatory has been completed and was inaugurated in March 2015. Currently, scientists are taking data while the observatory is being extended with a sparse array of "outrigger" detectors around the central HAWC array.

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Jason Carter, Kinesiology and Integrative Physiology

It's odd if you think about it. We have to spend a third of our lives unconscious or we can't function. And that's not I-forgot-where-I-parked function, that's everything from development to physical and mental well-being.

But for how much it dominates our lives, there is so much about the connection between sleep and our existence we're yet to understand. Jason Carter dreams of shedding light on those ties.

Supported by the National Institutes of Health, Carter's lab, in conjunction with healthcare providers, has been studying how sleep deprivation in women leads to an increased risk of hypertension, as well as the effects of interrupted sleep at various times throughout the night. Both genders are also susceptible to the effects of stress, a major factor Carter is studying.

Sleep science, as a field, is only about a third of a century old; there's a great deal we do not yet know, leaving a rich landscape yet to explore. "We are just beginning to realize the importance of getting a good night's sleep," Carter says. "There is a cumulative effect from not getting enough sleep."

The seven to eight hours of sleep we need per night is getting harder and harder to come by, and for those who work a disrupted schedule, the effects can be even more pronounced.

That much time devoted to sleep makes Carter wonder, just like the rest of us. "We spend one-third of our lives, more or less, asleep, and we still don't know the real physiological purpose."

It isn't that wonder that keeps him up at night, though. Despite being aware of the need for a good night's sleep, it doesn't always come easily to Carter.

He has insomnia.

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Raymond Shaw, Physics
Will Cantrell, Physics
Lynn Mazzoleni, Chemistry
Claudio Mazzoleni, Physics

High in the Sky

A Brocken spectre—also known as a “glory”—is a tight, tubular rainbow formed around a shadow, the Sun projecting the image onto the clouds below. The conditions and timing have to be just right. What if we can make atmospheric conditions just right, here in the Keweenaw, any time we want?

Atmospheric science researchers at Michigan Tech no longer have to cross their fingers for cooperative weather. The University’s cloud chamber allows them to make their own. The lab is one of only a handful in the world and the only one capable of sustaining clouds for hours.

But why is this study of clouds so important? Understanding clouds means understanding climate and the processes that drive our weather. The chamber is modular, allowing for instruments to be added or subtracted as needed. This means it can stay on the cutting edge long into the future.

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