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Methylation is responsible for sequence-dependent attraction between DNA strands


The laboratories of Professors Aksimentiev and Ha have uncovered the secret to DNA-DNA interactions in their latest Nature Communications article. Using molecular dynamics simulations and single molecule fluorescence resonance energy transfer, the authors directly demonstrate that double-stranded DNA molecules interact in a sequence-dependent manner that does not require the presence of proteins or Watson-Crick strand exchange. Additionally, the measured attraction involves DNA methylation instead of a previous hypothesis involving sequence homology. The methylation of certain nucleotides result in a stronger association between strands, which likely affects gene expression.

To read more about this work, you can view the original article here or read a featured interview with Aksimentiev and Ha.

1/21/2014 Jonathan Damery, ECE ILLINOIS

Fire rescue missions are rife with risk: floorboards and staircases that might collapse, a blaze hidden above a drop ceiling, supports disintegrating behind a masonry façade. Firefighters are trained to evaluate those dangers and respond accordingly. Yet not all dangers are visible. Last semester, three senior design students—Andri Teneqexhi, Lauren White, and Hyun Yi—prototyped a device that could protect firefighters from the most invisible danger of all: the searing temperature itself.

“This team just nailed it,” said Associate Professor Jonathan J Makela, the course instructor for Senior Design (ECE 445), who recognized the students with the Instructor’s Award, the highest designation granted among the 45 teams last semester.

The senior design team (L-R)—Lauren White, Hyun Yi, and Andri Teneqexhi—with the two components of their thermal sensing device.
The senior design team (L-R)—Lauren White, Hyun Yi, and Andri Teneqexhi—with the two components of their thermal sensing device.
“It’s not the most complicated project, but it was so well designed in terms of meeting the needs of the user.”

With modern firefighting clothing, every inch of skin is covered, insulating the firefighters from severe temperatures and exposure to gases and carcinogens. Along with fire-retardant outwear, there is a mask and self-contained breathing apparatus (SCBA), fitted over the face, keeping the air that they breathe relatively cool. But when the SCBA facepiece reaches a certain point—about 150˚C—those protections can become compromised. The polycarbonate lens of the firefighter’s mask begins to soften (a physical limitation of the material), and if the temperature continues to rise, the facepiece could fail, instantly exposing the firefighter to the dangerous temperatures. This is where the students’ device comes into play: something to warn the firefighters to exit, well before the temperatures reach that level. 

“Our system here has approximately one, two, three, four different temperature sensors, with about three different indicators,” said Yi, holding up the device, which fits onto and within a firefighter’s protective headgear. The interior portion, which mounts behind the self-contained breathing apparatus, has an LED warning light just below the field of vision and two buzzers that would alert the firefighters to the elevated temperatures. These components are designed with intentional redundancies. “Even if the electronics fail, this thing still goes,” Yi said, pointing to a mechanically based fuse in the external unit. 

Richard Kesler models a sensor designed by ECE ILLINOIS students. The sensor sits inside his mask.
Richard Kesler models a sensor designed by ECE ILLINOIS students. The sensor sits inside his mask.
The students designed the two sections to communicate via a wireless link, so that external and internal temperatures are processed by a microcontroller on the mask unit, and at the end of the semester, when the prototype was complete, they tested it in an enclosed variable heating chamber, ensuring that it would operate accurately and efficiently at real-world temperatures. “This is not something that we can have very large error bars on,” said Gavin Horn, the research program director at the Illinois Fire Service Institute, who advised the students throughout the semester. “We have to know exactly where we’re at, because a ten-degree difference in temperature of the facepiece could be very important.” 

To guarantee maximum practicality, the students not only attended to small design issues—using standard lithium batteries, for example, which can be easily replaced—but they also worked to keep the overall price under $30. “Keeping that budget was the most difficult part,” said Yi. “You could use something called a thermopile sensor, and that’s also very accurate and much easier to use [than our thermistors]…The reason we can’t use that though is that sensor alone cost $35, and then we’re already going to be blowing the budget on that.”

While additional testing and prototype development is still in order, everyone involved is confident that the device could become a useful component of firefighting protective gear. When the National Institute of Standards and Technology convened a workshop to address facepiece failures in 2011, a warning device was recommended as a possible solution. The students’ design responds to that call. “There is certainly potential for this to be a marketable solution,” said Horn. “The ability to sense the environment and to provide that additional feedback to the firefighter, we feel is critical, and hopefully, this will have a chance to address that concern.”

The students credit the successful design to their complementary skillsets and also to their active communication with one another and with fire safety experts. “I just think that’s very important, because imagine us not communicating with Gavin,” said White. “You don’t want to make something that they don’t want.”

Throughout the semester-long design process, as the students weighed conflicting needs and constraints, they would ask Horn which features would be most important in real-world scenarios. “Some of those, we’re able to give them straightforward answers and some of them we wanted to challenge them a bit and said, ‘Well, you have to make an engineering judgment on that,’” Horn recounted. “But they did a very good job.”

Early in the semester, the students also realized how important the electronics services shop (which provides circuit board fabrication) and the machine shop (which provides chassis fabrication) would be for the finished product. They worked hard to design those components and ordered them early. "Using all resources available to you is the key to success in this class," Teneqexhi suggested. “[And] it’s good to have a group schedule and try to keep up with it.”

Yet, overall, perhaps it was the real-world value of the device that was the ultimate motivation for the team’s success. “This is something that can actually help save lives, help reduce injuries,” White said. “You’re probably going to hear about this later…If you know a firefighter, I bet they’ll tell you, ‘I have this really cool unit made by students.’”