In a paper published today in Nature, North Carolina State University genetics researchers team with scientists from across the globe to describe the new reference manual – the Drosophila melanogaster Reference Panel, or DGRP. Dr. Trudy Mackay, William Neal Reynolds and Distinguished University Professor of Genetics and one of the paper’s lead authors, says that the reference panel contains 192 lines of fruit flies that differ enormously in their genetic variation but are identical within each line, along with their genetic sequence data.

These resources are publicly available to researchers studying so-called quantitative traits, or characteristics that vary and are influenced by multiple genes – think of traits like aggression or sensitivity to alcohol. Mackay expects the reference panel will benefit researchers studying everything from animal evolution to animal breeding to fly models of disease.

Environmental conditions also affect quantitative traits. But studying the variations of these different characteristics, or phenotypes, of inbred fruit flies under controlled conditions, Mackay says, can greatly aid efforts to unlock the secrets of quantitative traits.

“Each fly line in the reference panel is essentially genetically identical, but each line is also a different sample of genetic variation among the population,” Mackay says. “So the lines can be shared among the research community to allow researchers to measure traits of interest.”

The Nature paper showed that, in general, many genes were associated with three quantitative traits studied in fruit flies – resistance to starvation stress, chill coma recovery time and startle response – and that the effects of these genes were quite large.

“Until now, we had the information necessary to understand what makes a fruit fly different from, say, a mosquito,” Mackay says. “Now we understand the genetic differences responsible for individual variation, or why one strain of flies lives longer or is more aggressive than another strain.”

The study was funded by the National Institutes of Health, the National Human Genome Research Institute and the NVIDIA Foundation’s “Compute the Cure” program. Dr. Eric Stone, associate professor of genetics at NC State, is also a lead author of the paper, along with colleagues from Baylor College of Medicine and the Universitat Autonoma de Barcelona in Spain.

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“Chip manufacturers are now creating processors that have a ‘fused architecture,’ meaning that they include CPUs and GPUs on a single chip,” says Dr. Huiyang Zhou, an associate professor of electrical and computer engineering who co-authored a paper on the research. “This approach decreases manufacturing costs and makes computers more energy efficient. However, the CPU cores and GPU cores still work almost exclusively on separate functions. They rarely collaborate to execute any given program, so they aren’t as efficient as they could be. That’s the issue we’re trying to resolve.”

GPUs were initially designed to execute graphics programs, and they are capable of executing many individual functions very quickly. CPUs, or the “brains” of a computer, have less computational power – but are better able to perform more complex tasks.

“Our approach is to allow the GPU cores to execute computational functions, and have CPU cores pre-fetch the data the GPUs will need from off-chip main memory,” Zhou says.

“This is more efficient because it allows CPUs and GPUs to do what they are good at. GPUs are good at performing computations. CPUs are good at making decisions and flexible data retrieval.”

In other words, CPUs and GPUs fetch data from off-chip main memory at approximately the same speed, but GPUs can execute the functions that use that data more quickly. So, if a CPU determines what data a GPU will need in advance, and fetches it from off-chip main memory, that allows the GPU to focus on executing the functions themselves – and the overall process takes less time.

In preliminary testing, Zhou’s team found that its new approach improved fused processor performance by an average of 21.4 percent.

This approach has not been possible in the past, Zhou adds, because CPUs and GPUs were located on separate chips.

The paper, “CPU-Assisted GPGPU on Fused CPU-GPU Architectures,” will be presented Feb. 27 at the 18th International Symposium on High Performance Computer Architecture, in New Orleans. The paper was co-authored by NC State Ph.D. students Yi Yang and Ping Xiang, and by Mike Mantor of Advanced Micro Devices (AMD). The research was funded by the National Science Foundation and AMD.

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Note to editors: The paper abstract follows.

“CPU-Assisted GPGPU on Fused CPU-GPU Architectures”

Authors: Yi Yang, Ping Xiang, Huiyang Zhou, North Carolina State University; Mike Mantor, Advanced Micro Devices

Presented: Feb. 27, 18th International Symposium on High Performance Computer Architecture, New Orleans

Abstract: This paper presents a novel approach to utilize the CPU resource to facilitate the execution of GPGPU programs on fused CPU-GPU architectures. In our model of fused architectures, the GPU and the CPU are integrated on the same die and share the on-chip L3 cache and off-chip memory, similar to the latest Intel Sandy Bridge and AMD accelerated processing unit (APU) platforms. In our proposed CPU-assisted GPGPU, after the CPU launches a GPU program, it executes a pre-execution program, which is generated automatically from the GPU kernel using our proposed compiler algorithms and contains memory access instructions of the GPU kernel for multiple threadblocks. The CPU pre-execution program runs ahead of GPU threads because (1) the CPU pre-execution thread only contains memory fetch instructions from GPU kernels and not floating-point computations, and (2) the CPU runs at higher frequencies and exploits higher degrees of instruction-level parallelism than GPU scalar cores. We also leverage the prefetcher at the L2-cache on the CPU side to increase the memory traffic from CPU. As a result, the memory accesses of GPU threads hit in the L3 cache and their latency can be drastically reduced. Since our pre-execution is directly controlled by user-level applications, it enjoys both high accuracy and flexibility. Our experiments on a set of benchmarks show that our proposed preexecution improves the performance by up to 113% and 21.4% on average.

Protein labeling is used by researchers in a variety of fields to help them understand how these important molecules affect the normal functioning of cells. Currently, proteins are labeled for study simply by fusing them to other fluorescent proteins, which allows researchers to use microscopy to track their movements through a cell. This approach has several drawbacks, however, not least being that the fluorescent proteins are often large enough to affect the function of the protein of interest.

Dr. Alex Deiters, associate professor of chemistry at North Carolina State University, along with colleagues Drs. Jason Chin, Kathrin Lang and Lloyd Davis of the Laboratory of Molecular Biology at the Medical Research Council in Cambridge, U.K., have developed a way to attach a fluorophore – a fluorescent molecule about 20 times smaller than the fluorescent proteins currently in use – to a protein that is expressed in a mammalian cell.

Deiters and Chin developed a special 21^st amino acid that they added to cells that were specially engineered to incorporate this amino acid into the protein they wanted to study (there are normally only 20 amino acids). This 21^st amino acid has a “chemical handle” that only reacts with a specifically designed fluorophore, but not any cellular components. According to Deiters, “The reaction between the modified protein and the fluorophore is extremely fast, high yielding, and generates a stable link between both reaction partners. This novel methodology enables future cell biological studies that were previously not possible.”

The research appears in the Feb. 5 issue of Nature Chemistry.

“We found that our approach gave us a higher yield of labeled proteins and that the binding reaction was 50 times faster than with current methods,” Deiters says. “Additionally, it took less reagent to complete the reaction, so overall we have a faster, more efficient method for protein labeling, and less chance of interfering with the normal function of the proteins and cells being studied.”

The research was funded by the National Institutes of Health and the National Science Foundation.  The Department of Chemistry is part of NC State’s College of Physical and Mathematical Sciences.

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Note to editors: Abstract of the paper follows.

“Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction”

Authors: Kathrin Lang, Lloyd Davis and Jason W. Chin, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, UK; Alexander Deiters, Jessica Torres-Kolbus, Chungjung Chou, North Carolina State University

Published: Feb. 5, 2012 in Nature Chemistry

Abstract:
The site-specific incorporation of bioorthogonal groups via genetic code expansion provides a powerful general strategy for site-specifically labelling proteins with any probe. However, the slow reactivity of the bioorthogonal functional groups that can be encoded genetically limits the utility of this strategy. We demonstrate the genetic encoding of a norbornene amino acid using the pyrrolysyl tRNA synthetase/tRNA_CUA pair in Escherichia coli and mammalian cells. We developed a series of tetrazine-based probes that exhibit ‘turn-on’ fluorescence on their rapid reaction with norbornenes. We demonstrate that the labelling of an encoded norbornene is specific with respect to the entire soluble E. coli proteome and thousands of times faster than established encodable bioorthogonal reactions. We show explicitly the advantages of this approach over state-of-the-art bioorthogonal reactions for protein labelling in vitro and on mammalian cells, and demonstrate the rapid bioorthogonal site-specific labelling of a protein on the mammalian cell surface.

Cyrano is a 10-year-old tabby cat who was treated for bone cancer last year and is now in total remission. However, the disease and treatment weakened the bone in his affected back leg and Cyrano’s knee

Cyrano's implant is about the same size as a tube of lip balm. Image courtesy of Greg van der Meulen, BioMedtrix, LLC

deteriorated as a result. His owner, Sandy Lerner, felt that amputation would negatively affect the cat’s quality of life, and her search for other options brought them both to NC State and the team of orthopedic surgeon Dr. Denis Marcellin-Little and industrial and systems engineer Dr. Ola Harrysson.

Marcellin-Little and Harrysson are pioneers in osseointegration, a process that fuses a prosthetic limb with an animal’s (or human’s) bones. The NC State team, in collaboration with veterinarians and engineers from around the U.S. and abroad, will provide Cyrano with the first ever custom-made, osseointegrated feline knee replacement.

“Although total knee replacements in dogs are increasingly common, a cat poses some additional challenges, particularly regarding the size of the implant,” Marcellin-Little says. “Additionally, Cyrano’s existing leg bones were weakened by the cancer, so we must take care to be sure that the implant does not place undue stress on the remaining bone.”

If all goes well, Cyrano should be back to mousing at the family farm in about three months.

Cyrano’s case is unique, but Marcellin-Little hopes that this surgery will pave the way toward making feline knee replacements more commonly available. “This collaboration between NC State’s College of Veterinary Medicine,  College of Engineering, and outside implant designers and manufacturers allows us to design and make implants that we could only dream of, in the past. I am sure that this technology will help other patients with tumors, in the future.”

Clark is owner and president of Guy M. Turner Inc. a Greensboro-based company founded in 1924. The company specializes in heavy rigging, specialized transportation and crane services, and has 10 offices in seven U.S. states.

Clark received his Bachelor of Science degree in civil engineering from NC State in 1974 and is a registered professional engineer. He served as chair of the NC State Board of Visitors, and is a member of the NC State Engineering Foundation Board, Dean’s Circle, Student Aid Association, Alumni Association and The Walter Hines Page Society. He has also served on the Park Scholarship Selection Committee and has established the Jimmy D. Clark Distinguished Professorship for NC State’s Department of Civil, Construction and Environmental Engineering.

NC State’s Board of Trustees is composed of 13 members; eight are elected by the UNC Board of Governors, four are appointed by the governor, and the remaining member is the president of the student government.

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Sánchez will tour NC State’s Nonwovens Institute Partners Lab, which aims to transform research and development in air, blood and water filtration and demonstrates the university’s partnerships with leading companies across the globe. The tour – the first time that the filtration lab will be available for public viewing – begins at 2 p.m. in the Partners I building on NC State’s Centennial Campus. Sánchez will be available to speak with media after the tour.

He will also tour the Textile Protection and Comfort Center in the College of Textiles building and see the “Pyroman” mannequin that tests, under fire, protective garments for firefighters and first responders. That tour begins at about 2:25 p.m.

Sánchez will then speak to students, faculty and industry partners about the importance of advanced manufacturing in growing U.S. jobs and exports at 3 p.m. in the College of Textiles Convocation Center. He will be joined by NC State Chancellor Randy Woodson.

Media coverage is invited for both of the lab tours and the under secretary’s remarks. Contact Mick Kulikowski at 919/515-8387 for parking information.

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On Wednesday, Jan. 25, the day before the surgery, media are invited to meet Cyrano, view the implant, and speak with surgeon Denis Marcellin-Little and engineer Ola Harrysson at 3 p.m. in Room 2530 of the Terry Center at the NC State College of Veterinary Medicine. Parking is available in the Veterinary Health and Wellness Center lot located on William Moore Dr. For directions or questions, call Tracey Peake at (919) 515-6142.

Cyrano is a 10-year-old tabby cat who was treated for bone cancer last year and is now in total remission. However, the disease and treatment weakened the bone in his affected back leg and Cyrano’s knee deteriorated as a result. His owner, Sandy Lerner, felt that amputation would negatively affect the cat’s quality of life, and her search for other options brought them both to NC State and the team of orthopedic surgeon Dr. Denis Marcellin-Little and industrial and systems engineer Dr. Ola Harrysson.

Marcellin-Little and Harrysson are pioneers in osseointegration, a process that fuses a prosthetic limb with an animal’s (or human’s) bones. The NC State team, in collaboration with veterinarians and engineers from around the U.S. and abroad, will provide Cyrano with the first ever custom-made, osseointegrated feline knee replacement.

“Although total knee replacements in dogs are increasingly common, a cat poses some additional challenges, particularly regarding the size of the implant,” Marcellin-Little says. “Additionally, Cyrano’s existing leg bones were weakened by the cancer, so we must take care to be sure that the implant does not place undue stress on the remaining bone.”

Marcellin-Little and Harrysson began their work on osseointegrated pet prosthetics in 2005 with a cat named George Bailey, who was born without the lower half of his hind legs. Since then, the collaborators have done several implant surgeries, improving and strengthening the design and streamlining the manufacturing process, but Cyrano’s case was different enough to warrant additional collaborations – both with veterinary surgeons familiar with knee replacements in dogs, and with implant engineers and manufacturers. The result is a truly one-of-a-kind collaboration aimed at bringing feline knee replacements into the mainstream.

Cyrano’s case is unique, but Marcellin-Little hopes that this surgery will pave the way toward making feline knee replacements more commonly available. “This collaboration between NC State’s College of Veterinary Medicine,  College of Engineering, and outside implant designers and manufacturers allows us to design and make implants that we could only dream of, in the past. I am sure that this technology will help other patients with tumors, in the future.”

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“We’re optimistic that this new approach could lead to large-scale production of stretchable conductors, which would then expedite research and development of elastic electronic devices,” says Dr. Yong Zhu, an assistant professor of mechanical and aerospace engineering at NC State, and lead author of a paper describing the new technique.

The buckled nanotubes look like squiggly lines on a flat surface.

Stretchable electronic devices would be both more resilient and able to conform to various shapes. Potential applications include devices that can be incorporated into clothing, implantable medical devices, and sensors that can be stretched over unmanned aerial vehicles.

To develop these stretchable electronics, one needs to create conductors that are elastic and will reliably transmit electric signals regardless of whether they are being stretched.

One way of making conductive materials more elastic is to “buckle” them. Zhu’s new method buckles carbon nanotubes on the plane of the substrate. Think of the nanotubes as forming squiggly lines on a piece of paper, rather than an accordion shape that zigs up and down with only the bottom parts touching the sheet of paper. Zhu’s team used carbon nanotubes because they are sturdy, stable, excellent conductors and can be aligned into ribbons.

The new process begins by placing aligned carbon nanotubes on an elastic substrate using a transfer printing process. The substrate is then stretched, which separates the nanotubes while maintaining their parallel alignment.

Strikingly, when the substrate is relaxed, the nanotubes do not return to their original positions. Instead, the nanotubes buckle – creating what looks like a collection of parallel squiggly lines on a flat surface.

The carbon nanotubes are now elastic – they can be stretched – but they have retained their electrical properties.

The key benefit of this new method is that it will make manufacturing of elastic conductors significantly more efficient, because the carbon nanotubes can be applied before the substrate is stretched. This is compatible with existing manufacturing processes. “For example, roll-to-roll printing techniques could be adapted to take advantage of our new method,” Zhu says.

A paper describing the new approach, “Buckling of Aligned Carbon Nanotubes as Stretchable Conductors: A New Manufacturing Strategy,” was published online Jan. 23 in Advanced Materials. The paper was co-authored by Feng Xu, a Ph.D. student at NC State. The research was funded by the National Science Foundation.

In another new paper, Zhu’s team has demonstrated for the first time that carbon nanotubes can be buckled using a technique in which the elastic substrate is stretched before the nanotubes are applied. The substrate is then relaxed, forcing the nanotubes to buckle out of plane. The nanotubes form a ribbon that curves up and down like the bellows of an accordion. This second technique has been used before with other materials. This second paper, “Wavy Ribbons of Carbon Nanotubes for Stretchable Conductors,” was published Jan. 19 in Advanced Functional Materials.

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To make the Dean’s List, students must earn an academic grade-point average of 3.25 or higher if they are carrying 15 or more hours of course work, or a 3.5 grade-point average if they are carrying 12 to 14 hours.

The complete listing is available on the Web at: http://www.ncsu.edu/registrar/guides/deans/index.html

Those students with a perfect 4.0 average are noted on the list.

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NOTE TO EDITORS: The list of NC State students who made the fall 2011 Dean’s List can be obtained on the Web at: http://www.ncsu.edu/registrar/guides/deans/index.html

Access the above Web address and click on North Carolina for a county-by-county breakdown of Dean’s List students. If a student’s corresponding city is not listed under the appropriate county, it is because the student originally established residency in the county listed, but changed his or her mailing address for grades. Also, students with privacy blocks on their personal information are not included in the Web list.

If you cannot access the Web site or if you experience problems with this format, call NC State News Services at 919/515-3470 and we will fax, mail or e-mail you a list of students from your coverage area.

Who: NC State’s College of Textiles

When: Saturday, Feb. 11, 10 a.m. to 2 p.m.

Where:  College of Textiles building at 1000 Campus Drive on NC State’s Centennial Campus.

Cost: The open house is free and open to the public; no pre-registration is required.

Contact: For more information, contact 919/515-3780 or visit the Web.