This novel approach to gene modification was developed by Daniel Voytas, professor in the U of M’s Department of Genetics, Cell Biology and Development, along with colleagues at Iowa State University. Cited among the top 20 scientific “breakthroughs of the year” in a special issue of Science published December 2012, the technique involves taking a DNA binding protein (TAL) and fusing it to a nuclease that breaks DNA. When the chromosome break is repaired, it allows the incorporation of DNA sequence changes at a precise location in the genome.

This platform technology has broad applications in genome engineering including fundamental genetic research, crop improvement and treatment of human genetic diseases.

TAL effector nucleases represent a progression from zinc finger nucleases, or ZFNs, which originated more than a decade ago. ZFNs explore the DNA in a cell nucleus, probing with extensions, or “zinc fingers,” until they find the particular DNA sequences they have been designed to ferret out. They then chop those sequences out of the chromosome, replacing them with new sequences. But where ZFNs are difficult and expensive to produce, TAL effector nucleases work better and are far easier and cheaper to make.

The newly issued patents are part of a portfolio of patents and applications licensed exclusively to Cellectis, a French biotechnology company, by the U of M’s Office for Technology Commercialization. Cellectis commercializes these molecules under the trademark TALEN™.

Cellectis Plant Sciences, a subsidiary of Cellectis focused on plant genetics, operates a research and development facility in New Brighton, Minn. where Voytas serves as chief science officer. Voytas is interested in using the technology to improve disease resistance in plants and to make plants healthier by modifying plant oils and carbohydrates.

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Or consider the cancer patient, spared months of lengthy chemotherapy treatments through a simple med-loaded, controlled-release plastic disc implanted in the body. Once the medicine has been delivered, the plastic dissolves into safe byproducts, leaving no trace and no toxic after effects. This type of drug delivery is but one possible use of a new safe plastic developed by Chun Wang, PhD, of the U of M’s Department of Biomedical Engineering.

Both of these emerging technologies have received special awards and have been ranked in the top 20 percent of submitted innovations to this week’s National Innovation Summit and Showcase in Washington, D.C.

Dementia diagnosed on the phone

Pakhomov has a unique background combining linguistics, computer science and experience with business startups. His new technology is an efficient software tool that uses verbal fluency to detect problems such as dementia, Alzheimer’s disease, neurodegenerative disorders and learning disabilities. With a few modifications, it can also be used to test a person’s fluency in a foreign language.

Diagnoses that were once qualitative and dependent on physician assessments can be made accurately with a phone and a technician. The system overcomes the variability in expertise, subjective diagnoses and high-cost of previous diagnostics.

Amazingly, it doesn’t matter what language the patient speaks; the patient could speak Mandarin, Portuguese, English or Farsi and the software could diagnose the problem regardless. The secret is that the system analyzes pauses and gap-fillers (as in, “ummmm” and “ah”). It compares those against norms for a group and a norm specific to the individual.

As the population ages, early, inexpensive diagnosis of these age-associated problems is critical to quality of life and cost reductions. But the system also assists in long-term monitoring of patient progression and can be used by pharmaceutical companies developing new treatments, enabling quantifiable measurements of responses to various dosages and formulations.

The patented process has already been tested with 250 patients. Only three to four more studies are needed before the process is ready for commercialization.

Learn more about this technology

Biodegradable epoxy has multiple medical applications

Chun Wang, who oversees the U’s Polymeric Biomaterials Laboratory, researches polymers (a kind of plastic) for gene delivery, drug delivery and tissue repair. He has developed a new biodegradeable epoxy with potential for numerous medical applications. The epoxy polymer, similar to an epoxy glue, is easy to manufacture and can dissolve into safe, nontoxic components in the human body at predictable rates and in predictable conditions, making it superior to more commonly used medical polymers. Its uses include:

• coatings for medical devices
• adhesives
• controlled release drug delivery
• tissue engineering and repair

The substance is strong, flexible and clear; adheres well to cells; and requires no catalyst or solvents to create. The ease of production has the potential to reduce manufacturing costs and increase profits, while its compatibility with human tissue makes it safe. Medical plastics of this sort are a billion-dollar industry in the U.S.

The substance is one of several created by Wang that are currently undergoing commercial exploration; he has also developed a semi-solid polymer, or “liquid polymer,” with potential for use in controlled drug release delivery systems. The viscous liquid material can be included in topical creams or injected, can hold a wide range of drugs, and is compatible with human tissue. Like the epoxy polymer, it is biodegradable  The ease of application and time-release qualities should help patients comply with therapy, which improves treatment effectiveness and reduces costs.

The university is currently seeking business partners to help explore commercialization of these exciting new materials.

Learn more about this technology

Awards presented at May conference

The awards to these two innovations will be presented at the National Innovation Summit in Washington, D.C. May 13-16. The technologies were chosen based on their potential positive impact on a specific industry sector.

See a list of all TechConnect award winners

Post by Vincent Hyman, a freelance writer based in St. Paul, Minn.

Cargill research and development staff had been studying a problem related to poor aeration in their fermenting process for some time.  Poor aeration caused fermentation to underperform, sometimes at great cost to the company. In one recent case, suboptimal fermentation involved an increased cost of $2.5 million per year.

To analyze the fermentation issue, Cargill had been working with outside consultants to build and run computer simulations of mixing and aeration in industrial-sized fermenters. However, turnaround times were painfully slow and the process was prohibitively expensive. The team sought a quicker, more cost effective solution.

Cargill had previously worked with the Minnesota Supercomputing Institute on some small projects and was aware that MSI offered computing services to companies at reasonable prices. For the simulation project, MSI staff worked with Cargill to license and install specialized commercial software on an MSI computer, which Cargill staff could access remotely. The resulting arrangement has proved to be a success.

Using MSI resources, Cargill has been able to evaluate, over the course of four months, a variety of different aeration schemes and identify a solution to poor aeration. This solution will be tested at full scale this month.

“MSI’s computational resources are extremely affordable and most of our jobs run immediately on submission,” says Christopher Tyler, a senior research engineer at Cargill. “We’re also able to use our licensing effectively because of these resources, saving us additional costs. I would recommend MSI to my colleagues in Cargill or in other companies for their fast, courteous and cost-effective services.”

Visit the Minnesota Supercomputing Institute to learn more about MSI external sales and services.

Interested parties can also contact Bill Hellriegel at hellr@msi.umn.edu or 612-624-1356.

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Submitted by Bill Hellriegel, assistant to the director, Minnesota Supercomputing Institutute.

Photo by Andria Waclawski

Reblogged from Research @ the U of M:

A biospecimen can be anything from DNA and proteins to tissues and bodily fluids used for diagnostic, therapeutic and epidemiologic purposes. Since biospecimens are often collected at one location and used later in another location, preservation during transit and storage is critical. In fact, collection and storage of biospecimens has become a priority for several countries, some even establishing national biorepositories or biobanks. Despite the growing field and importance of biopreservation, many institutions do not have the resources to properly train staff.

The university’s Biopreservation Core Resource (BioCoR) fills that gap by providing education on the scientific basis for preservation and best practices. BioCoR offers short courses on preservation, an online library of videos/podcasts and protocol-specific training for university faculty, government agencies, professional groups and businesses.

Upcoming short courses

Preservation of molecular, cellular and tissue biospecimens, May 20-21, 2013
This annual course presents a scientific overview of preservation by experts in the field, including fundamentals of preservation, protocol development, modes of preservation (liquid storage, desiccation), regulatory issues and more.

Preservation of cellular therapies, Oct. 10-12, 2013
Learn about the fundamentals of preservation, protocol development, design of a storage facility, regulatory issues associated with preservation of cell therapies, clinical issues and more.

Email biocor@me.umn.edu for more information about these events and their services.

The goal of Agriculture Awareness Day is to showcase the critical role American agriculture plays in maintaining a strong economy, especially as the world population continues to grow. The event features interactive booths that give people the chance to see dairy cows, beef cattle, pigs, lambs and goats. Visitors also get the chance to learn more from a range of experts, including agricultural producers, associations, corporations and government agencies.

Click on the photos below to view a slideshow complete with interesting facts provided by the Agricultural Education Club.

Photos by Andria Waclawski

When traffic signals run efficiently, local road networks become faster and safer. With increasing congestion on our nation’s roadways, transportation engineers are looking for new ways to monitor and manage local traffic signal systems. Despite this growing need for traffic signal data and analysis, most existing signal control systems don’t make it convenient to monitor or archive traffic signal performance data. That’s where SMART Signal (Systematic Monitoring of Arterial Road and Traffic Signals) technology developed by University of Minnesota researchers comes in.

“In past research, we developed the SMART Signal technology to collect and analyze real-time traffic signal and signal system performance data and deployed that technology in several test projects,” says lead researcher Henry Liu. “In this most recent project, we’ve enhanced SMART Signal with plug-and-play technology that makes it extremely simple and much more cost-effective to deploy.”

The enhanced SMART Signal system features a single data collection unit that connects quickly to standard traffic signal controller cabinets. “The ultimate goal is to reduce the effort of customized installation as much as possible,” says Liu.

Funded by MnDOT, the latest SMART Signal research has also put real-time traffic data from one of the test projects—Minnesota’s Trunk Highway 13 in Burnsville and Eagan—live on the web, where both road users and traffic engineers can access it quickly and easily. Drivers can now use the new web interface to view real-time travel information, historical queue length, and real-time queue length at intersections equipped with the system. In addition, users can calculate actual travel time along the roadway between any two intersections, at any time of day.

Researchers expect that this innovative traffic signal technology will provide even greater benefits in the future. Researchers plan to use data from SMART Signal to develop an intersection safety monitoring system that will determine if a signal is properly timed to maximize safety, particularly under different weather conditions. Better signal timing could mean less red-light running, resulting in fewer crashes. The system could also be used to measure the frequency of red-light running and calculate the probability of related crashes.

The SMART Signal technology was invented by U of M civil engineering professor Henry Liu and his research team. Initial research was funded by the Minnesota Department of Transportation, Minnesota Local Road Research Board, the U of M Intelligent Transportation Systems Institute and Hennepin County. The resulting startup company, launched in November 2011, was facilitated by the Office for Technology Commercialization.

SMART Signal technology and its deployment in Minnesota was selected as a finalist in the 2013 Best of Intelligent Transportation Society (ITS) awards.

Watch SMART Signal’s new video

Republished with permission from the Center for Transportation Studies. From the April 2013 issue of CTS Catalyst .

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According to behavioral evidence, consumers crave choices, but become quickly overwhelmed when faced with too many options. So how do Internet users navigate the infinite choices available? Preceding the advent of Google, computer science professor John Riedl was instrumental in inventing recommender systems—Web-based tools that identify user preferences to help them find the products, information and people they value most.

Recommender systems combine user behavior data, such as ratings, purchases, searches and views with defined characteristics of specific items to predict a user’s preference for something else. For example, Amazon recommends books based on a person’s search history. Netflix suggests movies viewers will enjoy using ratings of films they have previously watched. Best Buy offers online shoppers accessories for the new cell phone they recently searched for.

Recommendations are based on two basic types of data filtering: content-based and collaborative. Content-based filtering (think Pandora) uses a series of characteristics associated with a specific item to provide recommendations for other items with similar characteristics. Collaborative filtering (think Amazon) uses information from a user’s past behavior or purchases as well as similar decisions made by other users to predict items that person may have an interest in.

“Twenty years ago, Riedl saw the opportunity to capture human ratings—millions of micro-opinions on information or products—and to computationally combine them into personalized and valuable guides to an otherwise overwhelming set of choices,” says Vipin Kumar, head of the Department of Computer Science and Engineering at the U.

In 1996, Riedl took what he learned about recommender systems and founded the startup Net Perceptions. During the eight years that the company was in business (until 2004), it developed and licensed online shopping solutions for Amazon, 3M, Best Buy, Kmart and JC Penney. Heralded as one of the most successful startups in U of M history, Net Perceptions grew to 300 employees and won a World Technology Award during its short but highly influential life.

Today, Riedl has broadened his research into the social web, seeking ways that intelligent technologies can help groups of people work together more effectively online. His research team, GroupLens, applies broader applications of interactive systems to the rich questions arising in the social web, investigating the remarkable profusion of online community activity, such as that on Wikipedia, Facebook and the League of Legends online game. As the face of the Internet has become social, his research team has been among the leaders of investigating the science behind these sites.

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Photo by Richard Anderson

Imagine looking at a live animal the same way you use Google Maps. Start with a bird’s-eye view and zoom in, past the hair, through the skin, down to an organ. Zoom again; now you see the vessels feeding the organ. Another zoom and you see the individual cells. Keep going, and you’re inside the cell, watching individual organelles at work, in real time.

That’s the vision for the University Imaging Centers, where, as program director Mark Sanders says, “the university sees the future.” Though the Google Maps of microscopes is not a reality yet, the Imaging Centers is approaching its vision.

A national center of excellence

The University of Minnesota’s Imaging Centers was recently acknowledged as a Nikon Center of Excellence–one of a select group of centers in the country. The designation recognizes the Imaging Centers for exemplary performance and as an integral component of fundamental research on imaging technology. Another plus: the Imaging Centers will evaluate and test cutting-edge imaging technology and expand its role as an international learning resource center.

Remarkably, as a business unit, the University Imaging Centers is just over three years old, consolidated from several imaging labs across the U. Since consolidation, the Imaging Centers has received three significant funding awards totaling more than $11 million, allowing it to improve facilities, add needed expertise and purchase new equipment.

The Imaging Centers’ state-of-the-art equipment allows it to work on an extraordinary variety of  projects and collaborate with researchers and institutes across the U. Because many of the digital files generated are so large (up to 20GB), the Imaging Centers partners with the Minnesota Supercomputing Institute for data storage.

Director Sanders notes, “We can use the same tools to solve all kinds of research problems. We work with animal and plant tissues, study crop pathogens, cancer mechanisms and treatments, everything from very basic research to business applications.”

For example, the Imaging Centers has helped anthropologists study the past by evaluating the material left on stone-age tools. “We could observe at the microscopic level the changes that took place in tools and look for signs of biological material on the tool,” Sanders explains. This information helps anthropologists determine the intended use of the tool, the materials being used by ancient humans and the foods being consumed.

Specialized service and training

Looking to the future, companies come to the Imaging Centers for a variety of purposes. Sometimes business research involves trade secrets or competitive concerns, so the Centers’ staff can train the business’s staff to use the imaging equipment, or the Centers can consult and collaborate with the business.

The Imaging Centers also hosts international guests who are training on and using the equipment. At a recent symposium, only two of twenty-four participants were from the university. Sanders notes, “The national and international outreach brings attention to the university as a center of excellence.”

Sanders is enthusiastic about the Imaging Centers and what it means to research. “Biology is the study of life. Before, we could only view tissue at the cellular level if it was no longer living. In the past 10 years, new technology has enabled us to view living tissues at increasingly refined levels—down to a hundred nanometers.”

By the numbers

The University of Minnesota Imaging Centers:

• Operates two facilities but will soon open a third for a total of 13,000 square feet
• Has over 450 active users, about 10 percent of whom are from outside the university
• Has about $7 million in hardware and 25 high-end instruments
• Has 8 staff, 4 of whom have PhDs
• Annually provides several symposia and many training sessions, training some 200 individuals
• Is guided by a 13-member advisory panel representing chemistry, biomedical engineering, electrical engineering, plant pathology, cell biology and development, neuroscience, cardio-cancer and more

Visit the University Imaging Centers to learn more.

Post by Vincent Hyman, a freelance writer based in St. Paul, Minn.; photography by Andria Waclawski

Education, research and, yes, sports may be what most Minnesotans think of and hear about the U of M. But the role of business is increasingly important as companies seeking to maximize limited resources draw upon the talent, facilities and expertise of large research institutions like the U.

Last Friday, the university announced the launch of an ad campaign that emphasizes the critical role of business at the U by highlighting university partnerships with three Minnesota companies—Boston Scientific, 3M and Land O’Lakes. The Partnering Illuminates Possibilities campaign, which features radio and print ads, focuses on innovations that are improving food safety and sustainability, developing lifesaving medical technologies and increasing the efficiency of solar energy.

While the campaign features just a few of the companies partnering with the U (there are many more), it represents a broader university-wide effort to expand the university’s connections with Minnesota businesses, both large and small. The MnDRIVE initiative, included in the university’s biennial budget request to the state, outlines a series of focus areas in which the U aims to partner with state-based companies to advance Minnesota’s economy, position the state as a leader in key industries, and improve quality of life for all Minnesotans.

In addition to partnering with existing businesses, the university has a history of helping to create them. The Venture Center, housed in the Office of Technology Commercialization, has helped to launch 34 new companies in the past five years. In addition, the U of M currently holds more than 300 technology transfer agreements with companies throughout the world. Visit the Office of the Vice President for Research to learn more about resources and services for businesses at the U of M.

We want to hear from you!
What are some other ways that the U partners with Minnesota businesses? What other companies, partnerships or innovations should our business community know about? Please share your thoughts in a comment below.

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