Tech Connect-Biodesign Issue-2010

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A Legacy of Industry Leadership Since the Avnet family started selling surplus radio parts in New York City in 1921, Avnet’s leaders and talented employees have defined what makes a world-class company. On December 15, 2010, Avnet will commemorate a milestone that only 350 other companies have ever achieved in the history of the New York Stock Exchange – we will celebrate our 50th anniversary on the NYSE. This milestone distinguishes Avnet as a premier company – one with global scale and scope, five decades of demonstrated adaptability, a strong global culture, and leading financial strength. It is these capabilities that

have allowed Avnet to grow consistently and profitably over time, and become the leader in technology distribution. Avnet would like to thank our 16,000 plus employees who have made our company so great, our trading partners who have placed their trust in us to deliver the highest service and value, our shareholders who invest in us as well as our business and community partners who work with us to help make the world a better place to live and work. We are proud of our legacy and look forward to achieving far more in the next 50 years than we can only imagine today!

View Avnet’s history on www.avnetondemand.com

What’s Inside

A r i z o n a’ s

Technology Magazine

The Focus

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Arizona IT community members build bridge to new business.

The Network

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X-rays as close as a computer when doctors need to trade notes.

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On the Cover :: The Bio Institutes Issue

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Feature

TECHNOLOGY MAGAZINE

TECHCONNECTmag.COM

A look at the latest discoveries from the state’s biosciences leaders

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Bio5 / TGen / The Biodesign Institute

INSIDE

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A R I Z O N A’ S

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WINNING WAYS

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DISCOVERY CHANNELS

THE

Bio Institutes ISSUE

Illustration by Michael Northrup/TGen

Contact us :: editor@techconnectmag.com

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010 Governor’s Celebration of Innovation

Find out who the members of this year’s class of winners are.

011 Drowning In Data

Businesses must remain on guard to protect their customers.

In Every Issue 006 President’s Letter 008 Editor’s Letter 024 Science Foundation Arizona 026 The University of Arizona 028 Arizona State University 029 Northern Arizona University 030 Capitol Watch

fan...

Take it from a Phoenix Business Journal

What has always impressed me is the Phoenix Business Journal staff ’s willingness to go beyond print... from sponsorships, online, videos and community outreach to their commitment and enthusiasm for the Valley.

They are a true partner to enhance our brand.

Al Maag

Chief Communications Officer, Avnet Inc.

TO SUBSCRIBE OR ADVERTISE, CONTACT MIKE MALL AT 602.308.6525

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Bio Brilliance n this edition TechConnect chronicles the progress of three of Arizona’s premiere bioscience research institutions: the Translational Genomics Research Institute (TGen), The Biodesign Institute at Arizona State University and the BIO5 Institute at The University of Arizona.

To underscore the value they and other members of the bioscience community in our state offer, here are some facts from the Arizona Commerce Authority’s Innovation Arizona Web site:

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Number of Establishments • 778 establishments • 579 are in the medical devices and equipment, and the research, testing and medical laboratories subsectors Number of Jobs • 84,234 bioscience jobs • 14,000 non-hospital bioscience jobs (a 23.4 percent growth during 2002-2007) Average Wage • $52,481 annually

Export • $1.122 billion in medical instrument exports in 2008 Core Competencies • neurological research • cancer research • bioengineering research • agricultural, plant science and environmental research All three facilities featured inside definitely contribute to the overall achievements.

The Biodesign Institute spurs scientific breakthroughs that improve health, protect lives and sustain our planet. Its research is aimed at predicting, preventing and detecting the onset of disease, developing renewable energy and reducing environmental damage, and developing innovations that safeguard our nation and the world. The Biodesign Institute focuses on bioscience infrastructure specializing in applied nanobioscience, bioelectronics and biosensors, bioenergetics, biooptical nanotechnology, biosignatures, discovery automation, evolutionary functional

genomics, infectious diseases and vaccinology, innovations in medicine, personalized diagnostics, single molecule biophysics, and sustainable health.

TGen is a non-profit genomics research institute established to employ genetic discoveries to improve disease outcomes by developing smarter diagnostics and targeted therapeutics. TGen conducts research on a number of human disorders, including Alzheimer’s and Parkinson’s diseases, autism, diabetes, and numerous forms of cancer and a variety of other complex human diseases. This internationally recognized institute has helped generate a strong foundation for Arizona’s growing role in scientific research and cuttingedge biotechnology. The emerging field of translational genomics research harnesses the power of new discoveries resulting from the Human Genome Project and applying them to the development of improved diagnostics, prognostics and therapies for cancer, neurological disorders, diabetes and other complex diseases.

BIO5 harnessed five disciplines—basic science, agriculture, medicine, pharmacy and engineering—to find solutions to the complex biology-based challenges affecting humanity today: How do we prevent, treat and cure the myriad diseases we face? How do we create more resilient crops, nutritious foods and new sources of fuel? How do we address the many environmental problems that surround us today? Scientists from the BIO5 disciplines are capitalizing on breakthroughs in the molecular life sciences to improve the quality of life in the 21st century and beyond.

In this issue of TechConnect, you will learn about the phenomenal progress and incredible discoveries of these institutions. As a member of the 75-member Arizona Bioscience Roadmap Steering Committee, I am proud to be affiliated with an industry and group of organizations that are impacting human progress in such a profound fashion. I know you’ll be just as proud to be an Arizonan after reading this edition.

Steven G. Zylstra

President & CEO, Arizona Technology Council

Editor’s Letter

Publisher Steven G. Zylstra Editor Don Rodriguez Art Director Jim Nissen, Switch Studio Designers Chaidi Lobato Carla Rogers

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Contributing Writers Cindy Brown John Cummerford Karen Dickinson Larry Fleischman Richard Harth Carol Hughes Pati Urias Bruce A. Wright Steve Yozwiak

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Back on the horse s any journalist would, I’ve always prided myself on being able to write well.

(I admit, some of you might disagree if you’ve read my work in this publication.) Once a topic comes up and I do my reporting, I can write about it. I’ve never been stumped on what to write.

Well, almost never.

A few years ago I was invited to an event to visit with Helios scholars who worked as interns during the summer at the Translational Genomics Research Institute (TGen) in downtown Phoenix. The eightweek biomedical internship open to Arizona high school, undergraduate, graduate and medical students annually gives participants the chance to work side-by-side with TGen researchers.

When I arrived the students were standing besides posters that explained the research projects in which they were involved. All were extremely excited and proud to describe their investigations. Who wouldn’t be?

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Then I started my interviews.

First one then another and another. At a certain point I was overwhelmed by the strangest feeling. It never happened in my years of reporting any story and I started to panic. I had no idea what they were talking about.

OK, that’s a slight exaggeration but not too far off the mark.

I understood the basics.

Likely enough to write one sentence per project. When you’re trying to write an article about something technical, six sentences is not ideal. I walked in with confidence—after all, chemistry was minor as an undergraduate—and walked out with my shoulders slumped and a little dizzy.

The result? You guessed it. No story. Not one word.

I’ve never forgotten that humbling moment. In fact, when I was developing themes for TechConnect that thought came back. Those students were long gone, but I knew I had to get back on that horse and share news about TGen. Well, let’s say I got back on the pony ride.

This time I stayed in my role as an editor and sought someone

who could make the most complicated information easy to follow (more for my sake than yours). I turned to the senior writer at TGen, Steve Yozwiak.

He’s been a colleague over the years and his work has been in this publication previously.

I also contacted The Biodesign Institute at Arizona State University and the BIO5 Institute at The University of Arizona, asking them about the most interesting developments that have been occurring at their facilities lately. Like Steve, they share their work and their stories with you inside.

You’ll be amazed what the researchers are up to. It’s even more amazing to consider they are all making history that will impact our lives for years to come. There are definitely no one-trick ponies in this elite group.

Don Rodriguez

Editor, TechConnect Magazine

Trademark // General Counsel Quinn Williams

E-mail editor@techconnectmag.com For queries or customer service, call 480-620-3759.

TechConnect is published by the Arizona Technology Council, One Renaissance Square, 2 N. Central Ave., Suite 750, Phoenix, AZ 85004.

Entire contents copyright 2010, Arizona Technology Council.

Reproduction in whole or in part without permission is prohibited.

Products named in these pages are trade names or trademarks of their respective companies. TechConnect is a trademark of the Arizona Technology Council. All rights reserved. Publication of TechConnect is supported by private-sector businesses, and is not financed by state-appropriated funds.

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Innovator of the Year/Start-Up Company WebPT in Phoenix Web-based system for physical therapists to keep records and schedules Innovator of the Year/Small Company Breault Research in Tucson APEX, an optical engineering application Innovator of the Year/Large Company IBM Corp. in Tucson System Storage Easy Tier application that uses solid state discs to speed access time to data on computers Innovator of the Year/Academia Arizona State University’s School of Life Sciences in Tempe Deep-brain stimulation technique to help various neurological and psychiatric conditions Teacher of the Year Robert Hobbins from Sonoran Science Academy in Tucson

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Governor's Celebration of Innovation honors the best of the best embers of the state’s technology community gathered to honor their own at the annual Governor’s Celebration of Innovation held recently at the Phoenix Convention Center. This year’s theme of The event was presented by the Arizona Technology Council and the Arizona Commerce Authority. Arizona in Motion was appropriate as companies continue to move forward in the light of the economic news.

This year’s winners and the reasons for their recognition are:

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OneNeck IT Services People’s Choice Lifetime Achievement Award Steve Sanghi, president and CEO of Microchip Technology in Chandler He is credited with leading the evolution of the company into one of the most successful microcontroller companies in the world as well as being a champion of science, math and engineering education in schools.

Chairman’s Award Sandra Watson, chief operating officer of the Arizona Commerce Authority Ed Denison Business Leader of the Year Robert Breault, president and founder of Breault Research in Tucson

William F. McWhortor Community Service Leader of the Year Dr. Jack Johnson, president of SciEnTeK-12 Foundation in Tucson.

Pioneering Award GlobalMedia Group in Scottsdale CapSure/CONi system that includes images in electronic medical records Green Innovator of the Year Global Water Resources in Maricopa FATHOM platform to help save water.

Global Competitiveness Leadership Michael Manson, co-founder and CEO of Motor Excellence in Flagstaff, which makes electric motors for vehicles ranging from bikes to cars

Students named Future Innovators of the Year Kurt Andres, Pusch Ridge Christian Academy in Tucson Project: “Augmenting Energy Efficiency

by Ameliorating Mass Imbalance in Wind Turbines” Scott Olson, Highland High School in Gilbert Project: “A Novel Fiber Optic Backlight System Utilizing Controlled Light Attenuation” Stan Palasek, Sonoran Science Academy in Tucson Project: “Heat Stress Reveals Hexose Transport Rates in Saccharomyces cerevisiae” Varun Ramesch, Hamilton High School in Chandler Project: “A Parallel Algorithm for Real-Time Hand Gesture Recognition” Legislators of the Year Sen. Barbara Leff, R-Paradise Valley, and Rep. David Stevens, R-Sierra Vista Tech Ten legislators Sens. Manuel Alvarez, D-Elfrida; Frank Antenori, R-Vail; Rebecca Rios, D-Apache Junction; and Reps. Chad Campbell, D-Phoenix; Bill Konopnicki, R-Safford; Lucy Mason, R-Prescott; John McComish, R- Ahwatukee; Michele Reagan, R-Scottsdale; Kyrsten Sinema, D-Phoenix; and Andy Tobin, R-Dewey.

There is nobody— and no business— that is not touched by the Web.

Writing by :: John Cummerford

n 1992 there were fewer than 15,000 domain names on the worldwide Web. Today there are about 200 million. In 2004 there was no Facebook.

Today there are 148 million registered Facebook users in the United States alone (more than registered Democrats and registered Republicans, combined!). There is nobody—and no business—that is not touched by the Web. It has changed the way we work and play, and shaped an entire generation.

Yet, hardly a day goes by without a story in the press about how someone’s financial or personal (or really personal) information got ferreted out and disclosed. If you have a business, you know the success of your company depends in large measure on how well you protect your customers. So, think about this:

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Your Customers Your customers depend on you to protect their personal information. If they think you are not dependable, they will go elsewhere.

Yet, as Bruce Schneier, the godfather of Internet security, once observed, “If McDonald’s offered a free Big Mac in

exchange for a DNA sample, there’d be lines around the block.” That is, your customers are nervous, but they don’t know what to be nervous about. Help them by not taking on more of them than you need to have. If you don’t need their home address, why ask for it?

Why do you need their cell phone number or their kids’ names? Those are just more data to lose; if you don’t have it, you can’t lose it.

Your Agreements.

You need to set expectations in your customer agreements. Ask yourself what you are really going to do with your customers’ information, tell them that clearly, get them to agree and then do what you promised.

Be fair, but don’t be overzealous. And don’t overstate your case. If you say, “We will never disclose your information to third parties,” imagine how that promise will sound when the “third party” asking has a badge with a gun and a subpoena in hand.

Your Technology and Your Practices Ask yourself, “If I wanted to steal information from my own business, how would I do it?”

The most sophisticated data encryption technology is worthless if your employees don’t lock doors, leave thumb drives out,

What Does the Future Hold?

What the Web will be like in 10 years is less predicable than the weather, because the weather will likely be pretty similar to what it is today— the Web sure won’t. Here are my predictions: • Privacy is a fetish that is going away. Soon everyone will know, or be able to find out, pretty much everyone else’s business. Keep in mind a right to “privacy” is relatively new-fangled.

• Governments will also lack privacy and find themselves as vulnerable as the rest of us. Just because Big Brother is able to read my emails doesn’t mean that nobody is snooping on Big Brother.

• Since everyone will, at least metaphorically, be able to see everyone else naked, we will have to learn to avert our eyes as matter of common courtesy. Snooping will be seen as bad form.

• Rather than rely on “official” opinions, we will turn to those we trust: our friends.

Thus, social networks will usher in a return to old fashioned values such as community, personal loyalty and trust.

John Cummerford is an attorney at GreenbergTraurig in Phoenix.

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Businesses need to be careful to protect themselves and customers

or are afraid to challenge strangers in the hallway. Corporate security should be a closed loop system. Teach your employees the best practices. Once they’ve learned them, get someone to try to get around those practices then share what you found out with those employees.

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Drowning in data

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Before marketing can implement demand creation programs, it’s essential to have a clear understanding with the sales representatives who will receive the output of these programs.

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Now that sales prospects are returning, here are three ways to optimize demand creation

s a B2B outsourced demand creation agency that works with high-tech companies to identify new customers, accelerate sales opportunities, and discover fresh, actionable market insight, we’re continually tasked with improving sales pipeline performance and growing top-line revenue in measurable ways. It’s complex stuff, which is why many organizations struggle with it.

Not to sound cliché, but there isn’t a silver bullet. Demand creation programs and tactics are relatively easy to implement, but truly optimizing demand creation is challenging. With budgets tighter than ever, every dollar spent must achieve maximum ROI. So optimization is essential, and it cannot be achieved until several critical issues are addressed. Let’s focus on the top three: alignment, enablement and integration.

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Writing by :: Larry Fleischman

Connect Sales and Marketing At the heart of the sales pipeline issue many organizations face is the inability of their sales and marketing teams to agree. Topping the list of disagreements is defining the elements of a qualified sales lead. Before

marketing can implement demand creation programs, it’s essential to have a clear understanding with the sales representatives who will receive the output of these programs. There must be some alignment.

Both teams should agree on the criteria that must be met for a sales lead to be qualified sufficiently so it’s worthy of sales rep acceptance and pursuit. The basic criteria include what is commonly known as BANT— budget, authority, need and timeframe.

Many organizations are familiar with this construct. Most important among these criteria is the “need” for your products because without a core problem, there’s not going to be a budget set aside to solve it, an established timeframe in which to address it, and no person of authority accountable for solving it. Focus on identification of need.

Also, on the sales and marketing alignment list is the lead hand-off process.

Assuming a prospect meets the qualification requirements that sales and marketing have pre-determined, there needs to be a clear process for passing the lead from marketing to sales. Too often leads are lost in the transfer for avoidable reasons. Two of the key ones include insufficient or inaccurate intelligence attached to the lead so the sales rep doesn’t have the right information about who they should speak with or what they should be talking about. Or the sales rep just may not be ready to accept the lead due to a number of reasons beyond marketing’s control. So the key lesson here is to have a clear, clean sales handoff process that ensures when a lead is passed by marketing to sales that it’ll have the care, attention and accountability it needs.

Human and Digital Intersect

Marketing automation is gaining widespread adoption. If your organization isn’t yet familiar with marketing automation, the leading providers, and the features of their systems, start doing the research because this is an important component of Marketing 2.0. The concept is fairly simple: Using technology to help you monitor the behavior of your prospects and manage what information they receive from you and when.

While the idea is straightforward and the concept has its place in an increasingly complex marketing environment, the common misconception is a digital marketing solution is the panacea. It is most definitely not, and organizations that develop their demand creation strategies and programs based on a premise that marketing automation is the end-all, beall are going to be disappointed. Unless, however, they deploy marketing automation in tandem with sound data practices and critical elements of human touch. Data is a long story we don’t have space for here, so let’s focus on human touch.

Larry Fleischman is practice director, branding and goto-market strategies & solutions at Televerde. He can be reached at larry.fleischman@televerde.com.

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A common cause of sales and marketing misalignment is lack of sales enablement.

Enablement requires sales reps have the tools, training, lead intelligence and support required to keep a sales opportunity engaged. Proper enablement includes ensuring sales reps have a set of relevant information (i.e., case studies, white papers, product data sheets, testimonials) to provide to their prospects.

They also need to have an understanding of what information is appropriate to provide to a prospect at the right time. Providing the wrong information at the wrong time can derail a prospect’s momentum. The sales rep must be sensitive to the journey that buyers take to make purchasing decisions, and must respect the buying cycle stages. Lead intelligence is a no-brainer these days; the sales rep simply must be armed with critical information about the prospect— what they’re interested in and why, when they want to solve their problem, how much they’re willing to spend on the solution, how much research they’ve done via your web site or social media, and the composition of the purchasing committee.

In terms of sales support, in many cases (and especially for large accounts), sales reps need help staying focused on the sales opportunity. At a basic level this could include help scheduling appointments. On the complex side of support, they may need help acquiring critical intelligence about their prospects and applying this intelligence in a prescribed manner. So for certain types of sales opportunities factor in the appropriate level of support that is needed.

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Right Tools and Support

Just like most almost anything in life, moderation and balance are also in order for those responsible for their organization’s demand creation initiatives. By this I mean integration. Applying only dialogue-based marketing techniques or only digital-based programs are not approaches that will yield optimized results. In today’s complex B2B demand creation environment, a robust mix of tools and approaches must be in play and deployed in ways that support each other.

Human touch is essential in this process.

It’s no different when it comes to demand creation. Marketing automation is very useful at helping identify who is coming to your web site and monitor their digital behavior.

It’s also helpful for assigning “scores” to these people so that when they hit a certain threshold after a set of activities, it comes to your attention immediately. Also, it’s useful for determining what email messages or other digital content should be automatically delivered based on certain buyer behaviors or scores.

There’s no math or science that tells us with certainty (not yet anyway) that a seller should speak with a buyer at pre-determined intervals. Or exactly how many digital touches should occur before a human touch should take place. At some point we need to pick up the phone and simply talk. It can be the breakthrough in a relationship. Listening to the other person can help us discern the difference between what we think they want and what they really want. It’s the integration of both these forms of contact that yields the greatest results.

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Beijing The group visited Zpark software park with over 200 software and IT companies employing 20,000 people.

While companies such as Oracle, IBM and Thompson Reuters are located in this software park, amazingly 95 percent of the companies in the park are Chinese. One of those companies is Beyond Soft, which won Best Employer in China in 2010. Beyond Soft is part of the burgeoning software outsourcing industry in China. It employs 4,000 developers in five countries, including the United States.

To customers from all over the globe, Beyond Soft provides services such as software and website development, application testing and localizing software for the Chinese market.

Nation's IT community rolls out red carpet to potential Arizona partners Writing by :: Karen Dickinson

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FINE CHINA

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s the world continues to recover from the recession, one lesson learned is businesses no longer can count on customers coming to them. To stay competitive, companies need to reach out, even if that means going to the other side of the globe.

With this in mind the Arizona Technology Council recently led a trade mission to China to introduce members

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of a delegation to business opportunities through meetings with government officials, industrial park leaders, peer companies, and consumers. The trip was organized in conjunction with the Arizona Department of Commerce and the Arizona U.S. Export Assistance Center.

I shared observations of cities visited in the 10-day trip that began Oct. 27 in a blog that was posted during our travels. The cities and highlights included:

Hangzhou Eighty of the top 500 Chinese private companies are headquartered here.

We visited the Hangzhou North Software Park Service Center, which provides one-stop free services to companies in the park. The companies include the creative industries— multimedia, Internet, advertising and entertainment—along with IT and software. We had a quick visit with a Chinese website development company, Panshi, with 1,600 employees helping companies in the Zhejiang province in which Hangzhou is located.

Suzhou We took a quick break in the city of Suzhou, known as the “Venice of China." Also known for its many traditional Chinese gardens, the delegation was able to visit one of those ancient gardens in Suzhou's Old Town, set in the midst of canals flowing toward the Grand Canal. We then bused it to Suzhou's brand spankin’ New Town. In that town is the Suzhou Industrial Park, a cooperative project between the Chinese and Singaporan governments. Once again, the scale of this industrial park, the sophistication of the technology and the beauty of the living areas are indescribable.

Shanghai A highly educated city, with 65 colleges and universities, 51 graduate schools, and half a million students. This large talent base, the lifestyle, and special incentives have drawn many companies to locate in the Zhangjiang Science Park, growing quickly after 2002 due to special preferential policies such as a 14 percent rebate on the usual 17 percent value added tax for software companies located in the park. Many large private and publicly traded Chinese companies—such as ZTE, Lenovo, Apexone and Shanda—join multinationals, such as Infosys, Capgemini, Dupont and Honeywell, in the park and our own ON Semiconductor and Freescale. In fact, Park is home to more than 5,000 companies with 150,000 hi-tech employees. That’s more than all the hi-tech employees in all of Arizona! And the companies at the park are provided support services such as human resources talent searching, a shared data center, even a patent processing center for free.

We were hosted by the Xi’an Hi-Tech Industries Development Zone, which was founded in 1991 as one of earliest high-tech parks in China. It now houses more than 14,000 companies employing 250,000 people. And there are 55 other high tech parks in China just like this one.

The park’s focus is on four areas: electronic information such as IT, software and telecom; biomedical; advanced manufacturing research and development for industries such as semiconductors and optics; and services such as law offices and design. Fifty new IP applications are filed by the companies in the park per day. While there are multinational companies with offices in the park—such as Applied Materials, NEC, Fujitsu, Intel, Micron, Oracle, Sybase, SAP and IBM—most of the companies are Chinese.

The software park alone has 80,000 employees working for 900 companies. Special incentives are offered for U.S.based software companies to locate in Xi’an software park.

Zhangjiagang The port city has an entrepreneurial government that has been one of the first to embrace each of the many changes since China opened to the West in 1979. Not surprisingly, Zhangjiagang has a burgeoning solar industry as well as major manufacturing. We were hosted by high-level government officials from the Zhangjiagang Economic Development Zone as well as the Investment Promotion Bureau. This is a “model” city, one that other city governments visit as an example of how to create a livable, economically successful city. In fact, the average annual income in this small city is one of the highest in China: $15,000. The Zhangjiagang government has created parkland and lakes, and has strict rules in the city regarding cleanliness and maintenance. Because of the city government’s intense focus on sustainability and environmental regulation, it is known as one of the most livable cities in China, and it certainly lived up to its reputation. This city really is the new China.

Karen Dickinson is an attorney at Quarles & Brady in Phoenix.

TECHCONNECTmag.COM

Xi’an

Because exports mean jobs. And lots of help is available for Arizona companies that want to export. A National Export Initiative (NEI) is now in effect focusing on five areas: access to credit, especially for small and mid size firms; more trade advocacy and export promotion efforts; removing barriers to the sale of U.S. goods and services abroad; enforcement of trade rules; and pursuing policies that will increase global economic growth so that there’s a strong worldwide market for U.S. goods and services.

Some first steps have been taken as part of the NEI that could be important to your business. For example, until now a U.S. exporter of encryption-based products, such as a cell phone or a network storage system, was required to request a technical review from the federal government prior to export, a process that takes between 30 and 60 days.

A proposed new rule could eliminate up to 85 percent of all the technical reviews of these products, helping U.S. companies access the global market more quickly.

In addition, Congress recently passed the U.S. Manufacturing Enhancement Act, which suspends duties on a number of imported goods that are of special interest to U.S. manufacturers. The bill provides relief to manufacturers from duties they had to pay for imported inputs, such as chemicals and specialty parts. This is expected to reduce the cost to U.S. manufacturers, making products competitive in the global market. And, the Small Business Administration has recently made changes making it easier for small and medium sized businesses to get export financing. More changes are planned as part of the NEI, so stay tuned.

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Why is this important to the economy and Arizona businesses?

Feature

TimeTree of Life

App quickly traces origins of species owering over the mightiest sequoia, nature’s tree of life holds the totality of the living world on its bountiful branches and limbs. Now, an innovative new application lets anyone with an iPhone tap into this astonishing abundance of life.

Download it from Apple Store for free by using TimeTree as a search term.

The TimeTree app harnesses a vast Internet storehouse of data on life forms ranging from fungi to foxhounds, putting this information in the palm of one’s hand. The intuitive interface is designed to answer a simple question, quickly and authoritatively: When did species A and species B share a common ancestor?

The Timetree of Life from an assembly of individual timetrees. Each of the 1,610 terminal branches represents a family or family-level taxon.

The new iPhone software is the latest extension of a project conceived by Sudhir Kumar, director of the Biodesign Institute’s Center for Evolutionary Medicine and Informatics at Arizona State University, and Blair Hedges, professor of biology at The Pennsylvania State University. Kumar also is a professor at ASU’s School of Life Sciences.

As Kumar explains, the evolutionary tree of life has two critical components: phylogeny and timescale. Phylogeny shows the branching relationships between species or other higher level groups within a particular kingdom, providing crucial information for understanding the inheritance of traits and for erecting schemes of classification. But pure branching order lacks a time component.

Timescale, on the other hand, identifies when species emerged. It provides a way to compare species evolution in one group directly with the evolution of other groups, and to relate these with geologic history, climate, extraterrestrial influences, and other features.

When phylogeny and timescale are combined, the result is a timetree—a powerful tool for understanding the interrelationships and diversity of living things.

Timetrees are critical for evolutionary biology, as well as for other fields. In the realm

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of human health, for example, they can be used to track the development and migration of disease-causing organisms through time.

Climatologists and atmospheric scientists use timetrees to compare the effects of various organisms on the early planet. Astrobiologists pondering the origin and development of life in the universe, construct timetrees to explore chemical changes in ancient rocks, which may be associated with primitive life.

Although the TimeTree iPhone app provides a sophisticated means of mining scientific literature, using it is easy. Simply type the names of two organisms—for example, swordfish and sardine—into the iPhone interface.

TimeTree searches its cavernous web archive and within seconds, returns its findings.

The swordfish and sardine shared a common ancestor some 245 million years ago, before swimming their separate ways. This app also works on other Apple devices, including iPAD and iPod Touch.

Along the left margin of the iPhone display, a geological timescale is provided, with data points marking each scientific study TimeTree used to reach its result. “One of the most important things about this knowledgebase,” Kumar says, “is that it makes it possible for anyone to see the current agreements and disagreements in the field—immediately.”

The ultimate goal of the Timetree of Life initiative, according to Hedges, is “to chart the timescale of life—to discover when each species and all their ancestors originated, all the way back to the origin of life some 4 billion years ago.” The first phase of this ambitious undertaking appeared last year with the simultaneous release of an online

resource called TimeTreeWeb (www.timetree.org), and an accompanying book titled “The Timetree of Life”.

Hedges and Kumar were the editors of the voluminous TimeTree text written by 105 leading authorities and covering a profusion of living forms, from primitive bacteria all the way up to humans. Just like the TimeTree book and the web resource, the new iPhone app draws on the National Center for Biotechnology Information’s comprehensive taxonomy browser, which contains the names and phylogenetic lineages of more than 160,000 organisms.

The TimeTree resources form a public knowledgebase, accumulating and cataloging thousands of divergence times for organisms available in the peer-reviewed scientific literature.

TimeTree is both easier and more versatile than traditional means of searching for information on the divergence of species. Timetree building is still in its infancy, Kumar and Hedges note, with millions and millions of species yet to be fully represented. Nevertheless, the new iPhone app allows anyone to explore an area at the forefront of comparative biology and find his or her place in the timetree of life.

Besides the Biodesign Institute, support for developing the Timetree of Life project, including its smartphone app, has come from the U. S. National Science Foundation, the Astrobiology Institute of the U.S. National Aeronautics and Space Administration, and Science Foundation Arizona.

Richard Harth is a science writer at ASU’s Biodesign Institute.

By Richard Harth

Life Imitates Art t

edge, is an example of a topological form.

“As nanoarchitects,” Yan says, “we strive to create two classes of structure— geometric and topological.”

Geometric structures in two and three dimensions abound in the natural world, from complex crystal shapes to starfish, and unicellular organisms like diatoms.

Yan cites such natural forms as a boundless source of inspiration for human-designed nanostructures.

Topology, a branch of mathematics, describes the spatial properties of shapes that may be twisted, stretched or otherwise deformed to yield new shapes. Such shape deformations may profoundly alter the geometry of an object, as when a donut shape is pinched and stretched into a figure eight, but the surface topology of such forms is unaffected.

Nature is also rich in topological structures, Yan notes, including the elegant Möbius. The circulations of earth’s warmer and cooler ocean currents for example, describe a Möbius shape.

Other topological structures are common to biological systems, particularly in the case of DNA, the 3 billion chemical bases of which are packed by the chromosome inside the cell, using topological structures. “In bacteria, plasmid DNA is wound into a supercoil,” Yan explains. “Then the enzymes can come in and cut and reconfigure the topology to relieve the torsion in the supercoil so that all the other cellular machinery can have access to the gene for replication, transcription and so forth.”

To form the Möbius strip in the current study, the group relied on properties of selfassembly inherent in DNA. A strand of DNA is formed from combinations of four nucleotide bases—adenine (A), thymine (T), cytosine

(C) and guanine (G)—which follow one another on the strand like necklace beads.

These nucleotide beads can bind to each other according to a strict rule: A always pairs with T, C with G. Thus, a second, complementary strand of DNA binds with the first to form the DNA double helix.

In 2006, Paul Rothemund at the California Institute of Technology demonstrated the process of DNA self-assembly could be used to produce pre-designed 2D nanoarchitectures of astonishing variety. Thus, DNA origami emerged as a powerful tool for nanostructure design. The method relies on a long, single stranded segment of DNA, used as a structural scaffold and guided through base pairing to assume a desired shape. Short, chemically synthesized “staple strands,” composed of complementary bases are used to hold the structure in place.

After synthesis and mixing of DNA staples and scaffold strands, the structure is able to self-assemble in a single step. The technique has been used to produce remarkable nanostructures of smiley faces, squares, disks, geographic maps, and even words, at a scale of 100 nm or less. But the creation of topological forms capable of reconfiguration, like those produced by nature, has proven more challenging.

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he enigmatic Möbius strip has long been an object of fascination, appearing in numerous works of art, most famously a woodcut by the Dutchman M.C. Escher, in which a tribe of ants traverses the form’s single, never-ending surface. Scientists at Arizona State University’s Biodesign Institute and Department of Chemistry and Biochemistry, led by Hao Yan and Yan Liu, have now reproduced the shape on a remarkably tiny scale, joining up braid-like segments of DNA to create Möbius structures measuring just 50 nanometers across—roughly the width of a virus particle.

Eventually, researchers hope to capitalize on the unique material properties of such nano-architectures, applying them to the development of biological and chemical sensing devices, nanolithography, drug delivery mechanisms pared down to the molecular scale and a new breed of nanoelectronics.

The team used a versatile construction method known as DNA origami and in a dramatic extension of the technique, (which they refer to as DNA Kirigami), they cut the resulting Möbius shapes along their length to produce twisted ring structures and interlocking loops known as catenanes.

Their work appeared in the online issue of the journal Nature Nanotechnology.

Graduate students involved in this work included Dongran Han and Suchetan Pal in the Yan group.

Making a Möbius strip in the everyday world is easy. Cut a narrow strip of paper, bring the two ends of the strip close to each other so that they match, but give them a half-twist before fastening the ends together with a piece of scotch tape. The resulting Möbius strip, which has only one surface and one boundary

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Möbius strip inspires creation of nano-architectures

Feature

Myth of a germ-free world: a closer look at antimicrobial products

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illing microorganisms has become a national obsession.

A pair of antimicrobial compounds known as triclosan and triclocarban are lately the weapons of choice in our war of attrition against the microbial world. Both chemicals are found in an array of personal care products like antimicrobial soaps, and triclosan also is formulated into everyday items ranging from plastics and toys to articles of clothing.

But are these antimicrobial chemicals, as commonly used by people across the nation, really safe for human health and the environment?

More pointedly, Rolf Halden do they even work?

According to associate professor Rolf Halden, of the Biodesign Institute at Arizona State University, the answer to these questions is an emphatic “No.” A biologist and engineer, Halden is interested in chemicals produced in high volume for consumer use. “I follow the pathways of these substances and try to figure out what they do to the environment, what they do to us and how we can better manage them.”

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Halden also is an associate professor in the School of Sustainable Engineering and the Built Environment at ASU’s Ira. A. Fulton School of Engineering.

The antimicrobial triclosan was patented in 1964, and began its use in clinical settings, where it was found to be a potent bacterial killer, useful before surgical procedures.

Since then, industry’s drive to convince consumers of the need for antimicrobials has been aggressive and highly effective.

Antimicrobials made their first appearance in commercial hand soaps in the 1980s and by 2001, 76 percent of liquid hand soaps contained the chemical.

Antimicrobials have become a billion dollar a year industry and these chemicals now pervade the environment and our bodies. Levels of triclosan in humans have increased by an average of 50 percent since 2004, according to newly updated data from the Centers for Disease Control and Prevention (CDC). Triclosan and triclocarban are present in 60 percent of all rivers and streams nationwide and analysis of lake sediments have shown a steady increase in triclosan since the 1960s. Antimicrobial chemicals appear in household dust where they may act as allergens, and alarmingly, 97 percent of all U.S. women show detectable levels of triclosan in their breast milk. Such unnecessary exposures carry risks which, at present, are ill-defined.

Halden and his team conducted a series of experiments aimed at tracking

the environmental course of the active ingredients in personal care products. The disturbing results of their research indicate that triclosan and triclocarban first aggregate in wastewater sludge and are transferred to soils and natural water environments, where they were observed to persist for months or years.

The chemistry behind these compounds, which contain benzene ring structures that have been chlorinated, make them notoriously difficult to break down. Further, they are averse to water or hydrophobic, tending to stick to particles, which decreases their availability for breakdown processes and facilitates long-range transport in water and air. A recent study demonstrated the accumulation of triclosan in dolphins from contaminated coastal waters.

Earlier, the EPA had been provided with industry-funded studies of wastewater treatment plant effluent, seemingly indicating elimination of triclosan and triclocarban during the treatment process. But Halden speculated that these chemicals might in fact persist in the solid byproduct left over after treatment—the sewage sludge. The group’s suspicions were confirmed through an initial testing of a large wastewater treatment plant serving 1.3 million people, located in the Mid Atlantic region of the U.S. In the first study of its kind, conducted by the team in 2006, it was determined that three quarters of the mass of triclocarban

The culture of fear leads people to make impulsive decisions and buy a lot of antimicrobial products that are not really needed.

–Rolf Halden, professor at the Biodesign Institute of Arizona State University

Francisco.” One half of this sludge winds up on agricultural fields. The potential for these chemicals to migrate into food or leach into groundwater, has not received adequate consideration. It is likely that antimicrobials are capable of moving up

exposed to them, thereby increasing the likelihood that a super-bug, resistant to the very antimicrobials developed to kill them, will emerge—with potentially dire consequences for human health.

On the positive side, Halden’s team identified

specific microorganisms adapted to not only tolerate but also break down pervasive antimicrobials. The research is part of a wider effort aimed at alerting the public and regulatory agencies, including the EPA and FDA, of the dangers of these chemicals as well as developing effective remediation strategies.

As Halden explains, “these microbes have the dual advantage of being resistant to destruction by antimicrobials and being able to break down these chemicals. You could put them to use for example by adding them to high-strength industrial wastewater before it gets combined with the domestic sewage.”

While effective regulation of these chemicals is badly needed, Halden says that the inertia of regulatory agencies is a formidable obstacle. In the meantime, the best hope is for consumers to avoid triclosan and triclocarban containing products.

“The culture of fear leads people to make impulsive decisions and buy a lot of antimicrobial products that are not really needed,” Halden says. “It’s a profitable market to be in, but not one that is ultimately sustainable or a good idea.”

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the food chain, through a process known as biomagnification.

Both triclosan and triclocarban have been linked to endocrine disruption, with potential adverse impacts on sexual and neurological development. Further, the accumulation of these antimicrobials in the environment is exerting selective pressure on microorganisms

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entering the wastewater treatment facility was simply moved from the water into the sludge.

Similar tests confirmed the accumulation of triclosan in sludge with 50 percent efficiency.

“We make 13 billion pounds of dry sludge per year,” Halden notes. “That is equal to a railroad train filled with sludge stretching 750 miles from Phoenix to San

Feature

Fast Track New UofA-based institute to boost bench-to-bedside research n an academic environment bustling with research activity such as The University of Arizona, scientists routinely make discoveries that hold the potential for new drugs, new medical treatments or new medical devices. However, it can take years for such a discovery to make it from the “lab bench” to the “bedside” in the form of a new treatment for patients.

To boost its bench-to-bedside science and position itself in a more competitive place to acquire translational research funding from the National Institutes of Health (NIH), the UofA has formed a Clinical and Translational Sciences Institute (CTSI) to provide the groundwork for therapeutic advances that will directly advance medical care.

“We want to bring to the people of Arizona the best that is available in medicine,” says William M. Crist, vice president for health affairs at the UofA. “A university of this size and caliber provides a perfect environment to translate innovative research directly into new therapeutic solutions.”

Specifically, the CTSI will: • Provide opportunities for practitioners with knowledge about what concerns and affects their patients to interact with scientists engaging in basic research.

• Provide those researchers with access to human tissue samples in which they can test new ideas.

• Facilitate interactions between fledgling biotech enterprises or established pharmaceutical companies and the university.

• Streamline the use of new drugs and vaccines found to be

Bio

By Deboran Daun

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Fernando Martinez, director of BIO5

effective in clinical trials without being hindered by ignorance about best therapeutic practices or lack of consideration of ethnic and cultural background • Serve as a hub for physician-scientists who treat patients and do research in “translational” areas that connect basic science to clinical treatment.

In traditional clinical settings, physicians often struggle with clinical obligations that take too much time away from pursuing efficient, outcome-oriented lab research.

In contrast, the CTSI will provide an “environment in which clinician faculty members have the resources, the mentorship and the encouragement to dedicate a significant proportion of their time to research,” says Leslie Tolbert, the university’s vice president of research, graduate studies and economic development.

The CTSI initiative is part of the university-wide transformation plan, through which UA is building strategically on existing strengths and resources to most effectively meet our missions in education, research and connection to the community.

Provost Meredith Hay has committed $6 million to develop a translational biomedicine program, which will connect bench research with medical care through the hire of new clinician-scientists who will attract significant translational medicine funding from the NIH. The institute will grow on a solid foundation formed by already established UofA programs and facilities, which together provide the crucial ingredients for translational medicine: drug discovery, genomics, proteomics, biostatistics and medical device development.

“Take our already strong drug discovery program, for example,” says Fernando Martinez, director of BIO5 and head of the Arizona Respiratory Center, who has been designated to lead the translational institute’s efforts. “There is no doubt that we will find molecules that we can commercialize for the university, thus providing revenue streams that become ever more critical in times where state funding goes down rapidly.”

Renaissance Man

Innovation is driving force for Horacio Rilo

Islet cell transplantation UofA surgeons are the first in the Southwest to perform successful auto-islet cell transplants in patients with severe chronic pancreatitis, an extremely painful condition.

Rilo is a world leader in this process, having established transplant centers in Pittsburgh, Chicago, Cincinnati, South Carolina, and now Arizona. Without an islet transplant, the chronic pancreatitis patient develops an extreme form of diabetes termed ‘brittle diabetes,’ which is much harder to manage and has more secondary complications than Types I and II diabetes.

In auto-islet transplant surgeons remove the patient’s pancreas, separate the insulinproducing pancreatic islet cells (called “islets”)

Wound healing and artificial skin Diabetes increases the severity of wounds, sometimes making them chronic wounds that don’t heal without intervention. Rilo collaborates with plastic surgeons on new ways to heal wounds more efficiently with skin grafts. His group has developed an innovative “glue-like” suspension of microscopic bits of the patient’s own skin that can fill the wound. These microscopic skin particles then grow together and heal the wound. With this method, doctors don’t need to rely on artificial skin grafts and don’t need as much of the patient’s own skin to cover a wound, thus reducing invasiveness and healing time.

Rilo also has engineered a novel device that can sew together biologically compatible threads into a matting of controlled size and thickness, which is then placed over a wound to promote healing. This success of this research would obviate the need to use the patients’ own skin harvested from another part of the body.

Nipple areola cryopreservation project When women undergo radical mastectomies today, the nipple tissue is not harvested, even when it is cancer-free. Thus, when later undergoing reconstruction, the shape of the nipple can be roughly re-created, but not the function or true color. Rilo’s lab is working with plastic surgeons and cancer physicians to find ways of cryopreserving cancer-free nipple tissue so that it can be re-attached during reconstructive surgery, thus salvaging both the form and function of the tissue.

Bioengineered tissue and stem cell therapy—Harvesting adult stem cells from fat and bone marrow, storing them, and then using them later to regenerate other tissue is part of Rilo’s research. Adult stem cells offer advantages over other stem cell strategies because they are the patient’s own cells that are transplanted back, and the new tissues don’t react with the body’s immune system. Avoiding this response increases the success rate of the transplant. Active projects include using stem cells to treat Parkinson’s disease, degenerative knee injuries, chronic-wound healing, and diabetes reversal therapy.

Kidney preservation for transplantation When kidneys are harvested from donors, the choice of fluid in which they are packaged and transported can affect the outcome for the organ recipient. Rilo’s lab has determined which fluid offers the best nutrients and environment for the organs, and he is working on ways to educate surgeons about what they should request before kidney transport. He also is determining if this fluid works well enough for kidneys that would normally be excluded from the donor pool due to age or time of death, to be transplanted.

Diabetes management and prevention project Diabetes is called the silent killer, because the disease can be quite progressed before a patient has symptoms. Rilo’s Diabetes Center goals include creating a multi-pronged approach to the prevention and management of the disease so that complications can be avoided. His most recent project, which was undertaken in partnership with several community groups, was to determine if patient education alone had a positive impact on blood sugar management. It did. Significantly.

The project involved using continuous glucose monitors, bioelectrical impedance analysis, activity monitors and grass roots outreach to underserved and out-of-reach populations in the local community. Armed with cutting edge, portable technology to track a person’s body functions can arm them with the facts, and Rilo found that, for many patients, that was enough to modify their behavior and reduce the possibility of complications.

Deborah Daun is communications director at the UofA’s BIO5 Institute.

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from the diseased organ, and then transfer the islets back into the patient’s body. Once surgically removed, the pancreas is rushed to Rilo’s specially designed “Class 10,000” clean room to harvest the islets, which are then returned to the operating room and infused into the patient’s liver where they then control the patient’s blood sugars.

Rilo also is interested in performing allo– islet transplants (using a donated pancreas) for Type 1 diabetic patients in order to reverse their diabetes. He is seeking FDA approval and can demonstrate that one of his previously Type I diabetic patients, who underwent this diabetes reversal therapy in 2001 is still insulin free.

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nnovator. Inventor. Surgeon.

Patient advocate. Community educator.

As a translational scientist and physician, Horacio L. Rilo has a keen interest in a wide variety of people and disciplines, from engineering, to physiology, to medicine and public health. His knowledge and understanding of disparate fields allow him to draw creative conclusions, which in turn moves innovation to patients’ bedsides faster.

For Rilo, nothing is impossible— the solution is just up ahead and he figures out the best way to get there.

Rilo is the director of the Center for Cellular Transplantation Horacio Rilo in the Department of Surgery and a BIO5 member. The thread that runs through all of his pursuits is regenerative medicine and a passionate drive to ensure that transplant patients get the very best that science and medicine can offer. The theme in his transplantation work is “yourself to yourself.”

In other words, he is finding ways to transplant your own cells into your body to treat and regenerate diseased tissues and physiological processes. Rilo’s work falls into three areas:

By Steve Yozwiak

Feature

TGen’s new link

to ASU

super fastest Cox Business LightWave Service connection, enhanced by Obsidian Strategics military technology, accelerates analysis of disease research

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new light-speed computer connection using a militarytested network provides the Translational Genomics Research Institute (TGen) with the nation’s fastest supercomputer link among life-science facilities.

This enhanced capability moves data up to 100 times faster between TGen and Saguaro 2, Arizona State University’s supercomputer, accelerating TGen’s molecular research into diseases such as Alzheimer’s, diabetes and many types of cancer.

The transfer and processing of data sets containing trillions of bits of DNA information that once took more than a week will now be done in just a few hours.

To make this possible, Cox Business Arizona has installed a 10-gigabit LightWave fiber-optic connection between TGen in downtown Phoenix and the Saguaro 2 supercomputer, 10 miles away at Arizona State University’s main campus in Tempe.

The new connection replaces a 1-gigabit line, increasing the speed of data transfer by up to 100 times because of data-encryption technology designed for military applications

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by Obsidian Strategics, a Canadian-based defense-intelligence contractor.

“Every advance in computer technology helps us move ever-closer to finding new and better ways to diagnose — and help select treatment for — patients who are counting on us to help improve their quality of life.

We expect this new system to be a significant step in that direction,” said Dr. Jeffrey Trent, TGen’s president and research director.

The new system, one of the first civilian uses of this military technology, will allow TGen scientists to more quickly analyze next-generation whole genome sequences — readouts of the entire 3-billion chemical letters in an individual’s DNA. “The field of biomedical research presents one of the greatest opportunities in transferring massive amounts of data from point to point. Our Cox LightWave Service accomplishes this quickly and with 100 percent security over our wholly-owned network. It’s ideal for enterprises like TGen, ASU and datacenters that transmit and receive information in terabytes,” said Hyman Sukiennik, Vice President-Cox Business Arizona.

Reducing transmission time will become even more critical in the future, with TGen’s next generation sequencers easily producing as much as 30 terabytes of data per experiment, or the equivalent of an iPod with 15 million songs.

To make full use of the Cox Business LightWave connection, each end of the 10-mile link will connect through an Obsidian Longbow, a high performance network product originally designed to meet the mission critical demands of the U.S. Department of Defense’s next generation Large Data communications architecture.

The Longbow is manufactured in Phoenix

by Suntron Corporation.

Cox’s Business LightWave connection uses Dense Wave Division Multiplexing technology, enabling two or more optical signals having different wavelengths to be simultaneously transmitted in the same direction over one strand of fiber.

Obsidian’s technology leverages existing optical networks. In a recent collaboration with NASA’s Ames Research Center in California and Goddard Space Flight Center in Maryland, full line-rate encryption was added to the enterprise class product. Strong encryption typically degrades throughput performance even on fast servers. In contrast, Longbow’s use of the High Performance Computing (supercomputing) InfiniBand protocol, combined with an integrated hardware cryptography engine, delivers virtually full channel throughput with or without encryption enabled.

While encrypting the information is critical to maintaining patient privacy and to the protection of intellectual property rights, the Obsidian Longbows go further to provide secure user authentication, preventing unauthorized access to Saguaro 2 and TGen’s sequencing equipment.

“With Longbow’s ability to achieve near perfect utilization of a 10Gb Ethernet connection, researchers at TGen should realize a 100X performance boost over their existing capability,” said Dr. David Southwell, Obsidian’s chief technology officer. “Though we remain very committed to our work with the military/intelligence community, it is gratifying to see our Longbow technology being adopted in other markets, especially in the area of bioscience and medical research.

Hats off to TGen for leading the way.”

Obsidian’s Longbow devices were used to win the bandwidth challenge at the Supercomputing 2009 show in November maintaining the highest throughput coast-to-coast link from the Supercomputing event in Portland to the Naval Research Laboratory in Washington D.C. The Saguaro 2 supercomputer used by TGen is located at ASU’s Barry M. Goldwater Center for Science and Engineering.

“ASU is pleased to enter into this relationship with TGen, Obsidian, and Cox Business,” said Lee Seabrooke, ASU’s Director of Knowledge Informatics. “The High Performance Computing Initiative at ASU, along with our extensive academic and scientific resources, uniquely positions ASU to be able to address the most critical challenges of our time.”

Edward Suh, TGen’s chief information officer, said the enhanced computer systems should help position TGen as a leader in biomedical data analysis.

“In addition to next-generation whole genome sequencing, the faster computer connections also will help data transfers in the emerging field of proteomics, in which TGen will identify protein biomarkers linked to the causes of disease,” said Dr. Suh. “We have to be mindful of patients. Anything we can do to expedite the path to treatment is a plus.”

Steve Yozwiak is the senior science writer at TGen.

for genomic data new computer data compression technique called Genomic SQueeZ (G-SQZ), developed by the Translational Genomics Research Institute (TGen), will allow genetic researchers and others to store, analyze and share massive volumes of data in less space and at lower cost.

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Created specifically for genomic sequencing data, the encoding method underlying G-SQZ and its software use are described in a paper published recently in the journal Bioinformatics.

Tests show that G-SQZ can compress data by as much as 80 percent while maintaining the relative order of the data and allowing for selective content access. This could save researchers and others millions of dollars worldwide.

Plans are to make the G-SQZ program freely available for research and academic use, and to explore commercial

opportunities in genomic data storage and processing. TGen has filed a patent application for the G-SQZ technology.

“Data storage and processing costs are becoming a large factor in research planning as high-throughput genomic sequencing studies continue to generate increasing amounts of data. G-SQZ has the potential to save individual institutes hundreds of thousands of Edward Suh and TGen’s dollars per year Computational Biology in storage costs,” Division team said Waibhav Tembe, the paper’s lead author and TGen’s senior computational scientist, who led the development of the G-SQZ algorithm and its software.

Enormous computing power is required to conduct today’s cutting-edge analysis of large volumes of genomic sequencing data. This data is critical in studying the genes that are a part of the 3-billion-letter DNA sequence, the entire genome of one person. Such analysis is enabling researchers to identify those genomic components that either prevent or contribute to diseases, such as cancer, diabetes and Alzheimer’s, and to discover treatments tailored to individual patients that can prolong and increase their quality of life.

Today’s genomic sequence analysis requires analyzing terabytes of data. Large sequencing centers are planning or have installed petabyte-scale storage. One terabyte is more than 1 trillion bytes of data.

One petabyte is 1,000 terabytes.

Edward Suh, TGen’s chief information officer described G-SQZ as a significant breakthrough in storing and analyzing everincreasing genomic sequencing data.

“As a non-profit research institute dedicated to advancing science for the public good, we at TGen are proud to be able to share aspects of this technology with other non-profit research institutes, especially in these times of tightened budgets,” said Suh, who also is a senior investigator at TGen and co-author of the paper.

James Lowey, TGen’s director of highperformance biocomputing and the third co-author of the paper, said reducing storage costs for genomic technology has the potential to eventually lead to a chain reaction of lower health costs for medical institutions and, ultimately, for patients.

“When you reduce the need for storage, you also are reducing your overhead costs, such as electricity and space, and that can save money,” Lowey said.

The software is available for download from http://public.tgen.org/sqz.

Tembe is moving ahead with improving his current design to accommodate what he calls “parallel computing.”

Because G-SQZ compression keeps the data ordered and indexed, the squeezed data can be split into smaller “chunks,” allowing multiple computer processors to decode and analyze different parts of the same file simultaneously, he said. For example, if a file is indexed at 1,000 places, it can be fed into a supercomputer, allowing 1,000 processors to analyze the data at the same time, speeding up the results.

Analysis tools using parallel programming approaches can take advantage of the G-SQZ encoding format.

“While indexed and compressed representation is ready, the parallel computing functionality is undergoing a testing phase,” Tembe said. “But this is where it is headed. Sequencing hundreds of billions of bases per run is now a reality.

The real impact of G-SQZ lies in the storage, transfer and processing of genomic sequencing data, where substantial room for improvement still exists.”

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storage needs & costs

Scientists get compact format for genomic data processing

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technology cuts

These distinguished generals have the knowledge, expertise and enthusiasm to propel this state’s A&D industry to its fullest potential.

Retired Brig. Gen. R. Thomas Browning

–William C. Harris, president and CEO of SFAz

Retired Lt. Gen. John F. Regni

ScienceFoundation Arizona ::

Retired Air Force generals to lead Arizona aerospace and defense initiative W riting by :: Pati Urias

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wo military officers have put retirement on the back burner as they take on a new command: an initiative to bolster the state’s aerospace and defense industry.

Science Foundation Arizona (SFAz) has attracted retired Brig. Gen. R. Thomas Browning and retired Lt. Gen. John F. Regni to be co-directors for an A&D Institute (ADI) that will work to strengthen the state’s military and defense sector and make Arizona a more viable prospect for growing companies.

Each year military and defense industries pump nearly $18 billion ($9.1 billion from military installations and $8.8 billion from private sector) into the state’s economy and create 190,000 jobs. Because careers of the 21st century require educated and skilled employees, the ADI will also address issues related to the availability of a well-qualified A&D workforce.

“These distinguished generals have the knowledge, expertise and enthusiasm to propel this state’s A&D industry to its fullest potential,” said William C. Harris, president and CEO of SFAz. “Their combined decades of experience in the defense, business and education sectors will be critical to providing

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a vision and necessary leadership to our state’s efforts to fortify, create and grow more high quality jobs in this sector.”

Browning, a highly decorated veteran and champion for statewide economic development, graduated from the Air Force Academy in 1964 with a bachelor’s degree in engineering science and received his master’s in public administration from Shippensburg State College in Pennsylvania. Browning served in Thailand and Vietnam, returning stateside in 1973 to Nellis Air Force Base as a pilot, instructor, flight commander and assistant operations officer. Later he served as chief of the operations division of the Directorate of Electronic Combat in Washington, D.C. The Scottsdale resident also served in leadership positions at installations in Texas, Japan and Arizona.

He retired from the Air Force in 1992.

Regni was chosen for his leadership and experience in the education and A&D industry. He was the superintendent (president) of the U.S. Air Force Academy, commanded the Air University overseeing the Air Force Institute of Technology as well as the Community College of the Air Force (the world’s largest community college) and commanded Second Air Force, operating

all the Air Force’s technical training schools in 250 job specialties. Regni’s 40-year Air Force career began at the Air Force Academy, where in 1973 he earned his commission as well as a bachelor of science in biology.

Regni has served in a variety of personnel, training and command assignments at the Pentagon and at bases in Korea, Italy, Alabama, Hawaii, Illinois, Mississippi and Texas. Over the years the Litchfield Park resident has served on the board of directors for the Civil Air Patrol and the Mountain West Conference, and represents Arizona on the Southwest Defense Alliance.

SFAz also will provide $1 million in grant funding to Arizona State University to work with a consortium of academic and A&D industry partners through an Aerospace and Defense Research Collaboratory, further developing and strengthening technologies used in aerospace and military applications.

The Collaboratory will focus on three interconnected areas of A&D technology: • machine-to-machine and human-tomachine interactions and integration • visioning, simulation, modeling and visualization • information management and information assurance

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the university’s Office of University Research Parks. “We need to devise strategies to enhance security while promoting the safe movement of goods, services and people across the border. If we can do that, we’ll create jobs and improve the quality of life for all of us in the border region.”

While The University of Arizona has been involved in border issues for decades, that expertise was recognized in 2008 when the university was named to lead the Department of Homeland Security’s Center of Excellence for Border Security and Immigration, known as BORDERS.

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t’s hard to turn on the news these days without hearing a host of concerns about Arizona’s border with Mexico.

While it’s certainly true that the state’s 350-mile international border presents significant challenges, what’s often overlooked are the many opportunities that the border itself presents.

Amid the sunshine and saguaros of the Sonoran Desert, Southern Arizona is quietly becoming a national leader in addressing a

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wide range of border issues – from security, to immigration, to commerce, to health and environmental issues, just to name a few.

Two new University of Arizona initiatives are propelling the state to national prominence in this area and will have a significant positive economic impact on the state as well.

“Our location on an international border presents us with a unique opportunity to take lemons and make lemonade,” says Molly Gilbert, director of strategic initiatives for

Merged Disciplines BORDERS is a consortium of 14 research institutions dedicated to improving technologies, processes, and policies related to border security, immigration, and trade.

The consortium’s innovative approach draws on lessons learned from information sciences, engineering, computer sciences, economics, political sciences, public policy analysis, and other fields. Its goal is to identify approaches to border management that are practical, effective, and demonstrate respect for privacy and civil liberties concerns.

A component of the university’s Eller College for Management, BORDERS is under the leadership of Jay Nunamaker, Jr., director and principal investigator, and Executive Director Elyse Golob.

“BORDERS’ research addresses real world issues that are of immediate concern to policy makers and citizens alike,” says Golob.

“Our approaches and recommendations are already being utilized to deal with current border security and immigration demands.”

To complement BORDER’s research expertise, the university recently launched the Border Security and Technology Commercialization Center (BSTCC).

Located at the U of A Tech Park, the Center will evaluate and assist in the commercialization of promising technologies–innovations that will enhance the safety and security of the border, support bi-national trade, and increase the efficiency of border operations.

Technologies may include advances in the areas such as deception detection, data fusion, cyber security, communications, and interoperability, among others.

“One of the benefits of locating the center at the Tech Park is that we have the ability to test technologies in the field – in conditions very similar to those in which they’ll be deployed,” says Gilbert. A test site at the Tech Park will simulate border points of entry and be adaptable for a wide variety of testing scenarios.

We need to devise strategies to enhance security while promoting the safe movement of goods, services and people across the border. If we can do that, we’ll create jobs and improve the quality of life for all of us in the border region.

–Molly Gilbert, director of strategic initiatives for the Office of University Research Parks Joint Effort The BSTCC is a collaborative effort of the university and its partner organizations, Alion Science and Technology Corporation and the Bi-National Sustainability Laboratory.

Alion is a technology solutions company that provides support to the Department of Defense and other public and private sector organizations. The company is headquartered in Virginia and has laboratories and facilities across the nation and in eight other countries.

Promising technologies may be brought to the BSTCC for testing either by federal or state agencies or by private sector

companies. Alion is responsible for designing third-party testing procedures and for conducting these tests according to the highest professional standards.

The Bi-National Sustainability Laboratory, located in New Mexico, will provide additional border locations for the Center as well as important linkages to prestigious national laboratories, such as Sandia and Los Alamos.

The BSTCC is beginning its pilot operations in 2011 with the evaluation of an innovative deception detection technology. A private Arizona company will fund these initial testing activities while a $3 million request to the

Department of Homeland Security to support a broader pilot study is pending.

Gilbert sees the BSTCC as an important component of Southern Arizona’s economic development strategy.

“Arizona has an amazing group of companies that are doing border technology work or have technologies that can be converted to border applications,” she says. “If we can help them to demonstrate the efficacy of their technologies, they will prosper and create jobs, benefiting the entire region.”

But the impact of work conducted at the BSTCC goes far beyond the region.

“Borders are everywhere,” Gilbert notes.

“The technologies we are creating and testing here have applications globally.

They can be exported around the world, to anywhere that people are working to balance the conflicting demands of border security and trans-border commerce.”

Bruce A. Wright is associate vice president for University Research Parks at the University of Arizona.

+ Get Connected BORDERS: www.borders.arizona.edu UA Office of University Research Parks: www.ourparks.arizona.edu

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Artist drawing of the new Southwest Regional Center for Aberration Corrected Electron

{ Update::asu}

Microscopy at Arizona State University in Tempe.

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he LeRoy Eyring Center for Solid State Science at Arizona State University, with a reputation for world-class instrumentation and highly skilled and qualified staff, is about to get a jolt to its image in the form of two new aberration corrective electron microscopes.

Funded by the National Science Foundation, the pair of new microscopes—one from Nion, the other from JEOL—are expected to produce the clearest possible views of matter at the atomic level. So special are these precision instruments that they will be housed in a newly constructed Southwest Regional Center for Aberration Corrected Electron Microscopy on ASU’s Tempe campus.

These new additions to ASU’s battery of instruments include Rutherford backscattering, X-ray photoelectron spectroscopy, Auger electron spectroscopy and particle induced X-ray emission. They will be on display during this year’s Industrial Associates Program Open House to be held from 7:30 to 11:45 a.m. Jan. 26 at ASU’s Tempe campus in the Old Main Carson Ballroom.

“Industry affiliates will have access to ASU labs to see up close the unique breadth of instruments and expertise in the silicon desert,” says Nate Newman, director of the Center for Solid State Science in the College of Liberal Arts and Sciences.

Microscopy pioneers John Cowley, LeRoy Eyring and Peter Buseck helped establish ASU’s nucleus of excellence in electron

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microscopy research and applications in the 1970s, says Newman.

That prowess has grown substantially in the past three years with a fusion of more than $15 million for new equipment, funded

by NSF and private investors, says Newman, along with the establishment of an Industrial Associates Program.

Industry affiliates will have access to ASU labs to see up close the unique breadth of instruments and expertise in the silicon desert.

–Nate Newman, director of the Center for Solid State Science

Key Users “Now we have more than 200 users, including more than 70 principal investigators and scores of associates from other universities and the industry,” says Newman, a professor in the Ira A. Fulton Schools of Engineering.

“The IAP is involved with myriad industries helping each to develop new processes, material, and quality assessments,” says coordinator Herb Finkelstein. “We are not directly involved in the research of new products as such, but we help industry bring

a more reliable and newly improved product to market.”

Among the technologies tapping ASU’s expertise are green technology, semiconductors, alternative energy, building, transportation, transportation safety, health, biosciences, wireless communications, homeland security, aerospace and defense, and household products.

Representatives from those fields and others who attend the open house will have an opportunity to see the transmission electron microscope and scanning electron microscope, each with a full range of associated imaging, diffraction and spectroscopy techniques.

The chief tour guide for the event will be ASU professor Ray Carpenter, who performed extensive research on materials for structural applications and nuclear power reactors at SRI International, Aerojet-General Nucleonics Corp. and Oak Ridge National Laboratory.

Attendees also will tour the Goldwater Material Science Facility to learn about available synthesis and characterization techniques, X-ray diffraction, topography, photoelectron spectroscopy, and Auger electron and Fourier Transform Infrared spectroscopy.

The Industrial Associates Program Open House is free and includes continental breakfast and presentations by the director and facility manager. Registration is required.

Contact Finkelstein at herb.f@asu.edu to register. For those unable to attend the open house, details about the equipment and facilities of the LeRoy Eyring Center for Solid State Science at ASU are online at http://lecsss.asu.edu.

Carol Hughes is senior director of media relations and public affairs at ASU’s College of Liberal Arts and Sciences.

{ Update::NAU} Paul Keim is director of NAU’s Center for Microbial Genetics and Genomics.

Time Travel DNA fingerprinting traces global path of plague

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devastating disease to prevent or control future infectious disease outbreaks.”

Tracking the worldwide spread of plague required identifying mutations in as many strains as possible. But transferring live bacterium across borders is highly regulated and difficult due to its potential danger, presenting a challenge to scientists.

Road Map To make this research possible, the team devised an innovative research strategy of decentralized experiments where scientists in worldwide locations worked with one or several of 17 complete plague whole genome sequences. By electronically combining all the research data, the team identified hundreds of variable sites in the DNA while assembling one of the largest dispersed global collections of plague isolates. That data was used to reconstruct the spread of plague pandemics, calculate the age of different waves of outbreak and was linked to descriptions in the historical record to better explain the current existence of plague. The results serve as a map of how the plague made its way around the globe.

Their collaborative research determined that the plague pathogen originated in or near China where it has evolved and emerged multiple times to cause global pandemics.

The international team also identified unique mutations in country-specific plague lineages.

Tracing its evolution, the plague spread over various historical trade routes as early as the 15th century. Chinese admiral and explorer

Zheng He’s travels may have taken the plague to central Africa. The Silk Road, which led from China to Western Asia and on to Europe as described by Marco Polo, also may have served as an avenue for disease. The latest plague pandemic of the late 1800s still persists.

“The plague found its way to the United States in the late 19th and early 20th centuries through multiple port cities by infected ship-borne rats,” said Wagner, assistant professor of biological sciences at NAU. “Based upon DNA variation detected from these comparisons, we determined that the original plague strains that infected the U.S. had their origin in Asia and likely made their way to California via Hawaii.”

While plague pandemics are something of the past, the disease has never fully disappeared. The bacterium remains ecologically established in animal populations around the world, and has resurfaced in Africa and Madagascar.

“This study gives one the exciting feeling that we are able to rewind time,” said Elisabeth Carniel, director of the National Reference Laboratory and World Health Organization Collaborating Center for Yersinia at the Institut Pasteur in Paris. “However, this should not lead us to consider plague a disease of the past. We are observing its re-emergence in countries where it has been silent for decades.

Therefore, far from being extinct, plague is a re-emerging disease.”

Cindy Brown is a public affairs coordinator in NAU’s Office of Public Affairs.

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n international team of scientists has traced major plague pandemics such as the Black Death back to their roots using DNA fingerprinting analyses.

Researchers from Ireland, China, France, Germany and the United States, including Northern Arizona University’s Paul Keim and David Wagner, have turned back the clock to examine the past 10,000 years of global plague disease events. Their findings regarding the plague pathogen, Yersinia pestis, will be published in an upcoming issue of the international science journal, Nature Genetics.

Keim, director of NAU’s Center for Microbial Genetics and Genomics and division director of Translational Genomics Research Institute, said that while the plague is less of a threat to humans than at other periods in history, such as the Middle Ages, the current plague research can be applied to ongoing health threats around the world.

This type of DNA fingerprinting can be used to characterize both natural and nefarious plague outbreaks—which is crucial when a bacterium is used as a biological weapon.

“This work is more of a model for our control of epidemic diseases such as salmonella, E. coli and influenza,” Keim said. “Plague took advantage of human commercial traffic on a global scale, just as the flu and food-borne diseases do today.

Future epidemiologists can learn from this millennium-scale reconstruction of a

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Capitol Watch

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business leaders, university presidents and policy makers will be engaged in a stronger, more-focused approach to economic development for Arizona.

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Arizona’s recovery demands we look at both short-term and long-term solutions.

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Arizona Comeback

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Advance state’s economy, competitiveness

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Writing By :: Gov. Jan brewer

made a promise when I took this office: to get Arizona back on track, to create quality jobs by attracting high-growth industries, and to advance our competitive position in the global economy. While our state’s massive budget deficit has clearly been center stage, strategically I have been focused on the future and how we bring Arizona back to its prosperous times so we can ensure it is stronger than ever.

For decades, Arizona’s rapid population growth has shrouded its uninspiring performance in building a strong

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foundation of base industries necessary to weather turbulent economic times. When the housing bubble burst and growth stopped, it quickly became apparent to everyone how ingrained our economy had become in the construction and financing of new homes.

Yes, Arizona needs short-term fixes for its current economic woes, but more critical is to be certain we are focused on rebuilding for the long-term with consistent strategies.

That is why I hired Don Cardon as director of the Arizona Department of Commerce and established the Arizona Commerce Authority by executive order on June 29. Our state’s top

This model is unique to Arizona; it’s designed to meet the needs of the state and the industries critical to our future.

As the Arizona Department of Commerce transitions into the Arizona Commerce Authority, borrowing best practices from economic models around the globe, all of Arizona wins. This new authority will be required to demonstrate a return on state dollars invested into the organization.

Arizona’s recovery demands we look at both short-term and long-term solutions.

The passage of Proposition 100 will help our state address immediate needs. And our new model for economic development will build a stronger foundation so our children and their children can avoid the difficulties of the recession from which we are now recovering with the Arizona Comeback. + Get Connected www.azgovernor.gov

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The non-profit trade association CompTIA supports and leads the global IT industry through educational programs, market research, networking events, professional certifications, and political advocacy. It is known worldwide as the leading provider of vendor-neutral IT certifications in various fields, such as security, network administration, computer repair, and server administration. www.comptia.org

As the largest independent provider of cash flow financial services in the United Kingdom, Bibby Financial Services has expanded its focus to growing small and mid-market companies across the United States and Canada. The company’s expertise encompasses receivables funding, purchase order and export finance, and specialist solutions for the staffing and transportation sectors. www. bibbyfinancialservices.com

Computer Skills Institute’s credentialed programs are short-term, combining hands-on training with the necessary skills to pass national certification exams. All classes are limited in size to provide more one-on-one attention with the certified instructor.

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CXT Software is a leading provider of software products that help businesses manage same day, time critical deliveries. It is dedicated to providing courier, messenger, distribution, and logistics companies with the tools necessary to compete and grow in an ever-evolving marketplace. www.cxtsoftware.com Using a process designed specifically for acquiring colocation data center space, the Data Center Advisory Services team ensures you get the perfect data center solution to house your most critical IT applications. It gains leverage in the negotiation process and helps its clients make complicated decisions about one of their most crucial assets in a streamlined and organized manner. eHealthTrust Arizona is the first, large-scale health record bank in the country.

It provides consumers with a private and secure online bank account for their health records, offering a platform for ongoing self-management of health and wellness. www.ehealthtrust.com Global Cabling Concepts is sole-source end-to-end provider of structured cabling design and installation services. It provides a network of structured cabling services for all data, voice and video cabling systems to the financial, healthcare and security markets in addition to Fortune 500 companies and largescale server providers. www.globalccaz.com

Global Connect Communications helps technology and healthcare companies articulate compelling stories. It can translate technical innovation into market advantage. Global Connect’s PR and social media campaigns allow its clients to level the playing field against entrenched competition or to show how new technologies can mean a whole new ballgame. www.globalconnectpr.com/.

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In today’s connected world, we expect instant, convenient communication.

Why should healthcare be an exception, when the inability to quickly obtain vital medical images and information can have life-threatening consequences?

–Mike Wall, CEO of DICOM Grid

ou’re anxious. Those headaches hadn’t stopped, so you came in for those x-rays of your brain. Now you’re waiting while a trio of the top neurological experts in the nation confer on the images. One is in Phoenix, another in Boston, the third in Anchorage—and you’re in Tucson. Instead of waiting days, even weeks for the images to be shipped back and forth to learn the course of your treatment, you get the news within the hour.

This isn’t a “some day” scenario. The tool that makes this possible now is DICOM Grid ImageCare, the first secure cloud computing platform that makes searching, sharing and exchanging medical images as easy as downloading a song from iTunes. The webbased application lets medical professionals collaborate and act on imaging data in real time or whenever it’s convenient from any location.

No costly travel or multiple sets of x-rays.

“In today’s connected world, we expect instant, convenient communication. Why should healthcare be an exception, when the inability to quickly obtain vital medical images and information can have life-threatening consequences?” asks Mike Wall, CEO of DICOM Grid, a Phoenix-based healthcare IT

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company that makes digital medical imaging accessible and affordable to medical facilities and physicians.

Patented Split-Merge technology lets ImageCare provide security and privacy that allow physicians to safely access imaging data over any Internet connection. It also provides an alternative method for mandated image archiving that can force a medium-sized hospital to store data rivaling the volume available through Google Earth. In fact, ImageCare platform exceeds regulatory requirements for offsite archival, disaster recovery, business continuity, and picture archiving and communications system (PACS) migration.

The general availability of ImageCare follows successful beta testing at hospitals, imaging centers and physician practices. “By using DICOM Grid’s ImageCare solution, two of our hospitals have been able to costeffectively achieve mandatory regulatory compliance with the added benefit of business continuity in the event of planned or unplanned PACS downtime,” says Scott Whyte, senior director of physician and ambulatory care IT strategy at Catholic Healthcare West. + Get Connected www.dicomgrid.com

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safety innovators

Honeywell is advancing flight safety through enhanced situational awareness.

On the ground or in the air, getting more information to pilots is critical for the safe operation of aircraft. That’s why we strive to create safety systems that not only surround pilots with the key information they need – weather, traffic and terrain – but also integrate these innovations into lightweight, cost-effective platforms. From intuitive displays and predictive sensors to integrated avionics, Honeywell reduces pilot workload while enhancing situational awareness with proven automated advanced avionics solutions.

www.honeywell.com

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