From the page to the world of three dimensions

Today, science students viewing cells in a textbook typically perceive microscopic worlds in the same manner as early Earth inhabitants who, gazing to the horizon, thought the world was flat. Two years ago, HudsonAlpha set a course of scientific discovery for students and introduced iCell. Since then, the interactive app iCell has reached 250,000 downloads on iTunes and more than 300,000 downloads across all platforms. HudsonAlpha iCell allows users to explore animal, bacteria and plant cells in a 3D display. 

"The purpose was to help students understand the cell a little better," said Adam Hott, Ed.D., coordinator of educational outreach. "Teachers are telling us students understand the formation and parts of a cell better than they ever have. For a student to truly see and grasp this precept is huge."

In iCell, users may drag, enlarge, shrink and rotate the cell, as well as tap on specific parts of the cell. Descriptions for each part are featured in basic, intermediate and advanced options of level of detail. Educators may also use the app in a classroom setting for teaching and testing.

"As iCell's presence grows, our purpose is broadening to how can we make iCell better, how can we include other types of cells and introduce more functionality and capabilities," Hott said.

The app has been featured across multiple outlets, including being named by Apple as "one of the best" free educational apps. Genetic Engineering and Biotechnology News listed iCell in its Best Science Apps column and CBE Life Sciences Education journal named it one of the most recommended cell biology apps available. 

HudsonAlpha iCell was developed in partnership with Digital Radiance and is available for free through the iTunes store, the Android Marketplace and Windows 8 store. But digital education at the institute doesn't stop with iCell. The educational outreach team has also developed the Progress of Science interactive timeline and Genome Cache. You can read about them below or follow the links to learn more. 

Progress of Science timeline

From domesticating the first animals used for food to creation of the first self-replicating synthetic bacteria, the Progress of Science interactive timeline links history with scientific discovery. Across the centuries, biotechnology's history can be traced in many thousands of stories of discovery -- a sampling of which is on the timeline. The timeline was originally developed as a 9-by-42-foot wall mural which is on display on the third floor hallway leading to the educational classroom. "The idea came to our director, Neil Lamb, that if we were going to inspire teachers and leaders and students about genetics and biotechnology, walking them down a sterile white hallway is probably not a good start to the experience," Hott said. "The timeline is just beautiful. It's a work of art." 

Genome Cache

Genome Cache is an interactive program that allows anyone to create a walkable path exploring the human genome. More than 20 paths are available in a digital or printable format and range in difficulty, making it a perfect exercise to learn more about the human genome through clues, fun facts and trivia questions. It's an app, a website, a print-out and a walking activity. It's a little bit of everything, Hott said. McMillian Park runs through the center of the HudsonAlpha campus and features a double helix walkway. The Genome Cache can also be organized along the walkway, turning the park into a giant human genome, essentially exploring and walking through all the chromosomes of the human genome. 

Teri Hasemeyer is a senior at the University of Alabama, double majoring in journalism and dance. She'll intern with the Tuscaloosa News during the fall semester with plans to graduate in December. Outside of the newsroom and dance studio, Teri can often be found sipping coffee or participating in a hot yoga class. Currently, she's working as a communications intern through BioTrain.

Celebrating five years, together

We recently celebrated the fifth anniversary of HudsonAlpha, and we're excited to see what the future holds. HudsonAlpha's president and director, Dr. Rick Myers, shares highlights of the past five years and his hopes for the future. We hope you'll enjoy reading Dr. Myers' thoughts as well as perusing some photographs from our anniversary celebration. We look forward to serving the Madison County community for years to come. 

Dear Friends,

The HudsonAlpha Institute for Biotechnology, the brainchild of founders Jim Hudson and Lonnie McMillian, opened its doors in 2008. The passion of these serial entrepreneurs to make the world a better place through genomic and genetic discoveries and applications has flourished in the five years since we started together, evidenced by the institute’s multifaceted growth.

I share Lonnie’s and Jim’s passion. The elation I feel for how far we’ve come in making a positive difference is eclipsed only by the excitement I have for what’s ahead. Genomic research, educational outreach and economic development; each of these mission areas is a precursor to advancing quality of life. Together, they are powerfully synergistic and at HudsonAlpha.

Progress has many measures. By sheer numbers, I can point to an expanding research team. We have added four faculty investigators running research and discovery laboratories since they institute’s debut, bringing us to a total of 10 faculty. Our educational outreach programs have expanded dramatically and have begun to have a major impact throughout the state and the whole country. We now have more than doubled the number of for-profit companies on our biotech campus since our opening ceremonies and additional companies are ramping up.

By many accounts, HudsonAlpha has made a mark on the world. Successfully competing for research initiatives in a highly competitive funding environment; continuing work on milestone projects like the ENCyclopedia Of DNA Elements, multiple cancer and treatment response studies, brain and heart disease projects and many others, all of which strive to identify genomic pathways of health and disease; filing patents for knowledge emerging from HudsonAlpha labs; advising leading technology companies on improving processes and productivity in data and knowledge acquisition; weighing in on how to advance science achievement in schools and shore up the nation’s workforce pipeline. These only skim the surface of a broader, deeper collective resource pool that beckons scientists, educators and business professionals.

Each institute and campus resident offers valuable insight, skills, opinions, questions and answers. Your questions also have great value. When I noted that it has been five years since we started, you are included. The passion to execute research, education and economic development activities on behalf of public good is inextricably linked to widespread understanding of benefits. As a nation, defending research investment equates to defending the health and livelihood of its citizenry. The evidence continues to mount that great benefits are ahead.

Want to learn more? Ask. Share the news. Spread the passion. Feel the excitement of scientific discovery and help make a positive difference.

You’re invited to participate. Please join us!

With warmest regards,

Rick Myers

So, you counsel my genes?

HudsonAlpha recently highlighted the challenges faced by many local families who are living with childhood genetic disorders. Kelly East, a genetic counselor at HudsonAlpha, shares why the project is so valuable and further explains the role of a genetic counselor.

When I tell people I’m a genetic counselor, I’m often met with a blank stare. When someone does respond, it often includes one of the following questions: 

1.     “You tell people whether they should have children?” Or 

2.    “So…you counsel my genes?” 

No, we neither counsel people’s genes (whatever that even means), nor do we tell couples whether they should have children. We are not in the family planning business. Genetic counselors work with individuals or families who either have, or may be at risk for, a genetic condition. We provide our patients with information about the features of a particular genetic condition and potential treatment and screening options. We discuss the cause of the condition, whether it can be inherited in a family and explain available testing options and results. The information and support provided by the genetic counselor greatly varies based on the reason for genetic counseling and the needs of the particular patient.

We are educators and supporters and help our patients understand complex genetic risk information so they can make decisions that are in line with their cultural and familial beliefs. Sometimes these decisions are extremely difficult with no apparent “good” solution. We’re not physicians so we don’t diagnose ailments, nor do we prescribe medications. However, we often work very closely with physicians and aid in the diagnostic process.

Genetic counselors have traditionally worked in prenatal, pediatric and cancer genetics clinics. However, genetic counselors have valuable knowledge and skills that may be applied in a variety of settings. It’s becoming more and more common for genetic counselors to work outside of the traditional clinic. These expanded roles include adult medicine, research, public health, education, industry and public policy. As science and medicine learn more about the impact of genetics on common diseases like heart disease, diabetes and macular degeneration, there will be a growing need for genetic counselors working in adult medicine and primary care.

Sound interesting?  

I was a junior in college before I heard about genetic counseling as a possible career choice.  I was on a pre-medicine track, but in the back of my mind, worried medicine was not the right field. For me, genetic counseling is the perfect marriage of genetics, medicine and education.

Genetic counselors are health care professionals with specialized master’s degrees in genetic counseling. Most genetic counseling programs are two years in length with the first year being a combination of coursework and clinical experience and the second year consisting largely of supervised clinical rotations. My best advice for those considering genetic counseling as a career would be to get a good foundation in biology and genetics, and then get out there – volunteer with support groups, help with community events, shadow genetic counselors – figure out for yourself if genetic counseling is the right career choice for you.

For more information about what a genetic counselor is, or to find a genetic counselor near you, visit the National Society of Genetic Counselors website. You can find a list of the accredited programs by visiting the American Board of Genetics website or learn about other genetic fields of interest here. 

Kelly East is a board-certified genetic counselor with a bachelor’s degree in microbiology and a master’s degree in genetic counseling from Auburn and UNC – Greensboro, respectively. Kelly is part of the educational outreach department at HudsonAlpha. Working with patients and the public, helping them to understand the impact of genetics on health and disease, is one of her favorite parts of being a genetic counselor.

Positive Exposure@HudsonAlpha

Dr. (Neil) Lamb first mentioned Rick Guidotti to me about a year ago. After some additional research and snooping, I knew this was something HudsonAlpha needed to be part of. It's hard to believe it's been nearly a year since that initial design meeting with our researchers. At the time, I couldn't remember Guidotti's name (sorry Rick) and all I could say was something like, "Neil... has a friend... TED Talk... photographer... must get him here for a photo shoot!"

Our team put together a great event a few months ago where the kids came out to the institute. All I had to do was keep rolling footage. I was excited to work on a project about such potentially pivotal research, and I was excited about connecting with another artist that also worked with scientists. Little did I know that was only the beginning of the excitement. 

Starting today, you can view Positive Exposure at the Huntsville Museum of Art. Each of the children photographed in the exhibit live in North Alabama. Like your children, they are smart and funny; they laugh and giggle; they play and sing. The difference is they have a genetic disorder that in many cases, has an unknown origin. The launch of Rick's work coincides with new research we're doing at the institute. Through a multi-faceted collaboration, researchers are looking at some of those childhood genetic disorders. The smiling faces you see in Rick's work and the video below could potentially benefit from some of this research. It's amazing.

It's one of my favorite projects the institute has been part of in my five years here, and I can't wait to see what happens next. If you're interested in learning more, please join us for our annual spring benefit where these guys will be our focus. 

I hope you'll visit the museum this week and see why I am truly inspired by these kids. 

JD Frey is the media manager at HudsonAlpha, as well 

as the resident videographer. When he's not behind 

the camera, you can often find him in his studio 

at Lowe Mill. But let's be honest, he's usually behind 

the camera there, too. His newest project includes 

boundless adorable videos of his new baby girl. 

Double Helix Dash

I am so excited to share HudsonAlpha's second-annual Double Helix Dash with you. It's one of my favorite events hosted at the institute. Where else can you run on the world's largest replica* of human DNA? Only here, folks. Only at HudsonAlpha.

Scheduled for April 2, the 5K race starts at 5:30 p.m. and the 1-mile twilight run begins after the 5K race is completed. My favorite part of both is the last stretch. (And no, that's not because it means I'm finished.) It's my favorite because runners finish on the double helix sidewalk that runs through McMillian Park. 

Last year, the race was at capacity and it's filling up quickly this year. If you think it sounds like a fun race,  you're right!  If you sign up now, you'll pay a lower registration fee. Prices go up starting Tuesday. 

You may register for the race through this link. Looking for more details? Go to the Dash website and Facebook page. Peruse this album if you'd like to see how much fun it was last year. 

So seriously, what are you waiting for? 

*Legally, I'm supposed to tell you we believe it to be the world's largest 

replica. We're waiting on Guinness to (technically) verify. 

-Victoria Cumbow, communications specialist

A new perspective on business

Along with genomic research and education, HudsonAlpha's mission encompasses economic development. When the institute opened in 2008, 12 companies leased space in the anchor facility on campus. During the past five years, the number of companies has doubled and a conference center and second building have been added.

The institute's economic arm is one of the things that makes HudsonAlpha different from most research organizations. Founders Jim Hudson and Lonnie McMillian, both serial entrepreneurs, believe that discoveries in the non-profit labs will be transferred into products and services faster through close contact and partnerships with for-profit groups.

One of the companies located at HudsonAlpha, Kirchner Private Capital Group, specializes in entrepreneurial business. You can learn more about company here, but in the meantime, here's a throwback blog from Kirchner on "Building a Business: A Lifecycle Perspective." 

When born, humans are an extraordinarily frail and dependent lot. Without proper care and nurturing, most infants cannot survive. As an infant matures into a toddler, child, adolescent, teen and adult, needed supports and guidance change. However, decisions made at various stages in one’s life can have profound consequences on the quality of life, wellbeing and even survival.

Businesses are similar. Without proper care and nurturing, most do not survive. Also similar to humans, businesses that survive move through several distinct phases during their lifecycle. At each phase the support and guidance that is needed also change. As with humans, the decisions you make at the plateau of each phase will have a direct effect on whether your business moves from the current plateau to the next in its lifecycle.

I am reminded of one of the “one liners” in our recent book, How Do You Know if You are an Entrepreneur: “If neither path at the fork in the road looks promising, but that doesn’t stop you”… you might be an entrepreneur. The fact you are at a fork typically means your business has reached a plateau in its lifecycle and the decision can make a difference in whether your business thrives or dies. Yet, some of us behave as if we have forgotten businesses can be and should be viewed in terms of the phases in their lifecycle.

When faced with decisions related to a new venture, even entrepreneurs who have been successful in a prior venture do not consistently identify the discrete phase or plateau that their business is positioned at a given point in time. They also may not appreciate the critical importance of decisions that are made at each at least four major plateaus in the lifecycle of the business. Most importantly, too often they do not adequately consider alternatives in the context of their related risks and possible rewards in moving from one plateau to the next plateau.

General lifecycle phases: While there may be many ways of characterizing the phases of the lifecycle of a business, for simplicity we will consider three broad phases: (1) startup; (2) growth, and; (3) liquidity event. During the startup phase, at least three discernible plateaus will be experienced. The first occurs after you have your “idea” or make your discovery. The second occurs after a prototype has been developed and market opportunities quantified. The third occurs after you have your first beta customer. During the growth phase, the may be many small plateaus, but for the sake of brevity in this blog they are grouped into commercialization activities. Finally, during the liquidity phase activities related to increasing market share are viewed in the context of increased valuation for and M&A, IPO or other liquidity event.

Value and reward versus risk: The point of laying out general lifecycle phases isn’t to engage in an academic exercise. Rather it is to illustrate that the resources, support and guidance needed at each of the plateaus raise a myriad of questions that must be addressed. The decisions that come from addressing those questions will likely make a difference in whether your business moves to the next plateau or stagnates and dies.

Your decisions should be guided by two sets of consi derations. First, how will various decisions ultimately affect the creation of value in my business? This is true, of course, since your ultimate reward will likely be directly related to the value that you have created. However, on the other hand such issues as time, other resource allocation required and investment requirements can be viewed in terms of a risk continuum. Most decisions that you will make should guide you to the right spot to place the fulcrum to achieve balance on the risk-reward seesaw.

The lifecycle perspective: This blog is not intended to imply that using a lifecycle approach to conceptualizing the birth and growth of a business is the only conceptual framework that might be useful. It is also not a full articulation of the many subtleties and nuances that actually should be considered with making decisions at each plateau.

Follow this link to a slideshare presentation.

Dr. Patrick McNees is a managing partner with Kirchner. He is a 

serial entrepreneur with 36 years of experience starting, developing and exiting 

companies and intellectual property. He was the founding CEO and Chief Scientist 

at Applied Health Science, Inc. and co-founder and President of North Rim 

Systems and Computer Associates, a computer software development firm.

You can lead a horse to water...

I’ve always found clichés annoying, but one more than others:

You can lead a horse to water, but you can’t make it drink.

Now I’m no expert on horses, but there seems to be some inherent problems with this phrase. First of all, if the horse is thirsty and there’s water around, you can’t keep it from drinking. Thirsty horses drink. Period. Second, if the horse isn’t thirsty, why are you leading it to water? Quenched horses don’t drink. Lastly, if the horse is thirsty but not drinking the water, then something is terribly wrong with the water.

Obviously I think too much about clichés, but I’ve heard this particular one used in reference to students. Students may be described as apathetic, unwilling to work, unmotivated or uninterested in academics. Or unthirsty horses, if you will. Many teachers see themselves as tirelessly leading these unthirsty horses to the water over and over again only to have the cooling waters of knowledge refused. Teachers wrestling with unengaged students turn to fellow educators for tips and hear: “Well, you can lead a horse to water….”

Each summer, I spend two weeks in a room full of thirsty horses; a group of engaged and dedicated educators. These teachers spend 14 days in a professional development course that leaves them drinking from a fire hose. It is our job as the facilitators to bring buckets of water by way of content knowledge and hands-on strategies. It is a thoroughly enjoyable experience. Teachers know that feeling because thirsty horses are awfully fun to teach.

Whatever the reason, teachers return to the classroom to find students unengaged -- or rather to find horses not drinking the water. Our job as educators is to hydrate those horses. Here are my thoughts on how to keep your horses thirsty:

• Ask what’s wrong with the water. Don’t get so busy that you forget to consider reasons that your students aren’t engaged. Perhaps they are full of water from a previous class and need time to digest. Perhaps they don’t recognize the water because they lack prior experience. Perhaps they are too busy thinking about food to realize they are thirsty. Perhaps your water is stale and could use some freshening up.
• Be thirsty yourself. With budgets tight it is harder than ever to find funding for professional development, but it is always worth the effort. Investing, both the money and the time in your professional growth pays off not only for you but also for your students. Seek out those opportunities that allow you to experience as a student. Solid professional development not only deepens your content knowledge, but also keeps you excited about the classroom.
• If you are full, leave the water alone. Find balance in your life. You are not just a teacher, or a parent, or a spouse or the chairperson of that committee. You are all of those things and you must not let any one responsibility overpower the other. If you are full, step away from the water.
• Hang out with other thirsty horses. There are unthirsty horses in the teachers' lounge too. Avoid them. Make an effort to spend time around other teachers who are determined to help students learn. You can identify the unthirsty teachers by noticing who says, “Well, you can lead a horse to water…..”

For additional resources from HudsonAlpha's education team, visit the education portal. 

Madelene Loftin works as an education specialist
at HudsonAlpha. She was named Mississippi's
Outstanding Biology Teacher of the Year in 2008.
Since joining HudsonAlpha, she's been inspiring
Alabama students to pursue careers in science while
inspiring science teachers to be better educators.

Could DNA store all the world's data?

Across several news outlets this week, there's been talk of storing the world's data on DNA strands. You can read one of those articles here while Neil Lamb, HudsonAlpha's director of educational outreach, gives a bit more insight into exactly how the process would work...

Scientists have developed a method for storing documents, images and sound files inside the strands of the DNA double helix. The technology could open new avenues to keep copies of your favorite photos, that short story you wrote in fifth grade or those home movies of Christmas and birthday parties. Best of all, the technology would be safe for thousands of years and would take up less space than a tube of lipstick.

Let’s back up for a moment and discuss storing data. Information, whether from text, image or sound, is digitally encoded as long strings of 0s and 1s. Eight of these digits make up a “byte” of information. A typed page is made up of 2,000 bytes while a movie download contains about a billion bytes. It’s been estimated that all of the world’s digital data takes up roughly three zettabytes (a billion trillion bytes).

DNA also uses a code to store information. In this case the code is four chemical “bases” – adenosine (A), thymine (T), guanine (G) and cytosine (C). Several years ago, scientists began to look at how the digital code of 1s and 0s could be stored inside the DNA. The digital string of 0s and 1s is rewritten as a series of A,T,C and G. (Keep in mind, the DNA fragments used for storage have no biological function and are kept inside a vial rather than inside a cell.) When stored under particular conditions, the DNA is stable for tens of thousands of years. When it’s time to recover the information, the DNA is sequenced and the order of the bases converted back to the corresponding bytes.

Early attempts to store information as DNA code directly mapped 0s and 1s onto the bases – for example, a 0 was represented by A or C and a 1 by T and G. Unfortunately, this approach is problematic when the string of 0s and 1s leads to a repeat in the DNA sequence – like CCCCC. Current DNA sequencing technology struggles to correctly identify these repeat regions, miscalculating how many “Cs” are present and introducing errors into the numerical data.

Here’s where the recent media attention comes into play. Nick Goldman and colleagues at the European Bioinformatics Institute in the UK have devised a method to minimize the likelihood of copying errors. Rather than use a direct link between 0s and 1s and DNA bases, they devised an intermediate code that prevents repeating bases. To further reduce errors, the original code is split into fragments four different ways, with the breakpoints occurring at different locations each time. This way, if an error does occur, other copies of the same region can be used as comparison.

The scientific team encoded multiple files, including part of an MP3 recording of Martin Luther King’s “I have a dream” speech, a text file of all the sonnets of William Shakespeare and a PDF of the 1953 paper by Francis Crick and James Watson describing the structure of DNA. All told, 757,000 bytes of information were encoded on over 153,000 DNA fragments. The scientists estimate their approach, which is described online in the journal Nature, can store over two petabytes (or two million billion bytes) of information on a single gram of DNA. That’s a mind-boggling amount of information contained in something about the size of 15 grains of sugar.

Speed and cost are the two biggest drawbacks to DNA-based storage. It took four days to synthesize the code into DNA and the process of sequencing and decoding the fragments required two weeks. The synthesis and decoding process costs $12,620 per megabyte of information – millions of times more expensive than storing data on magnetic tape. However, as technology continues to improve, both the price and timeframe are expected to drop dramatically. If current trends continue, the researchers estimate that in less than a decade DNA-based storage will be cost-effective for information stored 50 years or more. This could be especially useful for long-term archiving of governmental, historical or scientific data that only rarely would be accessed.

If you’ve ever had to search for a way to pull data from an old floppy disk, zip drive or VHS tape, you know how quickly digital storage technologies change. The researchers note DNA has been storing biological information for more than 3 billion years, meaning the odds are high it will be around in the future, available for conversion into whatever new technology civilizations are using to share data. Hang on to your CDs, DVDs and thumb drives a little bit longer, but this technology is certainly worth watching.

Dr. Neil Lamb is HudsonAlpha's director of 

educational outreach. Trained as a human geneticist, 

he now focuses his energy on creating programs and 

activities that help Alabama's teachers, students and the public understand genetics and biotechnology.

A thought process

So here’s a thought process I had a few months ago. It’s a trail, but just follow me.

I was reading an old edition of Edutopia’s Summer Rejuvenation Guide and the guide contained a try something new section which discussed Pecha Kucha nights:

Pecha Kucha is the onomatopoeic Japanese word for the sound of conversation. The equivalent English term is chit-chat. However, it tends to carry a slightly negative connotation like chitter-chatter or a frivolous exchange of words. (From Wikipedia).

[image credit]

According to Edutopia, Pecha Kucha is a fast paced speaking format in which speakers have only a few minutes and a few slides to make a point. Interesting, right? The article also mentioned Ignite, a competitive version of Pecha Kucha, with events all over the world. Ignite’s tagline is “enlighten us, but make it quick.” 

My brain is now fully engaged so I follow the links to watch a few streamed videos at Ignite Show.*

Warning: these will suck you in completely. With titles such as “Commutapult”, “How to Fight Dirty in Scrabble” and “The Secret History of Fonts”, it’s easy to waste lots of time. I learned about “Botanicalls”, an iPhone app that tells you when to water your plants, and what physical computing really is, and why they are teaching ethics using social media in Australia, and how to get the best deal on a new car ……. I said they would suck you in.

In all seriousness, these videos feature people talking about what they’re passionate about. They are pointed, opinionated, funny, short, and I’m learning the whole time.

My brain immediately jumps to how I see real-life classroom application. I’m thinking my colleagues would be wicked good at this. Can we craft a few genetics/genomics lessons that take advantage of available media and a YouTube attention span?

*Ignite is not an educational website. Not all content is appropriate for the classroom.

Madelene Loftin works as an education specialist
at HudsonAlpha. She was named Mississippi's
Outstanding Biology Teacher of the Year in 2008.
Since joining HudsonAlpha, she's been inspiring
Alabama students to pursue careers in science while
inspiring science teachers to be better educators.