April 4th, 2013 -Despite minor advancements, the ability to monitor and maintain our health remains largely dependent on the intervention of the medical community. Drawbacks are already apparent in low-income communities where medical staff and resources are stretched thin. In light of increasing medical costs and the dawn of the baby-boomers’ transition into elderly care, the question remains how we will adapt to the present time. Dr. Ellington matched up with ESI’s Hot Science, Cool Talks to discuss the next generation of biotechnology: low-cost, personalized, at-home diagnostics.
April 4th, 2013 - Dr. Ellington sat down with KUT’s Jennifer Stayton to discuss evolving technologies for self-diagnostics. Their conversation covers medical technology and history, ethics, consumer-driven models, and more. The full interview is available on KUT News’ website.
The Austin American-Statesman also interviewed Dr. Ellington on the topic. The full interview is available on the Statesman’s website.
The integration of cutting-edge research with education both engages scientists and is critical to improving American competitiveness in science. The University of Texas at Austin has developed an innovative, groundbreaking, faculty-initiated program to tap the considerable resources of the research university — energy, ideas, expertise, mentorship, and facilities — to create a generation of science-minded innovators through undergraduate research.
The Freshman Research Initiative (FRI) is transforming the undergraduate teaching model by turning a student’s traditional trajectory on its head, placing first-year students into advanced research labs at the beginning of their educational experience rather than at the end. They connect with faculty. They are embraced by the community of their small research cohort. They work on real-world problems.
Started in 2005, FRI is a two-year-long program that begins during a student’s first year by placing them in one of more than 30 faculty-led “Research Streams” working on real world applications. Each year, freshmen are recruited into an intensive set of degree-program courses that incorporate critical thinking, interaction with faculty, hands-on experimentation, data interpretation, student presentation, publication and peer mentoring. The model incorporates cutting-edge faculty research amenable to large-scale freshman training and experimentation, after which students are experienced in a broad range of techniques and all aspects of research from conceptualization through execution and presentation.
Originally developed in biology and chemistry, the FRI program has been running and expanding for seven years and now involves projects in biology, chemistry, biochemistry, physics, astronomy, mathematics and computer science. In the past seven years, more than 3,000 new UT Austin students have participated, and the program now serves over 700 first-year students each year in the College of Natural Sciences, more than 33% of the incoming college class.
FRI is not a select honors program. There are no prerequisites, and it is unique in its ability to attract and empower students who are traditionally underrepresented in the sciences. Partially due to the fact that FRI courses replace traditional lab courses, making participation less daunting for many students, undergraduate research and the doors it opens have become available to students who have traditionally not participated. For example: approximately one-third of students entering the program are first generation college students, more than one third are underrepresented ethnicities, one quarter have low test scores and one-quarter have high financial need.
Students are challenged to ask their own questions within the context of a larger science problem and to produce relevant results, and they are provided the techniques and mentorship to rise to this challenge. Grit, resilience, tolerance for short-term failure, determination, passion and problem solving skills matter more within FRI than high school statistics, test scores or even previous courses. FRI levels the playing field for science students and is producing young scientists with new perspectives to help solve global challenges.
And clearly, FRI works: 35% more students graduate overall with a science or math degree if they participated in FRI, and the program more than doubles the graduation rate for Hispanic students in science, technology and math. FRI students have higher GPAs and get more scholarships compared with other students in the College of Natural Sciences. Additionally, these students are true contributors to the scientific conversation. Since 2005, 143 FRI students have co-authored peer-reviewed papers on their research.
The DIY Disease Diagnostics Team
This year a new Research Stream is being pioneered by three faculty members here at UT Austin: CSSB Associate Director Andrew Ellington (Molecular Biosciences), Peter Stone (Computer Science) and Pradeep Ravikumar (Computer Science). Each of these faculty members is outstanding in their own fields, but have come together to share their expertise with one another and with new students in the novel “DIY Disease Diagnostics Stream.” In this stream, freshmen will be challenged to develop an interdisciplinary skill set that would be daunting even to an experienced clinician (which is precisely why they need to be challenged now, before they are experienced clinicians). They will be trained in molecular methodologies that will allow them to develop self-test diagnostics, will gain a basic understanding of laboratory robotics, will interface with computer scientists who will help automate the delivery of diagnostics, and will create their own social networks for assessing the context and impact of their diagnostic assays.
Advances in analytical chemistry, molecular engineering, biomarker discovery, and materials science have come together to begin a new age in diagnostics development. Whereas previously many medical tests were run in clinical labs or settings, point-of-care diagnostics can now be crafted for individual use. Much as home pregnancy tests altered the social landscape during the 1970s, home HIV tests are similarly providing a new means for consumers to empower themselves in medical decision-making. Similar tests for tuberculosis and other diseases will increasingly transform the interactions between clinicians and patients in resource-poor settings.
In parallel, there have been revolutions in computer science that will further transform the delivery of health care. Not only is laboratory automation changing the nature of how we do science, but the increasing automation of society now mandates that we even begin to think about the robotic driver in the next lane. How will similar advances impact how we think about who our health care provider is, and how we interact with them? Is it possible that the diagnostics made possible by better-living through chemistry will now be administered by a robot?
Finally, we continue to ride the wave of productivity and globalization released by the Internet. We now are intimately involved in the lives of individuals we’ve never met in person, and can crowd-source new data and new insights at a magnitude that was previously unimaginable. The aggregation of patient data will alter everything from the questions on a physical to the actuarial tables that determine insurance rates. Clinical trials will increasingly be carried out in a distributed fashion, with the results compared virtually. How will the glut of data that is being churned out every day by sequencing engines, and the coming glut of diagnostics data that will result from these sequencing insights, be handled not just by the medical profession, but by the consumers whom the data most directly impacts?
Making the Stream Possible
This Stream is only possible because of a generous gift from Bob and Cathy O’Rear, the involvement of the Gates Foundation, and UT Austin’s College of Natural Science, which is dedicated to providing the necessary research equipment, supplies, teaching assistants, mentors and student fellowships for this Stream.
In an effort to develop simple techniques for measuring caffeine in beverages, students in Dr. Jeff Barrick’s lab have engineered E. coli strains to feed off it.
Caffeine is often toxic to bacterial species. However, one P. putida variant contains a multi-enzyme pathway that can degrade caffeine into xanthine and formaldehyde. Xanthine in turn is an intermediate in guanine synthesis – which is necessary for growth. By introducing this P. putida gene set into an E. coli strain incapable of making guanine, new E. coli strains were engineered to be dependent on caffeine for growth.
Their results were published in ACS and should be simple enough to use in high schools to measure caffeine concentrations.
BEVERLY, MA (March 14, 2013)—Enzymatics, Inc., (www.enzymatics.com) announced that, in collaboration with scientists from UT Austin (including Dr. Andrew Ellington) it has developed a portfolio of Room Temperature Stable Library Construction Kits for the Illumina sequencing platform and is developing kits for the Ion Torrent platform. Enzymatics has filed patents on the proprietary room temperature stable library technology that has been shown to exceed performance of existing liquid-format library preparation kits by reducing reagent pipetting by 30%, simplifying library construction workflows and increasing application success rates. The kits can be stored at ambient temperatures, obviating the cold chain and dramatically reducing storage, logistics and validation costs.
Enzymatics’ new Room Temperature Stable Library Construction Kits feature master-mixed, lyophilized reagent mixes that are precisely aliquoted and QC tested, reducing pipetting and increasing experimental reproducibility. Lyophilization enables the kits to be stored at ambient temperatures, eliminating the need for dry ice shipping, freezer storage and lab bench ice buckets.
A typical library construction kit must be maintained at -20°C and ships in a large container with 20 pounds of dry-ice. This cold-chain requirement is wasteful and increases the risk associated with the product. Our Room Temperature Stable Library Construction Kits ship worldwide in an ordinary box and sit on the shelf until needed. Enzymatics is thrilled to be able to say that we’ve built an environmentally-friendly product that improves the quality and efficiency of the science it’s there to perform.Nowwe’re looking for great commercial partners to help us revolutionize the market, so please contact us to learn more!
-Enzymatics CEO Jon DiVincenzo
Enzymatics’ Room Temperature Stable Library Construction Kits include dried-down master mixes to perform the end-repair through ligation steps in DNA library construction. The products will be configured to support either the Illumina or Ion Torrent sequencing platforms, are manufactured in the USA under an ISO 13485:2003 Quality System, and are validated for performance using DNA sequencing.
The Georgiou, Marcotte, and Ellington labs have recently been featured in both PNAS and Nature Biotechnology.
In January, they published a new technique for retaining the heavy- and light-chain antibody endogenous pairs that are usually lost in high-throughput analyses after the bulk B-cell lysis stage. The full article can be seen here.
Then again in February, they published a new technique for determining the composition of the polyclonal serum response post-immunization. This should prove highly useful in measuring anti-body responses to vaccination as well as contribute to a deeper understanding of the entire (and complex) immune response. The full article can be seen here.
Once again, Dr. Marcotte’s work on the human proteome via model organisms was featured in the news. As did The New York Times previously, the Austin American-Statesman discussed the novelty of Dr. Marcotte’s research, which suggests that genes evolve in the same way that species do. He has found conserved genes between yeast and humans. In humans, the genes control angiogenesis (the formation of new blood vessels) and yet yeast do not have blood. The article marks his work as a credit to pure science and revolutionary in its development of new computational methods.
“Edward is a visionary and world leader when it comes to computational data integration, synthesizing biological knowledge by combining diverse strands of information … into association networks that provide fundamental insights into the functional organization and mechanistic basis of important biological processes.” Dr. Andrew Emili of the University of Toronto
You can read the Statesman article here or read more about Edward’s research here.
ABC News interviewed Dr. Sawyer on her most recent study with Dr. Matthew Porteus of Stanford. The two teams are investigating the mutation of both receptors key to HIV invasion and how such genetic modification can be used to create HIV-resistant T cells. This would be a novel therapy compared to the more prevalent anti-retroviral cocktail currently used against HIV. Their results were recently published in the January issue of the journal Molecular Therapy.
Researchers at The University of Texas at Austin have developed a menu of 61 new strains of genetically engineered bacteria that may improve the efficacy of vaccines for diseases such as flu, pertussis, cholera and HPV.
The strains of E. coli, which were described in a paper published in the January issue of the journal PNAS, are part of a new class of biological “adjuvants” that is poised to transform vaccine design. Adjuvants are substances added to vaccines to boost the human immune response.
“For 70 years the only adjuvants being used were aluminum salts,” said Stephen Trent, associate professor of biology in the College of Natural Sciences. “They worked, but we didn’t fully understand why, and there were limitations. Then four years ago the first biological adjuvant was approved by the Food and Drug Administration. I think what we’re doing is a step forward from that. It’s going to allow us to design vaccines in a much more intentional way.”
Adjuvants were discovered in the early years of commercial vaccine production, when it was noticed that batches of vaccine that were accidentally contaminated often seemed to be more effective than those that were pure.
“They’re called the ‘dirty little secret’ of immunology,” said Trent. “If the vials were dirty, they elicited a better immune response.”
What researchers eventually realized was that they could produce a one-two punch by intentionally adding their own dirt (adjuvant) to the mix. The main ingredient of the vaccine, which was a killed or inactivated version of the bacteria or virus that the vaccine was meant to protect against, did what it was supposed to do. It “taught” the body’s immune system to recognize it and produce antibodies in response to it.
The adjuvant amplifies that response by triggering a more general alarm, which puts more agents of the immune system in circulation in the bloodstream, where they can then learn to recognize the key antigen. The result is an immune system more heavily armed to fight the virus or bacteria when it encounters it in the future.
For about 70 years the adjuvant of choice, in nearly every vaccine worldwide, was an aluminum salt. Then in 2009, the FDA approved a new vaccine for human papillomavirus (HPV). It included a new kind of adjuvant that’s a modified version of an endotoxin molecule.
These molecules, which can be dangerous, appear on the cell surface of a wide range of bacteria. As a result, humans have evolved over millions of years to detect and respond to them quickly. They trigger an immediate red alert.
“In some of its forms an endotoxin can kill you,” said Trent. “But the adjuvant, which is called MPL, is a very small, carefully modified piece of it, so it’s able to trigger the immune response without overdoing it.”
What Trent and his colleagues have done is expand on that basic premise. Rather than just work with an inert piece of endotoxin, they’ve engineered E. colibacteria to express the endotoxin in many configurations on the cell surface.
“These 61 E. coli strains each have a different profile on their surface,” said Brittany Needham, a doctoral student in Trent’s lab and the first author on the paper. “In every case the surface structure of the endotoxin is safe, but it will interact with the immune system in a range of ways. Suddenly we have a huge potential menu of adjuvants to test out with different kinds of vaccines.”
One form might work better with cholera vaccine, another with pertussis (whooping cough) and another with a future HIV vaccine. Trent, Needham and their colleagues should be able to fine-tune the adjuvants with increasing precision as more E. coli strains are engineered and tested, and as their understanding of how they interact with the immune system deepens.
“I think we’re at the dawn of a new age of vaccine design,” said Trent. “For a long time vaccinology was really a trial-and-error field. It was a black box. We knew certain things worked. We knew certain vaccines had certain side effects. But we didn’t entirely know why. Now that’s changing.”
Trent said that an additional advantage of their system is that the E. coli can be engineered to express key viral and bacterial antigens along with the endotoxin. A single cell could deliver both parts of the one-two punch, or even a one-two-three punch, if antigens from multiple diseases were expressed in a single E. coli.
“It makes possible a vaccine that provides protection from multiple pathogens at the same time,” said Trent.
Trent and his colleagues are working on a second round of designer E. coli. They have also filed a provisional patent on their system and are working with the university to find a corporate partner to pay for clinical trials.
“This is ready to go,” said Trent. “I can’t predict whether it will actually make it to the market. But it’s very similar to the adjuvant that has already been approved, and my instinct is that if a company will undertake to do the trials, it will get approved. A company could call us tomorrow, we could send them a strain, and they could start working.”
Although his goal is to someday help destroy HIV and other viruses and retroviruses that form persistent, lifelong infections, biologist Chris Sullivan can’t help but admire the strategies that many of these viruses have evolved to evade our defenses.
“It’s brilliant,” says Sullivan, associate professor of molecular genetics and microbiology. “Take Herpes simplex virus 1, for instance, which is one of the masters. It goes in and infects very long-lived neurons, and then stays dormant, or latent, in that primary reservoir. It just hides out there, invisible to our adaptive immune system, waiting for the right time to attack.”
When it does attack, HSV-1 hedges its bets. It sends out viral particles that only go lytic—start replicating rapidly, destroying cells—when they’re at the surface of our skin, far away from the primary reservoir. The reservoir, meanwhile, stays hidden.
So even when we win the battle against the lytic cells, which manifest as cold sores, the war isn’t over. The latent virus remains in its hideout, running silent, waiting for the next opportunity to attack.
That’s where we stand now, in our wars against these viruses. It’s why in times of stress and illness the cold sores come back, for the roughly 60 percent of Americans infected by HSV-1. It’s why HIV can be managed but not eradicated. It’s why Kaposi’s sarcoma-associated herpes virus (KSHV), which is the virus that Sullivan has been studying most closely, can lay low for decades only to appear at the worst possible time, in the form of nasty tumors, when your immune system is compromised by AIDS or chemotherapy.
To win the war against these viruses in a more decisive fashion, something has to change. Our immune system has to be able to see and recognize these reservoirs of latent virus. Then all the squadrons of white blood cells that have become so good at fighting the viruses in their lytic form should be able to finish the job.
With the help of a $500,000 grant from the Burroughs Wellcome Fund, Sullivan is working to understand how latent viruses hide from our adaptive immune response, and whether there are any vulnerabilities that might be exploited to make them visible, so that we can kill them all.
“It’s the Holy Grail,” says Sullivan. “We call it ‘purging the latent reservoir.’”
To understand Sullivan’s strategy for finding the Grail, which revolves around small “suicide elements” in the viral genome, it helps to begin with the mechanism these viruses use to hide from our immune systems.
Our adaptive immune system has evolved to see and respond to viruses when they’re dangerous, which is when a lot of their genes are turned on and cranking out proteins.
In their latent state, however, most of their genes are turned off. The genes are still there, of course, but they’re hidden from the machinery in the host cell that makes proteins. The few proteins that are made only enable the virus to replicate and subsist. They don’t do any damage to the host cell, and so don’t trip any alarms.
When KSHV is lytic, for instance, more than 75 genes are turned on. These genes can generate thousands of virus particles in a single cell. During latency, by contrast, only three or four genes are turned on.
For a long time the virology community assumed that that was the end of the story. Very few genes turned on, very few proteins. Recently, however, scientists have discovered that the latency state isn’t quite so stable as was thought. A lot of the genes that are supposed to be turned off are “leaking.” Occasionally their blueprints become visible to the rest of the cell. If that leads to protein expression, as it typically would, that could mean trouble for the virus.
“It’s like a cliff,” says Sullivan. “You don’t sort of fall of a cliff. You either fall or you don’t. If you are a virus and you accidentally make proteins that haven’t evolved to be camouflaged, you alert the immune response, and you get cleared.”
The evidence of these leaks forced virologists to look again at the model. One possibility was that sufficiently few errant proteins were being made that the immune system remained clueless.
What Sullivan has begun to document is a considerably more elegant possibility. The viruses seem to have evolved a back-up plan. They have a way to take care of the leaks, and short circuit the process.
“We call them ‘suicide elements,’” he says.
Suicide elements, which Sullivan and his colleagues have found in KSHV, are small regions on viral mRNAs that are sensitive to whether the virus is in its lytic or latent state. If latent, then the suicide elements shut down the leaks, preventing the production of proteins.
If, however, the virus is lytic, these suicide elements actually flip their function. They help ramp up protein production, which makes the virus all the more nasty when it’s time for it to be nasty.
“We haven’t proven that these elements are necessary to keeping the virus hidden during latency,” says Sullivan. “But what we know for sure is that the viruses have them, and they are capable of cranking down expression. And the only thing that makes sense to me is that somehow this helps with latency, otherwise you are going to slow up your own replication cycle for no good reason.”
Sullivan believes that if he’s right about the purpose of these suicide elements, they could prove the key to a therapy that would purge the latent reservoir.
“What happens in my hypothetical world,” he says, “is you have a drug that disables the suicide elements. So now these protein leaks from the virus aren’t hidden from the immune response any more, and our own immune system can clear the infection.”
So far Sullivan has documented the suicide elements in KSHV and one retrovirus. He believes that they are likely to exist, at a minimum, in the seven other known strains of herpes, and very possibly in HIV. Which means that a treatment for KSHV, of the sort that Sullivan envisions, might be adaptable to those viruses as well. So no more cold sores, but also, more importantly, a true cure for HIV.