ASU Polytechnic team wins wildlife Quiz Bowl


February 10, 2016

Buoyed by the thrill of participating in the 2013 national wildlife trivia Quiz Bowl, held in conjunction with the annual conference of The Wildlife Society, four ASU Polytechnic natural resource management students returned from that contest with a big idea.

What if a similar Quiz Bowl event could be offered at the regional level? ASU Polytechnic students are regional wildlife Quiz Bowl champs ASU Polytechnic team members (from left) James Ecton, Jacquie Evans, Sky Arnett-Romero and Jessica Latzko accepted the Quiz Bowl "traveling plaque" from Quentin Hays (far right), president of the New Mexico Wildlife Society. The award was presented in front of the 400 professionals and students who gathered for the joint annual meeting of the Arizona – New Mexico Chapters of the American Fisheries Society and The Wildlife Society. Download Full Image

“Held closer to home, it would give more students the chance to compete — and also be a hook to get students engaged with the professional community of researchers and practitioners in wildlife biology and habitat management,” said Heather Bateman, associate professor of applied biological sciences in the College of Letters and Sciences, who took up the cause and chaired the committee that launched the first regional Quiz Bowl competition in 2014.

Three years later, the contest has become quite popular with student chapters, which now have the chance to compete at the Joint Annual Meeting of the Arizona and New Mexico Chapters of the American Fisheries Society and The Wildlife Society.

Last week, when the societies gathered for their 49th joint annual meeting at the Little America Hotel in Flagstaff, Arizona, from Feb. 4-6, the Quiz Bowl competition drew nine teams: one from Northern Arizona University, one from Prescott College, two from New Mexico State University, two from Eastern New Mexico University, two from Bosque School and one from ASU.

Coming full circle, this year’s Quiz Bowl committee was chaired by a member of that first ASU team to compete at nationals, alumnus Brett Montgomery, now with the Utah Division of Wildlife Resources. 

ASU’s 2016 team of James Ecton, Jacquie Evans, Sky Arnett-Romero, and Jessica Latzko — all applied biological sciences majors from ASU’s natural resource ecology program in the College of Letters and Sciences at the Polytechnic campus — finished strong in every round, earning a place in the finals.

“It was a repeat of last year’s final match-up — we once again faced a team from New Mexico State,” said Latzko, president of the Wildlife and Restoration Student Association at the Polytechnic campus and a veteran of the 2015 ASU team which took home second place.

But this year the Sun Devil team prevailed.

“None of us thought we would do as well as we did; we were just hoping that we didn't get crushed,” said teammate Jacquie Evans, who is president of ASU’s student chapter of the Society for Range Management. “We realized that we may have a chance when we watched the first round and knew almost all of the answers between the four of us. 

“The win was truly a team effort,” Evans continued. “We each had our own areas of expertise: Sky covered the reptile questions; Jessica got the fisheries questions; I knew about birds and plants; and James provided support, random trivia, and a really important quick reflex.” 

The finals drew a standing-room-only audience of more than 150 people — all on tenterhooks — for a contest in which teams not only need to know the right answer but must be quick to buzz in.  

“I was on the edge of my seat, trying to hide my emotions and had my hand over my mouth so I wouldn’t accidently ‘mouth’ any answers,” said ASU’s faculty coach, Stan Cunningham, wildlife biology lecturer on the Science and Mathematics Faculty in the College of Letters and Sciences. “It was tight but it was a good win.”

Cunningham, who also chaired one of the wildlife panels at the meeting, said he received numerous compliments on the caliber of ASU’s students, their overall turnout at the meeting (17 students attended), and the ASU Polytechnic program.

“This type of recognition does a lot for our program and, more importantly, our students’ ability to compete for professional positions,” he said. “We have an excellent natural resources ecology curriculum at the Polytechnic campus. Our students have done well with it, and it's nice to see it gaining visibility.”

In addition to competing, students participated in the full range of conference events, including fisheries and wildlife sessions focused on new research, technology, best practices, and the impact of climate change; poster sessions; as well as a timely plenary session, “Who Will Manage the Future of Our Public Lands,” which brought together elected officials, policymakers, conservation activists, and USDA Forest Service practitioners.

“I was glad so many of our students were able to be at these meetings and attend a plenary devoted to a current political and public policy debate that will directly impact their careers and our wildlife,” said Cummingham. 

Latzko said she greatly appreciates the friendships forged in competition. "Attending the conference the last three years, I've gotten to know some of the other students from different schools that we competed against. I think that’s what makes it fun! It's a healthy competition among friends — one that I think we'll look back on fondly when we're in our professional careers and likely still coming to the conference."

Maureen Roen

Director, Creative Services, College of Integrative Sciences and Arts

602-496-1454

Chemical cages: New technique advances synthetic biology


February 10, 2016

Living systems rely on a dizzying variety of chemical reactions essential to development and survival. Most of these involve a specialized class of protein molecules — the enzymes.

In a new study, Hao Yan, director of the Center for Molecular Design and Biomimetics at Arizona State University’s Biodesign Institute, presents a clever means of localizing and confining enzymes and the substrate molecules they bind with, speeding up reactions essential for life processes. Enzyme nanocages illustration Download Full Image

The research, which appears in the current issue of the journal Nature Communications, could have far-reaching applications in fields ranging from improving industrial efficiencies to pioneering new medical diagnostics, guiding targeted drug delivery and producing smart materials. The work also promises to shed new light on particulars of cellular organization and metabolism.

The technique involves the design of specialized, nanometer-scale cages, which self-assemble from lengths of DNA. The cages hold enzyme and substrate in close proximity, considerably accelerating the rate of reactions and shielding them from degradation. 

“We have been designing programmable DNA nanostructures with increasing complexity for many years, and it is now time to ask what can we do with these structures,” said Yan, who is also a professor in ASU’s School of Molecular Sciences in the College of Liberal Arts and Sciences. “There are numerous other applications from this emerging technology. Through our interdisciplinary collaborative effort, we here describe the use of designer DNA nanocages to compartmentalize enzymatic reactions in a confined environment. Drawing inspiration from nature, we have uncovered interesting properties, some unexpected.”

Zhao Zhao, a researcher in the Center for Molecular Design and Biomimetics, was the lead author of the paper, which was co-authored with researchers from ASU's Department of Chemistry, Rutgers and the University of Michigan.

Enzyme world

As chemical activators for virtually every reaction in the body, enzymes are key participants in the normal activity of cells, tissues, fluids and organs. Hundreds of thousands of metabolic enzymes are present in the human body, involved in diverse activities including DNA copying and repair and the transformation of glucose into useable energy. Elsewhere, some 22 digestive enzymes break down carbohydrates (amylases), fats (lipases ) and sugars (disaccharides), while so-called protease enzymes digest proteins.

Enzymes tend to be highly specific, not only in the useful functions they perform, but the precise substrates with which they will work. Substrate molecules of exactly the right size and shape bind with their appropriate enzymes as the correct key fits into the ridges and grooves of a lock.

Substrates latch onto enzyme molecules at a particular region known as the active site. Once enzyme and substrate have combined, a chemical product is formed and then released, returning the enzyme to its original configuration where it is ready to operate on a new molecule of substrate.

In order for such reactions to take place in an efficient manner, nature has devised methods of compartmentalization, forming natural reactor sites where enzyme-substrate reactions unfold. The cell itself is such a compartment, as are various membrane-bound organelles found in eukaryotes (cells containing a nucleus), including mitochondria, lysosomes and peroxisomes.

Compartmentalization of reactants helps to overcome a variety of challenges, bringing binding chemicals into cozy proximity, isolating enzyme-substrate complexes from competing reaction chemicals, improving the yield of product molecules produced and reducing the toxicity various intermediary chemicals can sometimes cause.

In order to induce or catalyze chemical reactions for a variety of purposes, synthetic biologists have copied a page from Nature’s recipe book, designing artificial compartments fabricated from proteins, lipids or the nucleic acids found in DNA (as in the current study).

Close encounters

Yan and his colleagues designed their synthetic reactors to house enzymes and their substrates, allowing chemical conversions to take place in a controlled environment. Each minute structure, measuring just 54 nanometers across, is something like a Faberge egg whose separate halves fit together to encapsulate their chemical contents. (A nanometer is one-billionth of a meter or roughly 80,000 times smaller than the width of a human hair.)

Using the base pairing properties of DNA’s four nucleotides — labeled A, T, C and G — allows nanoscale architects like Yan to construct myriad forms in two- and three-dimensions. In the new study, DNA nanocages were used to encapsulate metabolic enzymes with high assembly yield and fine-tuned control over reactants and products.

The construction of the nanocages takes place in two steps. First, individual enzymes are attached into open half-cage structures. Then, the half-cages are fitted together into a full, closed nanocage. To create the half-cages, a technique known as DNA origami is used. Lengths of viral DNA are prepared to self-assemble into a honeycomb lattice, with A nucleotides pairing with C and T with G.  

The open-sided half-cages of the DNA nanocages allow the access of large protein molecules into the nanocage’s internal cavity. The two half-cages are fitted together with the aid of short bridge DNA strands that bind with complementary DNA sequences extending from the edges of either half-cage (see animation below). The small gaps on each of the top and bottom surfaces of the DNA nanocage allow the diffusion of small molecules across the DNA walls.

Two-step nanocage: Individual enzymes (orange and green) are first attached to half-cage structures. Half-cages are then assembled into full cages, where reactants are brought into close proximity. Animation by Jason Drees for the Biodesign Institute at ASU

Probing the nanoscale

To examine the resulting structures Transmission Electron Microscopy was used, along with gel electrophoresis and single-molecule fluorescence experiments, which demonstrated that close to 100 percent of the DNA segments properly formed half-cage structures and more than 90 percent formed full cages. 

The study examined six different enzymes, ranging in size from the smallest, which measured ~44kD (kilodaltons) to the largest, ~ 450 kD. All six enzymes were successfully encapsulated in nanocages, though the yields varied according to enzyme size. The largest enzyme examined, known as β-galactosidase, showed the lowest yield of 64 percent.

Next, the activity of enzyme-substrate pairs was evaluated. In addition to bringing the enzyme-substrate pair into closer binding proximity, encapsulation in the nanocage is also believed to facilitate activity through the unique electrical charge density conditions within the nanocage.

Subsequent experiments demonstrated that most of the effect on enzyme-substrate activity in nanocages is due to the unique charge environment within nanocages, rather than enzyme-substrate proximity. The authors suggest that encapsulated enzymes exhibit higher activity within densely packed DNA cages as a result of the highly ordered, hydrogen-bonded water environment surrounding them.

An evaluation of enzyme activity showed a 4- to 10-fold increase for enzymes encapsulated in nanocages, compared with the activity of free enzymes. Enzyme turnover rate — defined as the maximum number of chemical conversions of substrate molecules per second — was inversely correlated with the size of encapsulated enzymes, with the smallest enzyme yielding the highest turnover.

Future cages

The DNA cages demonstrated their resiliency during the experiments, retaining their structural form throughout the enzymatic reactions. They also protected encapsulated enzymes from deactivation due to digestive chemicals, while permitting the uninterrupted diffusion of small-molecule substrates and reaction products through the nanopores of the DNA cage.

Encapsulation in nanocages was shown to increase the fraction of active enzyme molecules and their individual turnover numbers. The method thus provides a new molecular tool to modify the local environment surrounding enzymes and their substrates, opening the door to new applications in smart materials and biomedical applications. Among the latter are futuristic, programmable cages that could be used as nanoscale delivery mechanisms for a wide range of therapeutic agents.

 

Richard Harth

Science writer, Biodesign Institute at ASU

480-727-0378