BEYOND ROCKET SCIENCE: SEEKING SOLUTIONS TO COMPLEX, GLOBAL CHALLENGES THROUGH LIFE SCIENCE RESEARCH

Joe Colletti is the senior associate dean of the College of Agriculture and Life Sciences and associate director of the Iowa Agriculture and Home Economics Experiment Station.

By Joe Colletti

There’s no doubt we face complex, global challenges in food, environment, bioenergy and human health and nutrition. Solutions will rely on new ways of thinking, new technology and analytics, new partnerships and new transdisciplinary teams.

It’s not rocket science, folks. It’s more complex than that. Solutions must be economically viable, environmentally sound, socially acceptable and resilient. They must make sense for the time and for the place.

For anything new to have impact and endure, it needs to be built upon a strong foundation. For the College of Agriculture and Life Sciences, that foundation is life sciences.

We have more than 150 years of success focused on crops, livestock, food,  environment, nutrition and socioeconomics related to agriculture. What you may not know is that life sciences—including biology, biochemistry, ecology and genetics—have been and continue to be key to our success in science. It enriches our research portfolio, which today is both broad and deep, spanning so-called “basic science” to “applied science.”

In 2009, a National Research Council report, “A New Biology for the 21^st Century,” outlined an approach to addressing major societal challenges of food, environment, energy and health. A key to this approach was the integration of knowledge across the life sciences, mathematics and engineering. The report stressed that the “New Biology” would build upon, not replace, “fundamental and curiosity-driven” research.

A few examples of our “beyond rocket science” work shows how we are tackling global challenges through life sciences:

Research on zebrafish using advanced genetics called TALENS is poised to enhance food production and address human health concerns (see page 22).

Breakthroughs in understanding plant-parasitic interactions at the genetic level may lead to new ways to thwart a $1 billion annual loss nationally in soybean production (see page 25).

Double haploid technology allows corn breeders to more quickly produce corn inbred lines that better resist pests, respond better under extreme climatic conditions and have enhanced nutritional value.

New understanding of components involved in plant cell wall development is central to biorefineries producing the next generation of fuels and renewable products.

Scientists are learning more about a naturally occurring enzyme that converts glucose in plants directly into isobutene, a valuable, green fuel additive and  industrial chemical.

A blend of molecular virology, computational modeling, protein structure and function and veterinary pathology drives new vaccine strategies to combat a horse lentivirus and may shed light on a close cousin of the disease in humans, HIV.

Capturing genetic and biochemical blueprints of medicinal plants may lead to advances in drug discovery and development for improved human health.

Using biology and enzymology to understand how plants and animals repair DNA damage can benefit human health, including new options for cancer treatment.

Ecology and evolutionary biology using a unique eye model in mollusks could advance therapies for human diseases causing vision loss.

You get the idea. The college’s fundamental work in life sciences is the basis for solving complex, global challenges. It’s a key part of how we are engaged in learning, discovery, translation and service for the benefit of Iowa and the world.

It’s not rocket science, folks! It’s more complex, and more meaningful!

RESTORATION PRODUCES RIPPLE EFFECT AT CLEAR LAKE

Professor John Downing leads long-term regeneration research at Clear Lake in north central Iowa. Downing says the lake’s recovery has been “phenomenal,” with much improved water clarity and lake function.

By Ed Adcock

Clear Lake is getting closer to living up to its name after a restoration plan created by limnologist John Downing and his Iowa State team.

It began with a two-year study he compares with a medical diagnosis.

“We basically took that lake and the watershed apart and determined what wasn’t working right and then helped the community find a way to put it back in better shape,” says Downing, a professor of ecology, evolution and organismal biology and agricultural and biosystems engineering.

He credits the City of Clear Lake, Cerro Gordo County, the Iowa Department of Natural Resources and dozens of citizen volunteers with making the restoration successful.

“It’s a community that really threw a lot of energy into it, worked hard and did many special things to increase the chances of success,” Downing says.

The lake became a classroom for many of Downing’s students.

One became the coordinator of the Clear Lake Enhancement and Restoration (CLEAR) Project. David Knoll (’99 animal ecology) worked for Downing as an undergraduate. He collected samples at the lake, analyzed them and performed GIS work during the diagnostic and feasibility study preceding the restoration.

The work convinced him to pursue a career in water resources. In 2001, he joined the Iowa Department of Agriculture and Land Stewardship as an environmental specialist with responsibility for the CLEAR Project.

Although much progress has been made, Knoll says, the community around Clear Lake is still working on implementing the recommendations of the feasibility study.

“The fact that this is a relatively small watershed (about 8,500 acres) makes it easier, but it takes a lot of maintenance work and requires consistent attention,” Knoll says.

The lake’s recovery has been “phenomenal,” much better than expected. “The water clarity is substantially improved, the function of the lake is much, much better,” Downing says.

One of the concerns when they started the restoration was heavy nutrient and sediment loading from agricultural and developed areas in the lake’s watershed. Row-crop agricultural land represents 51 percent of the land in the watershed, and about 80 percent of the lake shoreline is developed. This meant that a lot of improvements needed to be made in the land around the lake to cut down on nutrient run-off.

Phosphorus coming into the lake was the main problem and is now down to a quarter of pre-restoration levels. Likewise,  suspended sediment in the lake has been reduced by more than 80%.

The Department of Natural Resources is managing the carp, which stir up the bottom when nutrients are rich and outcompete other fish. Restoring surrounding wetlands and Ventura Marsh was another factor, and dredging the small lake west of Clear Lake helped protect it from sediment and nutrient deposition.

Downing said Clear Lake became a model for about a dozen lake restoration projects. “We, as a state, learned a lot—how to do the studies and how to do the restoration—from the work at Clear Lake,” Downing says. “We also learned a lot about the value of water, which was very important.”

He collaborated with Iowa State economists Catherine Kling and Joseph Herriges from 1999-2005 on surveys of Iowans seeking to understand the return of investments in Clear Lake and other waterways. Water clarity was a prime factor in how Iowans decide to visit lakes and clean lakes were called extremely valuable to the 80 percent of Iowans who visit lakes each year.

The Lakes Valuation project found that 12 of Iowa’s 132 lakes generate spending of more than $40 million annually. Overall, Iowans spent more than $9 million on average per lake.

Lake visitation increased 33 percent from 2002–2009, the years in which lake usage surveys were conducted. Of the four lakes with the largest increase in usage, three had undergone major restoration efforts.

“I grew up around water and studied to be a limnologist,” says Downing, an Iowa native. “It’s a great thrill for me to give something back to society.”

NATURE’S PROMISCUOUS REVISERS: TRANSPOSABLE ELEMENTS

Thomas Peterson uses color in the cob and seed coat to phenotypically track the genetic doings of a transposon that controls red pigment in maize. The gene for red kernel color also produces a natural insecticide.

By Meg Gordon

Thomas Peterson, a leader in transposon biology, does fundamental research that pulls him deep into the swoops, swishes and switches of the corn plant genome.

Sixty-four years ago transposable elements were discovered in maize. Thirty years ago a Nobel Prize was awarded to the scientist who found them. Three years ago, the maize genome map appeared in the pages of the journal Science, confirming that eighty-five percent of the maize genetic hard drive involves transposable elements, “transposons”.

DNA with wanderlust

Transposons are pieces of genetic material that freely and unpredictably caper around the genome. They can contain one gene or many genes, and regulatory elements—the so called junk DNA that scientists now know is anything but junk.

“This is the raw material for evolution,” says Thomas Peterson, Pioneer Chair in Maize Molecular Genetics and professor of genetics, development and cell biology.

Peterson was a graduate student when Barbara McClintock received her Nobel Prize in 1983. “At the time, it was so remarkable that this little piece of DNA could move around the chromosome when common wisdom stated that genes stayed in place,” he says.

In the intervening years, transposable elements have been found within the genomes of most organisms—from Arabidopsis to Homosapien to Xanthomonas.

Mother Nature’s genetic engineering

Plant breeding depends on natural variability recombined to create favorable types of plants. New molecular techniques for engineering DNA such as transcription activator-like effector nucleases (TALENs), that target specific sequences and cut the DNA, are making it possible to place genetic modifications where they are most likely to succeed.

But dramatic contributions to natural variability come from transposons. They are Mother Nature’s way of introducing variability—genomic complexity—genetically engineering on a large scale.

Peterson describes their behavior as somewhat like a computer in which the select, insert and delete functions sporadically activate to delete, move, copy and paste chunks of text all over a document. The resulting copy can accumulate duplicate sentences and paragraphs. At first these additions might seem irrelevant or disruptive, but over time some of the duplicate text morphs into prize-winning prose.

”People would like to control transposons but they have a reputation for being wild—if the TALENs approach is a smart bomb then the transposon system is an atom bomb,” says Peterson. “No one wants to unleash the transposon system into their carefully controlled genetic material but, the potential benefit transposons offer is that they open up so many kinds of large changes that are not feasible using any other method.”

Where the fine-tuning begins

About 50 percent of genes present in the maize genus are duplicates. Many sit side by side; others are peppered throughout the genome. Peterson studies relative activity rates and the mechanisms transposons employ to copy, slot in, slip out, or invert whole sections of DNA in maize. A transposon containing the maize gene for red kernel color allows Peterson to track its activity phenotypically (visually) through cob and kernel.

Transposon capering is enabled by an enzyme called transposase that frees the element with what Peterson believes is a clean cut to the DNA. Whether the transposon reinserts as a simple relocation or a large chromosomal rearrangement appears to be determined by the number of surrounding transposons and which end of a given transposon is cut and therefore activated.

Furthermore, environmental stresses such as heat and cold appear to encourage transposon-enabled gene duplication. Peterson’s current work proposes a new mechanism whereby endpoints of neighboring transposons contribute the scaffolding for rapid reprinting of side-by-side copies of a gene or its removal.

“Once you make two copies of a gene, one can change or adapt, developing a new function such as coding for a protein that recognizes a specific pathogen and confers disease resistance,” says Peterson. The other copy preserves the original function. Alternatively, deleting or disrupting a gene that has a negative effect on the organism can confer new advantage.

SCIENTISTS DISCOVER HOW NEMATODES ATTACK

Plant pathologists Thomas Baum (right) and Tarek Hewezi, developed a new approach to studying microRNAs, powerful regulators of gene activity, to better understand how nematodes change gene activities in plants.

By Ed Adcock

Soybean cyst nematodes have been found in fields in every Iowa county. The plant-parasitic microscopic roundworms cause an estimated loss of $1 billion dollars annually to U.S. soybean producers.

The pests get their name from the shell-like cysts, each containing hundreds of eggs, that persist in the soil until a susceptible plant is within reach.

Iowa State plant pathologists have made a breakthrough in the understanding of how cyst nematodes attack plants at the genetic level, providing the possibility of giving soybeans a way to fend off the pest.

Rosetta Green, an agricultural biotechnology company, licensed the technology last summer with the goal of developing nematode-resistant plants. The company’s agreement with the Iowa State University Research Foundation is based on research deciphering how cyst nematodes infect plants.

The research is led by plant pathologists Thomas Baum, professor and chair of plant pathology and microbiology, and Tarek Hewezi, an associate scientist.

Cyst nematodes are damaging pathogens of plants worldwide. The pests feed on plant fluids by attaching to the host plant’s roots.

Scientists previously discovered that nematodes hijack plant development by injecting cells with chemical signals that cause hundreds of cells to fuse into a feeding site.

Baum and Hewezi sought to understand how the nematode changes the plant’s gene activities for the purpose of turning it into a food source. The researchers’ new approach was studying microRNAs, which are powerful regulators of gene activity.

“These worms learned to communicate with these plants’ cells in a very subtle way,” Baum says.

The researchers used the plant Arabidopsis as the model because it has a relatively small genome, and studied how sugar beet cyst nematodes attacked it. They discovered a relationship one microRNA had with two genes that are associated with growth regulation.

Hewezi and Baum used molecular biology techniques to generate experimental plants in which the microRNA levels are elevated in roots attacked by cyst nematodes and they found these plants were not as susceptible to the nematode. And when they adapted the target genes to be unaffected by the microRNA, they found these plants were less susceptible as well.

“Our results indicate that the microRNA, together with its target genes, has a real function in the interaction and it’s required to a certain degree for the pest to attach to plant roots,” Baum says.

The Iowa Soybean Association funded research that led to the discovery, and the National Science Foundation recently funded a three-year study for $607,875 to continue work with Arabidopsis micro-RNAs during cyst nematode parasitism.