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New study sheds light on origins of life on Earth through molecular function

Published May 17, 2017
DNA
  • Debate exists over how life began on Earth, but a new study provides evidence for a “metabolism-first” model.
  • Scientists at the University of Illinois mined the Gene Ontology database to trace the origins and evolution of molecular functions through time.
  • The study shows metabolism and binding arose first, followed by the functional activities of larger macromolecules and cellular machinery.


URBANA, Ill. – In the primordial soup that was early Earth, life started small. Elements joined to form the simple carbon-based molecules that were the precursors of everything that was to come. But there is debate about the next step.

One popular hypothesis suggests that ribonucleic acid (RNA) molecules, which contain the genetic blueprints for proteins and can perform simple chemical reactions, kick-started life. Some scientists refute this idea, however, saying RNA is too large and complex a molecule to have started it all. That group says simpler molecules had to evolve the ability to perform metabolic functions before macromolecules such as RNA could be built. This idea is appropriately named “metabolism-first,” and new evidence out of the University of Illinois backs it up.

“All living organisms have a metabolism, a set of life-sustaining chemical transformations that provide the energy and matter needed for the functions of the cell. These metabolic transformations are assumed to have occurred very early in life, in primitive Earth. Organisms probably replaced chemical reactions already going on in the planet and internalized them into cells through development of enzymatic activities,” says Gustavo Caetano-Anollés, bioinformatician and professor in the Department of Crop Sciences at U of I.

Caetano-Anollés and Ibrahim Koç, a visiting scholar in the department, found evidence for the “metabolism-first” hypothesis by studying the evolution of molecular functions in organisms representing all realms of life. For 249 organisms, their genomes – or complete set of genes – were available in a searchable database. What’s unique about this particular resource, known as the Gene Ontology (GO) database, is the fact that for each gene product – a protein or RNA molecule – a set of terms describing its function goes with it.

“You can take an entire genome that represents an organism, like the human genome, and visualize it through the collection of functionalities of its genes. The study of these ‘functionomes’ tells us what genes do, instead of focusing on their names and locations. For example, we can find out what kinds of catalytic, recognition, or binding activities a gene product has, which is much more intuitive,” Caetano-Anollés notes. “The best way to understand an organism is through its functions.”

According to Caetano-Anollés, the number of times a function appears in a genome provides historical information. So the team took the GO terms describing all of the molecular functions in each organism and counted them up. The idea was that an ancient function, such as the catalytic activity of metabolism, is likely shared by all organisms and will be found in large numbers. On the other hand, more recent functions are found in lower numbers and in smaller subsets of organisms.

The team used the information and advanced computational methods to construct a tree that traced the most likely evolutionary path of molecular functions through time. At the base of the tree, close to its roots, were the most ancient functions. The most recent were close to the crown.

At the base of the tree, corresponding to the origin of life on Earth, were functions related to metabolism and binding. “It is logical that these two functions started very early because molecules first needed to generate energy through metabolism and had to interact with other molecules through binding,” Caetano-Anollés explains.

The next major advancements were functions that made the rise of macromolecules possible, which is when RNA might have entered the picture. Next came the machinery that integrated molecules into cells, followed by the rise of functions allowing communication between cells and their environments. “Finally, as you move toward the crown of the tree, you start seeing functions related to highly sophisticated processes involving things like muscle, skin, or the nervous system,” Caetano-Anolles says.

The research doesn’t just shed light on the past. Knowing the progression of these molecular functions through time can help predict where life on Earth is headed. “People think of evolution as looking backwards,” Caetano-Anollés says. “But we could use our chronologies and methodologies to ask what novel molecular functions will be generated in the future.”

The work has applications for bioengineering, an emerging field that uses biological information and computation to produce novel molecules. Engineered molecules could combat disease and improve the quality of everyday life, according to Caetano-Anollés. “The best way to reengineer biological molecules with novel and useful molecular functions is to learn principles from clues left behind in their past,” he says.

The article, “The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data,” is published in PLoS One.

Herbicide considerations for replanted corn

Published May 16, 2017
wet corn field

URBANA, Ill. – Following recent and excessive precipitation, many Illinois corn producers are now scrambling to replant before the final planting date on June 5. While there are many agronomic considerations associated with replanting, University of Illinois weed scientist Aaron Hager says farmers should keep weed control/herbicide issues in mind.

“Herbicide-resistance traits in the replanted hybrids should be taken into account,” says Hager, an associate professor in the Department of Crop Sciences at U of I. “For example, if you initially planted a glyphosate-resistant corn hybrid and have areas that need to be replanted, you can replant with a similar glyphosate-resistant hybrid or choose to replant with one that’s not glyphosate-resistant. If you take the second option, you will have to take special precautions to reduce drift with any postemergence glyphosate application, as these plants will be extremely sensitive to glyphosate.”

Hager says farmers should consider the interval between the last herbicide application and corn replanting. “For soil-applied corn herbicides, replanting can proceed whenever field conditions are feasible,” he says. “However, for some postemergence corn herbicides, there are intervals between application and replanting. If replanting a corn field previously treated with Spirit, for example, four weeks must elapse between the herbicide application and planting. For NorthStar, the interval is 14 days. For Permit or Yukon, you need to wait one month.”

While most soil-applied herbicides allow more than one application per season, a few, such as Acuron and Resicore, can be applied only once. In instances where small areas of a field will be replanted, Hager says some farmers may elect to simply replant without applying any additional residual herbicide. “However, if you decide to make a second application of a particular corn herbicide, keep in mind that many product labels indicate a maximum per-acre rate that can be applied during one growing season,” he notes.

If farmers need to control corn from the first planting, Hager recommends tillage as an effective first choice. Several herbicides can control existing corn plants if tillage isn’t an option, but Hager says careful attention must be given to what, if any, herbicide resistance trait(s) the existing corn plants contain.

“As you might imagine,” Hager says, “glyphosate is very effective for controlling existing stands of corn sensitive to glyphosate. Corn replanting can occur immediately after application, but control might be improved if at least 24 hours elapses between application and replanting. Glyphosate also would control sensitive weeds that might have emerged with the initial stand of corn. Be very cautious to avoid drift when spraying glyphosate, especially if spraying around wet holes.”

Other herbicides to control emerged corn include paraquat and glufosinate (only hybrids sensitive to glufosinate), although previous research with these herbicides has demonstrated that complete control is not always achieved. Performance of these products can be improved when applied in combination with atrazine or metribuzin. Paraquat and glufosinate would also control a broad spectrum of emerged weeds.

Corn hybrids resistant to glyphosate, glufosinate, or both can be controlled with Select Max prior to replanting field corn. According to label specifications, farmers should apply 6 fluid ounces per acre to control glyphosate-resistant field corn up to 12 inches tall.

“Applications should include NIS and AMS (do not use a COC or MSO in this particular use), and care must be taken to avoid in-field overlaps or excessive injury to the replanted corn might occur. Glyphosate can be tank-mixed with the Select Max to control emerged broadleaf weed species. Do not replant fields treated in this way sooner than six days after application or severe injury to the replanted corn can occur,” Hager says.

Product labels of ACCase-inhibitors including Poast, Poast Plus, Fusion, Fusilade, Select, and Assure II require an interval between application and rotation to or replanting with grass crops such as corn. These intervals range from 30 (Poast, Poast Plus, Select) to 60 (Fusion, Fusliade) to as many as 120 (Assure II) days, making these products unlikely choices for this particular use. Severe injury to replanted corn can occur if soil residues of ACCase-inhibiting herbicides are taken up by emerging corn plants.

For more information and handy reference tables, please visit the Bulletin.

News Source:

Aaron Hager, 217-333-4424

2017-18 Market prospects for corn and soybeans

Published May 15, 2017

URBANA, Ill. - In the May 10 World Agricultural Supply and Demand Estimates (WASDE) report, the USDA released the first projections for U.S. corn and soybean supply and demand in the 2017-18 marketing year. While the projections on crop production received quite a bit of the focus, the projections for marketing-year consumption levels provide essential information in forming expectations for corn and soybean prices in the 2017-18 marketing year, says University of Illinois agricultural economist Todd Hubbs.

The consumption projections for both crops reflect the potential market size under a scenario consisting of substantial supplies and lower prices. 

The U.S average corn yield is projected at 170.7 bushels per acre, and production is projected at a record 14.06 billion bushels. The U.S. average soybean yield is projected at 48 bushels per acre. Soybean production is projected at a record 4.255 billion bushels. “The currently projected corn yield maintains the previous projections from USDA presentations and does not reflect, as of yet, any of the potential issues associated with the cold and wet spring experienced by large portions of the Corn Belt,” Hubbs says. “Yield potential for both crops will unfold over the next few months and will be determined by weather conditions.

“Additionally, planted acreage levels are yet to be determined and still have a significant amount of uncertainty due to planting conditions. The USDA’s June Acreage report will provide more clarity as of June 30.”

In the corn market, corn use for ethanol is forecast at 5.5 billion bushels, 50 million bushels above the revised projection for the current year. The corn use for ethanol projection is a record consumption level for a marketing year and reflects the strong levels of domestic ethanol production thus far in the 2016-17 marketing year, Hubbs explains. “The importance of ethanol exports and continued growth in gas demand are key variables in meeting this projection. Corn exports are projected at 1.875 billion bushels, 350 million bushels lower than the revised projection of 2.25 billion bushels for the current marketing year. Export projections sit at levels between 1.8 to 2.0 billion bushels, which was common before the 2016-17 marketing year.

“Lower prices may help to stimulate exports, but the large crops of South American corn are expected to limit demand growth in export markets and generate significant competition for U.S. corn,” he adds.

Feed and residual use of corn is projected at 5.425 billion bushels, 75 million bushels lower than the 5.5 billion bushels projected for the current marketing year. Despite growth in livestock production, Hubbs says the projection represents a lower level of consumption and reflects the impact of distillers’ grains and ample supplies of other feed grains on corn use in feed. The feed and residual projection is below the peak consumption of 6.15 billion bushels in 2004-05 and 2005-06 when distillers’ grains supplies were still small. Consumption for all uses, including non-ethanol domestic processing, is projected at 14.30 billion bushels, 345 million bushels less than projected for the current marketing year. 

For the soybean market, the domestic crush is projected at 1.950 billion bushels, 25 million bushels above the projection for the current year, and constitutes a record projected crush level.  Exports are projected at 2.15 billion bushels, 100 million bushels above the projection for the current marketing year. The record level of soybean exports in the presence of a large world soybean crop reflects an expectation of a 5 percent increase in global soybean imports. “This growth in world demand for soybeans is dependent on continued demand growth in Asian markets,” Hubbs says. “Total consumption, including seed and residual use, is projected at 4.235 billion bushels, 142 million bushels above use during the current year. Projections reflect expectations of continued demand growth both domestically and in foreign markets.”

Ending stocks of U.S. corn for the 2017-18 marketing year are projected at 2.110 billion bushels, down 185 million bushels from current marketing-year ending stock projections. The reduction in ending stocks is directly related to the expectation of significantly lower production levels and reduced growth in corn consumption. Ending stocks of U.S. soybeans are projected at 480 million bushels, up 45 million bushels from current marketing-year ending stock projections.

“The increase in ending stocks is directly related to the expectation of significantly higher production levels,” Hubbs says.

The 2017-18 marketing-year average farm price of corn is projected in a range of $3.00 to $3.80. “Current bids for harvest delivery in much of Illinois are slightly above the middle of that range. If there are substantial planting delays and slow progress through mid-May, production and acreage concerns may increase and create a stronger price response,” Hubbs says. “The 2017-18 average price for soybeans is projected in a range of $8.30 to $10.30, with harvest bids in much of Illinois currently below the middle of the range. It is still too early for significant production concerns for soybeans. The ability for U.S. soybeans to expand exports next year will be essential in meeting the increase in soybean consumption and will merit close monitoring as we move into the next marketing year.”

News Source:

Todd Hubbs, 217-300-4688

Soybean sleuth and researcher to be keynote speaker

Published May 12, 2017
Dr. Hymowitz in the lab

URBANA, Ill. – The email addresses of most of the faculty and staff at the University of Illinois are the first initial and a portion of their last name. Not so for U of I Professor Emeritus Theodore Hymowitz. His email address speaks to his passion and lifelong pursuit: soyui.

Hymowitz will be a keynote speaker at the World Soybean Research Conference, Sept. 10-15 in Savannah, Georgia. How appropriate, as this year’s conference is celebrating 250 years of soybean in North America. Hymowitz hasn’t been studying the soybean that long, but he is as well, or even better, known as a soybean historian than a crop scientist. On an unfunded, freelance basis during his career, he traveled the world sleuthing the soybean and its roots.

In 1983, Hymowitz and his colleague J.R. Harlan published a paper attributing the introduction of the soybean to North America to Samuel Bowen in 1765. Later, Hymowitz pinpointed the entry of the soybean to the United States to be Savanah. But it wasn’t until Jan. 2016 that the Georgia Historical Society recognized his discovery. A historical society marker was erected at the Skidaway Institute of Oceanography to commemorate the soybean’s arrival.

After receiving his Ph.D. from Oklahoma State University, Hymowitz joined the faculty at the University of Illinois in the Department of Crop Sciences in the College of Agricultural, Consumer and Environmental Sciences. He spent his entire career at Illinois working on breeding, genetics, and the history of the soybean.

While at the University of Illinois he conducted research on the variation in and genetics of biologically active and anti-nutritional components of soybean seed and conducted plant exploration trips to Asia, Oceania, and Australia to locate potential germplasm resources for soybean varietal improvement.

In 2015, Hymowitz completed a decade-long effort with University of Arizona scientists Monica Schmidt and Eliot Herman. The team of researchers yielded a new soybean with significantly reduced levels of three key proteins responsible for both its allergenic and anti-nutritional effects. The work is described in a paper published online in the journal Plant Breeding.

For more about the conference, visit http://wsrc10.net/program/keynote-speakers/.

 

Deeper understanding of environmental values gained through broader collaboration

Published May 11, 2017
Children on streets of community near the Anchicaya River in Colombia
One of the research projects in the study looked at how a community along the Anchicaya River in Colombia was impacted by developments from a hydroelectric dam.
  • Social and behavioral science disciplines can help interpret values of nature and provide another level of understanding in environmental research projects.
  • Interdisciplinary research can help communities voice their opinions and articulate the multiple values of an environment.
  • In the study of ecosystem services, a broader social perspective can lead to more informed decisions and effective and lasting policy change.

URBANA, Ill. – It’s understood that chemists and geologists come from very different science disciplines, but people tend to file all social scientists under one category—social. But within the social sciences, a psychologist is very different from an anthropologist or an economist. A University of Illinois study illuminates the need to engage social scientists from a specific discipline to solve problems by bringing their distinct disciplinary perspectives.

In social science, one size doesn’t fit all, according to Carena van Riper, environmental social scientist and assistant professor in the College of Agricultural, Consumer and Environmental Sciences Department of Natural Resources and Environmental Sciences at the University of Illinois. She participated in a sort of think tank, hosted by the National Science Foundation, to bring different kinds of scientists together to solve complex problems. Van Riper’s group focused on cultural ecosystem services—recreation, cultural identity, relationships to places, etc.

“The problem we tackled includes all of the different factors taken into consideration when trying to understand how people put a value on the environment,” Van Riper says. “If you want to effectively solve a problem, researchers should engage multiple social scientists’ perspectives.”

The outcome is what van Riper refers to as a roadmap for researchers. “We drew from research in multiple social science disciplines to think about how they could enhance the study of ecosystem services. Psychology, sociology, geography…” she says. “We packaged it all together.”

After developing a model and showing how different disciplines interfaced with it, the group applied the model to three different cases, using actual research projects in the United States, Colombia, and Australia. “We showed how the studies engaged with the model but in an incomplete way. Adding various social science perspectives would help researchers identify a more accurate value of nature.”

One of the research projects looked at how a community along the Anchicaya River in Colombia was impacted by developments from a hydroelectric dam. After a tremendous amount of sediment was released below the dam, the community united to request compensation for their losses. “How do you put a price tag on that environment? Fortunately, the research team was interdisciplinary and helped the community advocate for their wellbeing.”

According to van Riper, a lot of the work in BioScience is published by folks in the natural sciences. The goal of her working group was to speak to this audience and show that the social sciences are not a homogeneous field.

“Human beings are complex. In the social sciences, there are lots of pieces, so you have to look at more than one discipline. There are internal processes like values, beliefs, attitudes, emotions. These are things that people process on the inside. And then external factors, like policies, institutions, cultures,” she says. “They are all critically important pieces of a puzzle that help us understand how society values the environment.”

Van Riper says after the working group examined the three cases, they developed questions to engage researchers and managers. “If you’re doing research, what are the questions you can ask to accommodate different ways of viewing the world?” She goes on to explain that the working group really tried to stir the pot and get people thinking about the intangible and non-material values people associate with nature.

“It’s a guide for researchers to engage with social scientists, essentially,” van Riper says. “We need to take a more interdisciplinary, if not, transdisciplinary, approach to solving problems. There are benefits that come from engaging with different types of disciplines.”

“Researchers need to know this, but also managers in agencies dealing with environmental challenges. It’s about embracing multiple forms of knowledge and multiple kinds of methods,” van Riper says. “Real innovation lies in research that bridges engineering, the natural and physical sciences, humanities, and the social sciences.”

The study, “Incorporating Sociocultural Phenomena into Ecoystem-Service Valuation: The Importance of Critical Pluralism,” is authored by Carena J. van Riper, Adam C. Landon, Sarah Kidd, Patrick Bitterman, Lee A. Fitzgerald, Elise F. Granek, Sonia Ibarra, David Iwaniec, Christopher M. Raymond, and David Toledo. It is published in BioScience.

The article originated from a Conference for Sustainability IGERTs and a subsequent workshop, both funded by the National Science Foundation.

 

Photos more credible, cartoons more persuasive

Published May 10, 2017
photo and cartoon brochures
  • With all else identical in a brochure, when a cartoon is swapped for a photograph, the cartoon is more cognitively engaging.
  • However, photographs are believed to be more credible.
  • Using cartoons may be a more effective way to communicate difficult scientific concepts in the classroom as well as to a general audience.

URBANA, Ill. – If you’re creating a message to educate, inform, or persuade, don’t underestimate the power of a well-executed cartoon.  A new study at the University of Illinois suggests if you’re trying to convince the public to change their stance on a topic such as wind energy, you may be more successful if you use a cartoon rather than a photograph.

“Photographs were shown to be more credible, but cartoons were more likely to change behavior,” says U of I agricultural communications professor Lulu Rodriguez who led the study. “A cartoon grabs people’s attention long enough to deliver the message. That’s what you need in today’s message-heavy atmosphere. Why not use a tool that has proven ability to cut through the others and inform people in a way that actually works?”

In the study, participants were shown one of two versions of the same set of brochures. Each set was designed to debunk a myth about wind energy, the intent being to give readers scientific information about wind energy and assuage their fears. Each pair of brochures was identical in design, text, color, size, etc. The only difference was that the originally designed brochures featured a beautiful, professional photograph of wind turbines, while the look-alike brochures created for the study swapped out the photograph with a cartoon.

“You have to spend more time with a cartoon to figure out the meaning of the illustrations, and the situation,” Rodriguez says. “People look at cartoons longer, so they’re more cognitively engaged with the cartoon. Usually it includes humor and people work hard at figuring out the punch line. The photos used to represent wind energy on the original brochures were just beautiful scenic shots of the turbine blades or a landscape dotted with turbines so people didn’t look at them as long.”

Interestingly, the respondents said the content was better in the cartoon brochures (even though the text was identical), but the credibility was lower than the brochures using photographs.

“It may be because of the more light-hearted approach of cartoons,” Rodriquez says. “Cartoons make a topic like wind energy, which may be a bit scary to people, more accessible. But this notion of credibility is a different issue. We teach students to be conversational in writing. Don’t put on your ‘tuxedo’ language. And yet, people associate big words with credibility.”

Rodriguez says the use of comics has already been shown to be effective in explaining scientific concepts and principles in high school chemistry classrooms. (Rodriguez is also the director of the agricultural communications program in the College of Agricultural, Consumer and Environmental Sciences and the College of Media.) She says she has not seen the comparison of photos versus cartoons studied in non-classroom settings.

In addition to educational settings, the power of cartoons to persuade can be of value to agencies working to educate the public about a science-laden concept—one for which they would like to change opinion, intentions, or behaviors.

“My interest is in making science more accessible to the public,” Rodriguez says. “This study offers real recommendations to communicate science better to a general audience. Understanding the science helps get people past whatever might be controversial about a scientific breakthrough or innovation. The controversies usually arise out of a lack of understanding.”

In terms of wind energy, Rodriguez says, people worry about claims that the turbines kill birds, when in fact, cars kill more birds. “We kept hearing scientists say that people do not fully understand wind energy. So we thought, how can we deflect that misunderstanding?”

Rodriguez cites communicating about GMOs as another possible case in which incorporating cartoons may inform people.

“Most people don’t know about all the regulatory layers at the local and national level involved in producing GMOs. If you try to describe that for people in text, they may not get it or they may not be motivated to read lines and lines of words. Perhaps a cartoon showing safety regulations or the similarity of genetic engineering to natural crossing of plants would be more convincing,” she says.

“I have a colleague who actually did this to explain how they got the vitamin A into golden rice using a cartoonish infographic. Not very scientific—but people get it. It’s a lot easier to explain complex scientific concepts that way.”

Rodriguez admits that text and photos may be the easier route to take.

“Truth be told, this is easy to recommend, but cartoons and effective information graphics are difficult to create. You have to hire someone with real skills to do it. Making things easier to understand is a difficult thing to do,” she says. “And, when people hire an advertising agency to create a brochure for their product or cause, they may lean toward using photos because they convey prestige or credibility. It may be difficult to convince them to use a cartoon because they think it reduces the classiness of the brochure.”

The article, “The impact of comics on knowledge, attitude and behavioural intentions related to wind energy,” is published in an issue of the Journal of Visual Literacy. The research was conducted by Lulu Rodriguez, University of Illinois; and Xiao Lin, Quixey, San Jose.

 

 

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