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Piglet brain atlas new tool in understanding human infant brain development

Published October 10, 2014
brain imaging
A map created using the MRI based averaged piglet brain atlas. University of Illinois.

URBANA, Ill. – A new online tool developed by researchers at the University of Illinois will further aid studies into postnatal brain growth in human infants based on the similarities seen in the development of the piglet brain, said Rod Johnson, a U of I professor of animal sciences.

Through a cooperative effort between researchers in animal sciences, bioengineering, and U of I’s Beckman Institute, Johnson and colleagues Ryan Dilger and Brad Sutton have developed a magnetic resonance imaging (MRI) based brain atlas for the four-week old piglet that offers a three-dimensional averaged brain and anatomical regions of interest. 

This averaged brain atlas, created from images from multiple piglets, will serve as a template for future studies using advanced MRI techniques that can provide important information on brain macro- and microstructure during this critical period of development. The template, as well as tissue probability maps that were also created, are available online and are freely distributed.

“The piglet brain is similar to the human brain in that it is gyrencephalic and experiences massive growth and development in the late prenatal and early postnatal periods. We are concerned that environmental insults such as infection or poor nutrition during these early periods may alter the trajectory of brain development,” Johnson said.

“Pigs provide an excellent translational model for biomedical research. This is a new tool that may be useful to others in the biomedical community,” he added.

While an atlas did already exist for the adult pig, Matthew Conrad, a doctoral student in Johnson’s lab said the previous atlas was created from a single adult animal. “The benefit to using an averaged brain is that it will produce a template that is a better representation of the population. The more animals included the better.”

The atlas was created by taking MRI images of the brains of 15 four-week-old York breed piglets—nine females and six males. The images were then reconstructed into 3D volumes for each pig. Through a series of deformations and averaging of the data sets, the images were eventually aligned to create the final averaged brain.

Conrad explained that having an averaged brain template available will allow better use of the software needed for more advanced techniques in studying the volume of brain regions.

An example of these techniques includes voxel-based morphometry (VBM), which can be used to detect volume difference in the brain. Additionally, diffusion tensor imaging (DTI), which looks at white-matter track development and connectivity in brain regions, and magnetic resonance spectroscopy (MRS), which looks at white matter and neurochemical changes in the brain, are being conducted.

“The atlas will be used as the population average. When new data sets are brought in, you first line up the new brain images to this template,” Conrad said.

In addition to the average brain atlas, Conrad said they also created population averages for white and gray matter as well as cerebrospinal fluid (CSF). “This is another data set that helps predict the tissue classification,” he said.

Previous studies using MRI imaging of piglets have looked at the effects of iron deficiency on brain development. “For that we did MRI imaging and manual segmentation, and with manual segmentation you are looking at volume changes within very large areas of the brain, but with VBM we can pinpoint smaller changes within discrete brain areas,” Conrad said. “We are now reanalyzing data from those piglets and replicating this study with new protocols, which will allow us to see changes that we didn’t see before.”

Another study is looking at the effects of postnatal infections, such as pneumonia, on brain development. “These types of infections are common in infants, and again it’s a period of time when the brain is undergoing rapid development,” Johnson said.

A third study funded by the National Institutes of Health is focused on maternal viral infection during pregnancy. “The goal is to assess how mom’s immune response to infection influences brain development and future behavior of her piglets,” Johnson explained.

Conrad added that the piglet brain is now being recognized for its potential as a translational animal model for neurodevelopmental studies.

“Much of the research on the effects of pre- and postnatal factors on brain development has been done in rodent models, but the rodent brain develops very differently.  Therefore, the piglet can provide a complementary model wherein results better translate to humans,” Johnson said.

The brain atlas project and related studies are funded by a grant from the National Institutes of Health.

The atlas and other resources created during this project are available online at

An in vivo three-dimensional magnetic resonance imaging-based averaged brain collection of the neonatal piglet (Sus scrofa)” was recently published in PLOS ONE and is available online at Matthew S. Conrad, Bradley P. Sutton, Ryan N. Dilger, and Rodney W. Johnson were coauthors of the study.

Organic Gardening Day Nov. 1

Published October 9, 2014
rows of organically grown crops

URBANA, Ill. – This year’s Organic Gardening Day will take place on Saturday, Nov. 1, from 8 a.m. to 4:30 p.m. at the Urbana Plaza Hotel and Convention Center (formerly the Holiday Inn) in Urbana.

Chuck Voigt, University of Illinois vegetable and crops specialist and coordinator of the event, said that experts from around the country will present educational sessions to inspire organic gardening.

William Woys Weaver, from Devon, Pennsylvania, will give two presentations. One of his talks will be about the kitchen garden, and the other talk will be about the health benefits of heirloom food plants. William is the author of books on heirlooms, local foods, Pennsylvania Dutch cooking, herbal cures, and more. “He is a very in-demand speaker and we are lucky to have him with us this year,” Voigt said.

Marty Travis, of Spence Farm in Fairbury, Ill., is the seventh generation living the small farm life on a family farm settled by his ancestors in 1830. “Marty, along with his wife Kris and son Will, grows a great variety of crops and livestock organically,” Voigt said. “He has also grown a wide variety of grain crops, often on a rather small scale. He’ll share some of the basics of producing diverse grain plants, either in the field or the garden. The diversity of what’s produced at Spence Farm is amazing.”

In addition to the speakers, there will be a retail area selling a broad range of gardening products.

Online registration is available until Oct. 27. The cost for the day is $60, which includes an organic lunch buffet. For more information, contact Linda Harvey by calling 217-244-1693 or send an email to

On-site registration on Nov. 1 begins at 8 a.m., will continue only as long as space allows, and will not guarantee lunch. The first educational session begins promptly at 9 a.m.



Test Bill Test

8:52 AM to Friday, October 10, 9:52 AM
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This is a Food Security Event

Invasive plant wins competition against its native cousin

Published October 8, 2014

URBANA, Ill. – Because of its aggressive behavior and its harmful effects, the invasive prairie plant Lespedeza cuneata has been added to several noxious weed lists.  Research at the University of Illinois on how soil bacteria interact with the plants’ roots to form nodules that fix nitrogen demonstrated that the invasive variety had superior performance when pitted against the native plant variety Lespedeza virginica.

“We expected Lespedeza cuneata to be a strong competitor when up against its native cousin that’s planted primarily for prairie restoration,” said U of I microbial ecologist Tony Yannarell. “There are a number of studies showing that L. cuneata grows quickly, is able to shade out its competitors, and has a high rate of nitrogen fixation, which allows it to ‘self-fertilize’ on unproductive soils.”

Yannarell explained that Lespedeza plants establish a “partnership” with bacteria in the soil to form nodules that fix nitrogen. “We wanted to demonstrate that the partners in this symbiosis matter,” he said.

Because the nitrogen-fixing gene is in the bacteria, the first step in the research was to identify bacteria that have the gene. “We started with isolating a pool of 50 bacteria [from the root nodules of invasive and native Lespedezas] and discovered that some of them weren’t traditional nodule-forming bacteria.”

Ultimately, seven bacteria were identified and used in a three-month greenhouse experiment in which various combinations of native and invasive varieties of Lespedeza were grown together in pots. Of the seven, five bacteria were found to benefit the invader and two did not benefit either of the plant varieties.  

“We were hoping to be able to change the degree of competitiveness by using different varieties of Lespedeza by varying the bacteria,” Yannarell said. “It turned out that none of the bacteria seemed to be better for the native plant.

“A really intriguing pattern that we found is that a lot of these strains of bacteria that are good for the invader belong to the Bradyrhizobium genus of bacteria that’s been shown in other parts of the world to be good at fixing nitrogen so this was one more confirmation of that information,” Yannarell said.

Yannarell said that this study provides yet another piece in the ecological puzzle.

The invasive Lespedeza cuneata was intentionally brought into the United States from Japan near the end of the 1800s. At the time, people liked its nitrogen-fixing capacity and soil fertilization. It was intended to be used to stabilize river banks and rehabilitate poor soil. Yannarell said that it has been recommended as wildlife forage, and some think that it has tannins that can act as a deworming treatment for goats. Now, however, it’s considered to be a noxious weed that grows in the South and Midwest. It is commonly called silky bush clover.

Yannarell stressed that there are a lot of different species of Lespedeza that are native to North America and indicative of high-quality prairie. Although Lespedeza cuneata isn’t a plant that would be intentionally planted by prairie restorationists, it has been seen in prairie seed mixes.

“Invasive Lespedeza cuneata and native Lespedeza virginica experience asymmetrical benefits from rhizobial symbionts,” was published in Plant and Soil and was co-authored by Lingzi Hu, Ryan R. Busby, and Dick L. Gebhart. The work was supported by a grant from the U.S. Army Engineer Research and Development Center and by the Cooperative State Research, Education and Extension Service, U.S. Department of Agriculture.


Additional Images:
  • Root nodules

Utilizing cornstalks despite wet weather

Published October 7, 2014

URBANA, Ill. - Wet, rainy weather conditions are beginning to cause headaches for farmers. Besides the obvious delay in harvest, additional moisture is negatively affecting grain and cornstalk quality for cattle producers that normally utilize the crop residue to extend the grazing season, according to a University of Illinois Extension beef educator.

Excess rain causes leaching of nutrients available in cornstalks, Travis Meteer explained. It also decreases palatability of the crop residue. Lower intakes of a less nutritious feed will result in poorer animal performance.

According to Meteer, grazing cornstalks is still a valuable tool for cattlemen looking to hold costs in place. The cost of grazing cornstalks is low first because the cows graze and harvest their own feed, and second, because all costs of producing the plant for grain production are attributed to the row-crop operation, he explained. “Even with the cost of a temporary fence—which many farmers already have—and water, the use of grazing cornstalks is more economical than feeding higher-priced hay.”

Meteer also explained that even with lower palatability due to wet, damp stalks, cattle will eat the more digestible and higher-protein portions first. “Therefore, a good mineral is probably the only supplementation needed for the first few weeks unless the herd includes fall-calving cows or stocker calves,” Meteer advised. “For them, a supplement will be necessary to meet nutrient demands of lactation and growth, respectively.”

Normally, one acre of cornstalks is needed to feed a cow for 30 days. If wet, rainy conditions persist, at least two to three acres will be needed due to faster degradation and more trampling of the residue. Strip grazing will limit trampling if the supply of available cornstalks is low.

Meteer said producers need to scout fields for several things. “First, look for ear drop and down corn areas. A significant amount of grain loss in fields can cause acidosis or founder in animals,” he said. “Fields with these areas will need careful management via strip grazing or completely fencing the problem areas out.

“Second, look for molds on remaining ears of corn. Some reports of Diplodia have been surfacing which will not cause major problems if ingested by cattle, but Diplodia will open the grain up to other fungus such as Fusarium and Gibberella. These molds can produce mycotoxins, including fumonisin, deoxynivalenol (DON or vomitoxin), and zearalenone,” he added.

Because cattle select the grain portion first when grazing, Meteer explained that toxic levels can be ingested if low to moderate levels of mycotoxin are present. “Because accurately sampling residue can be challenging, it is recommended to use mycotoxin levels in the grain to determine risk. If the grain contains less than 1 ppm of DON (vomitoxin) or less than 3 ppm of fumonisin or zearelenone, the cornstalks are likely safe to graze and the risk is very low,” he said.

Meteer pointed out that baling cornstalks in a wet fall can pose many challenges. “Obviously, wet cornstalks do not keep well in a bale. They are subject to mold, heating, and large amounts of spoilage. Cornstalks that have been rained on will also have higher levels of soil contamination, which will increase ash levels in the nutrient analysis of the baled forage. Soil contamination will decrease the nutritive value of the already poorer-quality feed,” he said.

For producers asking if compaction issues surface after grazing cornstalks, Meteer pointed out that research conducted at the U of I’s Dudley Smith Research Farm shows that compaction from grazing cattle does not even approach agronomic effect. “In these trials, cattle are removed in early winter to be provided a diet that better meets nutrient requirements. Cattlemen and landowners should not worry about compaction as long as cattle are stocked appropriately and removed in a timely manner,” he said.

All in all, Meteer said the wet weather is causing the quality of cornstalks to decline. “Producers need to increase acreage available compared to last year to accommodate a similar number of cows. Scouting fields is a must. Looking for ear drop and ear molds will be necessary to mitigate risk. Some supplementation may be needed if cows are required to graze cornstalks longer than 30 days. Cattlemen should still take advantage of grazing crop residues; however, more management may be needed in comparison to a normal, dry-weather fall,” he said.