UWMadScience https://uwmadscience.news.wisc.edu Behind the science & research that makes the news at UW–Madison Wed, 13 Feb 2019 17:33:02 +0000 en-US hourly 1 https://wordpress.org/?v=4.9.9 Disaster watch: meet the meteorologist who keeps campus safe https://uwmadscience.news.wisc.edu/climate/disaster-watch-meet-the-meteorologist-who-keeps-campus-safe/ https://uwmadscience.news.wisc.edu/climate/disaster-watch-meet-the-meteorologist-who-keeps-campus-safe/#respond Wed, 13 Feb 2019 17:33:02 +0000 https://uwmadscience.news.wisc.edu/?p=3358 Seven days before the polar vortex blanketed Madison in nearly record-low temperatures, researchers, meteorologists  and UW administrative leaders were already discussing how campus would be affected.

Immediately after learning of the impending cold, Shane Hubbard began to work with UWPD’s Emergency Management Unit to advise and prepare campus . A research scientist in the Space Science and Engineering Center, Hubbard develops geospatial models for hazard events like floods, tornadoes and winter storms.

“We had spent multiple days thinking about what the appropriate response would be for our campus,” Hubbard says. “Closing campus is a very difficult thing to do, so many people were involved in making that decision.”

Hubbard first began working in emergency management for the state of Wisconsin, and now uses that expertise along with his knowledge of meteorology to prepare campus for disasters.

“I realized how important it was for emergency management to have a strong sense for the weather,” Hubbard says. “So ever since I had been in that position, I try to connect emergency management groups with what I study.”

Hubbard works as a research scientist in the Space Science and Engineering Center.

When snow is involved, Hubbard and his colleagues closely watch for what areas of campus will be hit the hardest. They always recommend that the university take coordinated action whenever more than six inches of snow are forecasted.

“A lot of times the forecast doesn’t include finer details like flooding, so I provide emergency management recommendations based upon our weather outlooks,” he says.

With the sharply rising temperatures that occured recently, Hubbard carefully evaluated which areas of campus were most susceptible to flash floods. As freezing rain appeared in the forecast, Hubbard notified campus of high-risk areas.

His experience with flood evaluation extends well beyond Wisconsin’s borders as well, as he previously worked in Iowa City, Florida, Georgia and Indiana. In Iowa City, a place much more prone to flooding than Madison, Hubbard developed a time-based model to assess which buildings would be damaged first as a flood worsened .

Hubbard adds that climate change has caused more rapid rains and floods in recent years.

“What’s happening now is that people that aren’t expecting to get flooded, are getting flooded,” he says. “We’re not beating our old flood records by 5 percent anymore, we’re beating them in some cases by double.”

That kind of unexpected flooding was on full display this past summer when one large rainfall pushed the lake level in Mendota to near record levels. These rapidly developing storms have become more frequent across the country — which can be especially challenging for buildings near flood boundaries.

A road hazard sign warns of high-standing water flooding West Shore Drive along Monona Bay in Madison, Wis., during summer on Sept. 6, 2018. Area lake levels continue to rise after a record-breaking storm on Aug. 20 dumped more than 10-inches of rain on parts of Dane County, also flooding areas of the University of Wisconsin-Madison campus lakeshore. (Photo by Jeff Miller / UW-Madison)

A road hazard sign warns of high-standing water flooding West Shore Drive along Monona Bay in Madison, Wis., during summer on Sept. 6, 2018. Area lake levels continue to rise after a record-breaking storm on Aug. 20 dumped more than 10-inches of rain on parts of Dane County, also flooding areas of the University of Wisconsin-Madison campus lakeshore. (Photo by Jeff Miller / UW-Madison)

“The problem is that communities build right up against flood boundaries, and with the changing precipitation patterns, this could be the worst thing we could do,” Hubbard says. “One of the issues we have in this country is we continue to map our flood boundaries based on the last big flood we had, so a little bit more water can affect a lot more people.”

Hubbard and his colleagues are already making predictions for this summer’s precipitation and flood possibilities, especially regarding lake water levels. Though the city and county periodically issue their own reports on lake levels, Hubbard also helps estimate lake levels in real-time to keep campus updated.

Hubbard’s role in the university is unique. By combining his knowledge of disaster preparation and weather forecasting, Hubbard helps the Emergency Management Unit maintain the everyday safety of students, faculty and staff.

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Fructose can trigger viruses in the gut’s microbiome https://uwmadscience.news.wisc.edu/uncategorized/fructose-can-trigger-viruses-in-the-guts-microbiome/ https://uwmadscience.news.wisc.edu/uncategorized/fructose-can-trigger-viruses-in-the-guts-microbiome/#comments Wed, 06 Feb 2019 20:50:51 +0000 https://uwmadscience.news.wisc.edu/?p=3350 This is a guest post by Amelia Liberatore, a marketing intern with the UW–Madison Department of Food Science.

The human gut is a complex ecosystem dominated by bacteria that help digest food and keep one’s gastrointestinal tract in check. One population that lives in the gut are so-called lysogenic bacteria, which are bacteria that contain dormant viral DNA. When these lysogenic bacteria are exposed to a stressful condition, the viral DNA is activated and produces viruses. Recently, it has been suggested that diet, specifically dietary sugar, can be one of these triggers.

After nearly four years of testing, Jan-Peter van Pijkeren, a University of Wisconsin–Madison professor of food science, and his research team have unraveled a mechanism that explains how fructose — a sugar increasingly common in the diet — triggers the production of viruses in the gut. When the gut symbiont Lactobacillus reuteri is exposed to a fructose-enriched diet, it produces acetic acid, which in turn triggers the production of viruses.

“Approximately 50 percent of the viruses that we carry along in our gastrointestinal tract are derived from those lysogens,” explains van Pijkeren, whose research focuses on understanding the mechanisms that underlie bacteria-host interactions. “Up until this point, we had no understanding of what the underlying mechanisms were that contribute to this [activation of viruses].”

The role of bacterial viruses in the gut remains unclear. While the new findings demonstrate that the production of viruses reduces intestinal survival of L. reuteri, it is possible that these viruses can still help L. reuteri by killing other competing bacteria. Further research defining the ecological role of lysogenic bacteria combined with van Pijkeren’s latest findings could provide new avenues of research to tailor the composition of select organisms in the gut, including probiotics.

Jee-Hwan Oh, Jan Peter van Pijkeren, and Laura M. Alexander in their lab at UW Department of Food Science in Babcock Hall

Jee-Hwan Oh, Jan Peter van Pijkeren, and Laura M. Alexander in their lab at UW Department of Food Science in Babcock Hall

L. reuteri lives in many vertebrates, including humans. The van Pijkeren laboratory developed several genome-editing tools, which allowed them to develop L. reuteri as a model to study its viruses. They found that the normally dormant viruses of L. reuteri become activated as they move through the digestive track, resulting in the production of viral particles.

The next step was to investigate to what extent dietary sugars promoted virus production. The team decided to focus on fructose because of its abundance in the food chain. Since the development of high-fructose corn syrup as a cost-efficient sweetener in the early 1970s, average fructose consumption has increased fourfold.

Mice were fed high-fructose diets along with L. reuteri. The research team found that mice that ate fructose experienced a significant increase in the production of L. reuteri viruses in the gut when compared to animals fed glucose.

“That was an exciting observation, but we wanted to know what the mechanism was by which fructose increased virus production. So, we basically searched the DNA sequence of L. reuteri to find genes whose products could be involved in fructose metabolism. These results predicted that L. reuteri can metabolize fructose to subsequently produce acetic acid using a pathway that is conserved among bacteria.”

Focusing on the metabolic pathway, the research team found that consumption of fructose and L. reuteri increased acetic acid production in the gut of mice. When the research team inactivated the pathway responsible for acetic acid production, virus production by L. reuteri was nearly abolished. “These results could mean that acetic acid itself is a trigger for virus production,” explains van Pijkeren.

Acetic acid is a member of a group of chemicals known as short-chain fatty acids, which cells can use for energy. The dominant short-chain fatty acids in the human colon include acetic acid along with propionic and butyric acid. The researchers tested each of these chemicals and found that exposure to each type of fatty acid promotes the production of viruses via the same pathway that L. reuteri uses to produce acetic acid.

“So not only does fructose metabolism promote the production of viruses following acetic acid production by L. reuteri, but it’s also the exposure to short-chain fatty acids that is a trigger,” explains van Pijkeren.

Van Pijkeren’s report paves the way for future studies aiming to understand how the metabolism of a bacterium is linked to virus production, and how this can be influenced by our diet. Important questions remain, including what role these viruses play in the gut. Understanding diet-induced virus production is expected to ultimately allow researchers to tailor the robustness of select organisms, such as probiotics, in the gut and develop better ways to alter gut microbial communities

The research was published in the journal Cell Host and Microbe in their online issue on January 15 and in print in the 2019 February issue.

The Petri-dish is filled with solid growth medium that is covered by a lawn of bacteria. When these bacteria are exposed to a virus to which they are susceptible, one outcome is that the bacterial cells are killed. Bacterial cell killing results in a ‘clearing’, i.e. a plaque, which is depicted by the transparent circles on the plate.

The Petri-dish is filled with solid growth medium that is covered by a lawn of bacteria. When these bacteria are exposed to a virus to which they are susceptible, one outcome is that the bacterial cells are killed. Bacterial cell killing results in a ‘clearing’, i.e. a plaque, which is depicted by the transparent circles on the plate.


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The polar vortex should kill bugs, right? Not so much. https://uwmadscience.news.wisc.edu/bugs/the-polar-vortex-should-kill-bugs-right-not-so-much/ https://uwmadscience.news.wisc.edu/bugs/the-polar-vortex-should-kill-bugs-right-not-so-much/#comments Wed, 30 Jan 2019 19:46:03 +0000 https://uwmadscience.news.wisc.edu/?p=3314 The post office suspended mail delivery. Schools and campuses across the Midwest closed down. Temperatures in Chicago, Madison and other Great Lakes cities dipped lower than those in Antarctica.

Surely that means some of the peskiest insects we know don’t stand a chance in the polar vortex, right?

Well, not so fast, says University of Wisconsin–Madison bug guy, PJ Liesch.

“The cold weather will undoubtedly have some impacts, although it’s difficult to predict at this point,” Liesch says. “The snow we’ve received over the last few weeks has created an excellent insulating layer that will protect many overwintering insects from the full force of the cold.”

Students and pedestrians walk along snow-covered sidewalks near Agricultural Hall at the University of Wisconsin-Madison during a winter storm that brought several inches of snow to campus on Jan. 23, 2019.

Students and pedestrians walk along snow-covered sidewalks near Agricultural Hall at the University of Wisconsin-Madison during a winter storm that brought several inches of snow to campus on Jan. 23, 2019. (Photo by Bryce Richter /UW-Madison)

So what does that mean for the emerald ash borer, responsible for wiping out several thousand square miles of ash trees across Wisconsin, and tens of millions of ash trees in 30 states?

“Insects like the emerald ash borer will likely be impacted by the cold, but their reproductive capacity should allow them to ‘catch up’ in the long-run,” Liesch explains.

What about ticks, those creepy arachnids infamous for carrying diseases like Lyme, Rocky Mountain Spotted Fever, and even red meat allergies? (Why, yes, you can find Lone Star ticks in Wisconsin and they’re really disgusting.*)

Liesch delivers some more bad news: “Ticks overwinter down amongst leaf litter, meaning that they should be well insulated at this point.”

Well, surely those smelly, annoying stink bugs will perish in the arctic blast … right?

Turns out, they’re just more likely to cozy up next to us as we huddle for survival in our heated homes.

“The invasive brown marmorated stink bug, which has been a nuisance to many Wisconsinites, likes to invade homes and other structures which would provide sufficient warmth during this cold spell,” Liesch says.

Adult brown marmorated stink bug.

Adult brown marmorated stink bug. Photo Credit: PJ Liesch, UW Insect Diagnostic Lab

Ok, ok. Mosquitoes. We had a really hellish year here in southern Wisconsin last year, given the record-breaking flooding. So this deep freeze will give us the break we deserve …

She can’t yet say for sure, but probably not, says UW–Madison Entomology Professor, Susan Paskewitz, co-director of the Centers for Disease Control and Prevention Midwest Center of Excellence for Vector-Borne Disease: “We have a good snow cover and usually that should give some insulation down where the eggs are overwintering.”

While there is some potentially good news — “I’d expect that insects overwintering in more exposed locations (such as exposed egg masses) or recent invaders from more southern areas would be impacted the most,” Liesch says — it sounds like we’re just going to have to find ways to make do with these cold conditions and remember that summer, and its bugs, will be here before we know it.

Hoofer Sailing Club members bring their windsurfing boards and sailboats in for the evening near the Memorial Union Terrace at the University of Wisconsin-Madison as the summer sun sets over a Lake Mendota pier on Aug. 31, 2016.

Hoofer Sailing Club members bring their windsurfing boards and sailboats in for the evening near the Memorial Union Terrace at UW–Madison. (Photo by Jeff Miller/UW-Madison)

*No really, read this: –Nymphs and larvae of the lone star tick will often feed on humans, and can sometimes be present in large numbers.  These are sometimes called “seed ticks” in the southern USA.  It is not uncommon for a person to pick up 20 to several hundred seed ticks at a time.

Source: http://labs.russell.wisc.edu/wisconsin-ticks/wisconsin-ticks/amblyomma-americanum-lone-star-tick/

For more info about insects and insect-borne diseases and invasions:

Centers for Disease Control and Prevention

Ticks: https://www.cdc.gov/ticks/

Midwest Center of Excellence for Vector Borne Disease: http://mcevbd.wisc.edu/

University of Wisconsin–Madison Insect Diagnostic Lab: http://labs.russell.wisc.edu/insectlab/

United States Department of Agriculture Animal and Plant Health Inspection Service: https://www.aphis.usda.gov/aphis/resources/pests-diseases/hungry-pests/the-threat/emerald-ash-borer/emerald-ash-borer-beetle

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New insight into gene expression in all living things https://uwmadscience.news.wisc.edu/basic-science/new-insight-into-gene-expression-in-all-living-things/ Tue, 08 Jan 2019 17:18:21 +0000 https://uwmadscience.news.wisc.edu/?p=3306 A study published today (Jan. 8) in eLife, led by University of Wisconsin–Madison Professor of Biochemistry and Bacteriology Robert Landick and his research team, reveals for the first time the elemental mechanism behind transcriptional pausing, which underlies the control of gene expression in all living organisms.

It also provides new understanding of the enzyme RNA polymerase, an important drug target for treating conditions such as Clostridium difficile infections and tuberculosis. The findings could ultimately improve our understanding of how certain drugs work against the enzyme and aid in actively targeting it.

Gene expression is the process by which DNA is translated into all the proteins and other molecules living organisms need. Though it’s a process introductory biology students everywhere learn about, scientists are still far from fully understanding it.

The process occurs in two steps. Transcription is the first, where RNA polymerase reads the information on a strand of DNA, which is then copied into a new molecule of messenger RNA (mRNA). In the second stage, the mRNA moves on to be processed or translated into proteins.

To help control gene expression levels, transcriptional pausing by RNA polymerase can occur between the two stages, providing a kind of ‘roadblock’ where transcription may be terminated or modulated by the cell if need be.

A new study from UW–Madison’s Robert Landick, professor of biochemistry and bacteriology, reveals for the first time the mechanism behind transcriptional pausing. Image: Landick lab

“A sequence that causes pausing of RNA polymerases in all organisms, from bacteria to mammals, halts the enzyme in a paused state from which longer-lived pauses can arise,” explains Landick. “As the fundamental mechanism of this elemental pause is not well defined, we decided to explore this using a variety of biochemical and biophysical approaches.”

The team’s analyses first revealed that the elemental pause process involves several biological players, which together create a barrier to prevent escape from paused states. The process also causes a modest conformational shift that makes RNA polymerase ‘stumble’ when feeding DNA into its reaction center, temporarily stopping it from making RNA.

“We also found that transcriptional pausing makes RNA polymerase loosen its grip and backtrack on the DNA while paused,” says Landick. “Together, these results provide a framework to understand how the process is controlled by certain conditions and regulators within cells.”

He adds that these insights could aid future efforts to design synthetic genes, for example to direct the pausing behavior of RNA polymerase in a way that yields desired outputs from genes. It could also help our understanding of how certain drugs, known as RNA polymerase inhibitors, target the enzyme.

“For now, we would like to try and generate structures of paused transcription complexes obtained at a series of time intervals,” Landick concludes. “This would allow us to see exactly how parts of the enzyme move as it enters and leaves the paused state.”

Story adapted by biochemistry science writer, Kaine Korzekwa, from a press release by Emily Packer for eLife. A link to the story from the Department of Biochemistry can be found here.

Elm tree conservation stayed by hybrid species research https://uwmadscience.news.wisc.edu/botany/elm-tree-conservation-stayed-by-hybrid-species-research/ Wed, 12 Dec 2018 18:20:06 +0000 https://uwmadscience.news.wisc.edu/?p=3289 In July of 2018, a stalwart tree that had towered over the University of Wisconsin–Madison campus for generations and provided shade and residence for countless organisms was cut down. The American elm was one of the many long-standing elms in the U.S. to succumb to Dutch elm disease. Despite great efforts over the last two decades to prune and maintain the old elm, the disease soon spread to most of the immense tree.

A kingpin of horticultural studies, “Elmer” maintained a strong presence in the College of Agricultural and Life Sciences. Not only were students provided with great swaths of shade in their hot summer journeys across campus, but many biochemistry and horticulture students used the vast history of the tree as a point of study in their courses. Elmer’s cultural role on campus was outlined in a recent eulogy on the biochemistry department’s website.

Researchers at UW–Madison have often used elm trees in horticultural studies, and Elmer provided a snapshot of genetic history. Johanne Brunet, a USDA-ARS evolutionary biologist and professor in the Department of Entomology, has researched elm trees and their hybrid species.

“Elmer was a cherished tree and a relic of the majesty of the American elm over urban landscapes,” says Brunet. “Although our work did not directly examine the American elm, it was guided by its story.”

A Detroit neighborhood, captured in 1973 (top) and again in 1984 (bottom), shows the effects of Dutch elm disease. Photo credits: Jack H. Barger, USDA Forest Service.

The decline of the American elm is the unfortunate result of the introduction to the U.S. of Dutch elm disease, which originated in Asia and was accidentally introduced to the U.S. by means of infected timber that was meant for furniture production in Ohio. It was first described by Dutch pathologists, hence the name.

Elm populations have continued to decline as the disease proliferated following its introduction in the early 1930s. By 1989, it was estimated that over 75 percent of the American elm population had been lost.

The disease is caused by a fungus that infects the trees and whose spores are spread by bark beetles. These beetles burrow into the bark of elm trees, which makes them difficult to locate once they’ve settled on a tree.

Elm trees, once infected, plug their own vascular tissue, known as xylem, to prevent further spread. The xylem is key for delivering nutrients and water throughout the tree, and this blockage eventually starves the tree and kills it.

Hailed for their fast growth and hardiness in low-quality soil, like that near city streets, American elms were once common along neighborhood roads. Their cathedral-like, splayed branches create a shady canopy for those underneath.

American elm trees once lined many suburban streets, creating shady canopies for street-goers.

American elm trees once lined many suburban streets, creating shady canopies for street-goers. Photo credit: Joseph O’Brien, USDA Forest Service.

Disease containment remains an ongoing effort in the U.S., and several types of preventative treatments exist. Prominent trees, like Elmer, are heavily pruned to remove and burn the diseased branches. Chemical fungicides can also be injected into the trees, with varying levels of success. Unfortunately, none of these treatments truly eradicate the disease once it is introduced to the tree.

Not all hope for elms is lost, however. Research into disease-resistant hybrid trees has a long history at UW–Madison. The late Professor Eugene Smalley developed various strains of disease-resistant elm, notably the Sapporo Autumn Gold, New Horizon, and American Liberty varieties.

Sapporo Autumn Gold was developed using Asian hybrid cultivars, and has become one of the most successful hybrid cultivars. The strain was sent to Smalley by researchers at Hokkaido University in Sapporo.

New Horizon elms have dense foliage and a pyramidal shape, contributing to their unique appearance from other elm species. Photo by Wikimedia Commons.

New Horizon (left) is currently grown outside the Wisconsin Alumni Research Foundation, and is a cross between Japanese and Siberian elms. An upright and slow-growing tree, New Horizon has a distinct appearance from the classic splaying branches of the American elm.

American Liberty has been used in a variety of street-side planting and has found limited success. Smalley described the strain as “not as resistant as the Asian hybrids, but it still has the look of a classic American Elm.”

To replace American elm, an Asian elm species with some resistance to Dutch elm disease, Siberian elm, was planted over the landscape. In Brunet’s research on elm tree hybridization, they found that negative effects resulted from crosses between this introduced Asian elm species and our native slippery or red elm species.


“The issue is that the Asian trees cross with our local red elm species and create hybrids, and these hybrids cross back to the Siberian elms more often than to the native elm, which over time eliminates the native elm genes,” says Brunet. “If this process continues, it could result in the disappearance of the native elm species.”

The elm hybridization work was started by Juan Zalapa, then a postdoctoral associate in the Brunet and Guries laboratories. Raymond Guries, Emeritus Professor of Forestry and Wildlife Ecology, recently retired and was the university’s last dedicated elm breeder. But Brunet says that there is currently a national effort to encourage more people to join the field of plant breeding.

Advancements from researchers at UW–Madison have ensured the proliferation of elm trees for generations to come. While we may not see a direct replacement of Elmer the elm tree for some time, we can remember that with it as an inspiration, generations of elm trees will live on for decades.

This story was updated on 12/26/18.

Header photo by Steve Hall. 


Vote for IceCube’s cosmic ray discovery as breakthrough of the year https://uwmadscience.news.wisc.edu/uncategorized/vote-for-icecubes-cosmic-ray-discovery-as-breakthrough-of-the-year/ https://uwmadscience.news.wisc.edu/uncategorized/vote-for-icecubes-cosmic-ray-discovery-as-breakthrough-of-the-year/#comments Thu, 29 Nov 2018 17:40:30 +0000 https://uwmadscience.news.wisc.edu/?p=3264 Update on December 7: Thanks to your votes, IceCube made it to the finals! Now’s your chance to vote once more for IceCube’s cosmic ray discovery to be Science magazine’s breakthrough of the year.

Four billion years ago, in a violent clash of matter and energy, an otherworldly type of particle known as a neutrino was created and began its long journey to Earth. In September of 2017, the neutrino’s cosmic collision course came to an end as it crashed into an atom of ice beneath the South Pole, generating a brief flash of light. That light was captured by dozens of sensitive detectors frozen in the ice, triggering worldwide alarm bells that something worth watching was happening in the night sky near Orion’s left shoulder.

That neutrino, and the associated bursts of electromagnetic radiation captured by telescopes around the world, produced our first good evidence of where cosmic rays come from, solving a century-old mystery of their origin. With neutrinos loath to interact with most matter, the surest way to intercept them is to stick a lot of mass in their way. That’s where IceCube, headquartered at the University of Wisconsin–Madison, comes in. A billion tons of ice beneath the South Pole surveyed by thousands of light detectors, IceCube constantly watches the entire sky for these slippery particles, giving us insights into some of the universe’s most extreme events, including those capable of creating the highly energetic particles constantly raining down on Earth known as cosmic rays.

Now’s your chance to vote for IceCube’s groundbreaking discovery as Science magazine’s Breakthrough of the Year, an annual competition that surveys the past year’s biggest scientific advances and elevates one to the top slot. The first round of voting is open until Wednesday, Dec. 5, and the finalists will be up for a vote starting Dec. 6. The top vote-getter will be announced as the people’s choice award on Dec. 20, along with the magazine’s own selection.

A representation of the September, 2017 neutrino event in IceCube. The strings carry sensitive light detectors, and those detectors that captured the neutrino event are in color.

A representation of the September, 2017 neutrino event in IceCube. The strings carry sensitive light detectors, and those detectors that captured the neutrino event are in color.

Cosmic rays were first identified in the early 20th century as mysterious radiation coming not from the ground — where radioactive elements had recently been discovered — but from the sky. In 1912, Austrian physicist Victor Hess proved that the radiation increased with elevation by taking his instruments up in hot-air balloons, demonstrating that cosmic rays came from space. Scientists soon confirmed that cosmic rays are a collection of energetic particles, such as protons, bombarding Earth, where their collision with the atmosphere releases a shower of radiation.

But the ultimate origin of cosmic rays remained obscure. Because they are charged particles, cosmic rays do not travel in a straight line from their origin to Earth, but are whipped around by the magnetic fields pervasive throughout the universe. Neutrinos — tiny, nearly massless subatomic particles — don’t have that problem. They are neutral, and so travel unimpeded by magnetic fields. Their rare interactions with normal matter also mean they can pass through dust, planets and stars without stopping, making them ideal messengers of cosmic events. And because neutrinos are produced in the same events capable of producing cosmic rays, they can report information about these very energetic, violent cosmic events.

A blazar pointing its stream of matter toward Earth

An illustration of a blazar ejecting neutrinos and gamma rays toward Antarctica, where IceCube is based.

What the neutrino captured by IceCube in 2017 pointed to was a distant galaxy in the Orion constellation known as a blazar. Blazars are galaxies shooting out twin jets of matter from rapidly spinning, supermassive blackholes at their centers. The neutrino’s incredible energy triggered an automated alert from IceCube to other telescopes around the world and in orbit. Turning toward the blazar, those telescopes saw a burst of gamma rays coming from the same source, further pinpointing the blazar in that part of the night sky as the likely source of both the neutrino and the gamma rays. The dual messengers of neutrino and gamma rays also demonstrated that the blazar was indeed powerful enough to accelerate cosmic rays to their high energies. The nail in the coffin came from IceCube’s trove of historic data, which showed a burst of neutrinos coming from the same source in previous years.

IceCube’s cracking open of the enduring mystery of cosmic rays was announced with dual papers in Science magazine on July 12, 2018 and at a press conference at the headquarters of the National Science Foundation, the principal funder of IceCube, which is an international collaboration of hundreds of scientists. Take the time today to vote for IceCube’s discovery, and come back in a week to vote again in the final round.


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Grasslands among the best landscapes to curb climate change https://uwmadscience.news.wisc.edu/ecology/grasslands-among-the-best-landscapes-to-curb-climate-change/ Thu, 15 Nov 2018 20:11:16 +0000 https://uwmadscience.news.wisc.edu/?p=3256 By Bekah McBride, Nelson Institute for Environmental Studies

A study published Wednesday, November 14 in Science Advances by The Nature Conservancy and 21 scientific partners in the United States and Europe highlights the power of natural landscapes to resist climate change in the U.S.. Because grasslands, wetlands, forests and other ecosystems naturally absorb and store carbon, the study shows that protecting and preserving these features of the natural world could allow for the annual absorption of one-fifth of all U.S. greenhouse gas emissions – the equivalent to emissions from all U.S. vehicles.

While numerous studies have examined the climate-related effects of forests and agricultural lands, the new study is among the first to analyze the benefits of grasslands and coastal wetlands. This is due, in part, to the efforts of two UW-Madison co-authors: Tyler Lark, researcher in the Nelson Institute’s Center for Sustainability and the Global Environment (SAGE), and Seth Spawn, a graduate student in geography at SAGE. The two scientists led the study’s analyses of grassland conservation and restoration, and helped reveal the power of grasslands to fight climate change.

In fact, of the land management approaches assessed by the study, Lark and Spawn were able to demonstrate that maintaining grasslands is among the most cost-effective and scalable solutions to mitigating climate change. Grassland is categorized as any managed or natural area dominated by herbaceous or non-woody vegetation, like tall grasses and prairie plants, and these landscapes are well-known for their ability to absorb and store carbon in roots and soil.

A goldfinch perches on amid a sea of flowering prairie dock, purple gayfeather and rattlesnake master plants at the Curtis Prairie at the University of Wisconsin-Madison Arboretum

A goldfinch perches on amid a sea of flowering prairie dock, purple gayfeather and rattlesnake master plants at the Curtis Prairie at the University of Wisconsin-Madison Arboretum (Photo by Jeff Miller/UW-Madison)

“We’re really excited about this study, as it brings together leading expertise from all these individual climate solution pathways – from forest and fire management to cover crops and wetlands, and for the first time lines them up, allowing us to compare apples to apples,” says Lark. “It reveals what the priorities are and encourages a united effort by showcasing what can be accomplished, collectively. It’s a great example of something we could learn only by breaking out of traditional research silos and reaching across scientific disciplines.”

To study the specific effects of grasslands on the atmospheric carbon budget, Lark and Spawn combined data from several sources, including satellite imagery. With it, they built modeling tools to assess where grassland is being lost or converted to other types of landscapes and to determine how much carbon moves into the atmosphere as a result. Using this information, they calculated the overall cost and carbon sequestration achievable through grassland conservation and restoration throughout the U.S..

“At a time when we increasingly see and feel the negative effects of climate change and the challenges it poses, this research squarely focuses on the solutions and opportunities we have on hand to mitigate climate change,” Lark explains. “What we found is that there are a number of relatively cheap and easy solutions, such as maintaining and restoring grasslands and forests, that are win-wins for producers and land managers as well as society and the environment.”

A bumblebee pollinates flowers of a blossoming buckeye tree at the University of Wisconsin-Madison Arboretum. (Photo by Jeff Miller / UW-Madison)

For instance, maintaining grasslands near agricultural fields can boost crop production, Lark says, because grasslands promote biodiversity, support pollinators and host predators that can help suppress potential pests. They also help improve biodiversity, soil health and water quality.

However, other studies show that grasslands are disappearing from the landscape of the U.S.. Some estimate grasslands are being lost at a rate of more than one million acres per year and as much as 28 percent of the carbon stored in grasslands may subsequently be released into the atmosphere.

“Carbon emissions are costly to society” Spawn says. “As the primary cause of global climate change, these emissions can be detrimental to agricultural productivity and human health. Keeping grasslands on the landscape and their carbon in the ground can therefore be beneficial to everybody.”

The new study also highlights the benefits and potential of cover crops to combat climate change – grains, grasses or legumes planted alongside or in rotation with a cash crop like corn or soy. Cover crops are not meant to be harvested, but instead offer a natural solution to issues such as soil erosion, weeds and pests. Cover crops were shown to help with carbon sequestration and are another viable way to reduce carbon in the atmosphere where maintaining grassland is not possible.

“We tend to think more about technological solutions to climate change,” said Spawn. “But this study demonstrates that low-cost, scalable solutions can be readily achieved by tweaking the ways we manage our lands.”

This realization has been significant for cities and states looking to mitigate climate change on a budget. At the Global Climate Action Summit hosted in San Francisco September 12–14, 2018, scientists and public leaders met to discuss these kinds of solutions and brainstorm other ways to keep global temperature increases below the two degrees Celsius set forth by the United Nations Paris Agreement. The study was also presented at that summit.

“With the significant loss of grassland on an annual basis, we’re not yet headed in the right direction and every day that we don’t act, emissions continue,” says Lark. “Fortunately, we now know the impact of this and other natural climate solutions; so it’s time to begin implementing.”

To learn more about climate change mitigation potential and the cost of each select pathway in your area, check out the latest tool from The Nature Conservancy and other Nature4Climate partners at: https://nature4climate.org/u-s-carbon-mapper/

How to make an open-source, computerized map of the brain https://uwmadscience.news.wisc.edu/biology/how-to-make-an-open-source-computerized-map-of-the-brain/ Fri, 09 Nov 2018 16:50:25 +0000 https://uwmadscience.news.wisc.edu/?p=3246 This post was contributed by Mason Muerhoff, who is the Associate University Relations Specialist for the Waisman Center. 

In search of a way to improve how scientists analyze brain images, researchers at the University of Wisconsin–Madison Waisman Center decided to build a brain.

Or at least, a brain model.

Waisman Center senior scientist Alexander Converse and colleagues from several international universities recently published a rhesus macaque brain atlas aligned to a magnetic resonance imaging (MRI) template. The result is a three-dimensional, computerized map of the rhesus brain.

Senior scientist Alexander Converse used PET scans to analyze how the brain works.

Senior scientist Alexander Converse used PET scans to analyze how the brain works.

The map, Converse says, offers a tool for comparison for the positron emission tomography (PET) scans that he conducts in his research. Scientists use PET scans to reveal how organs and tissues in a subject are functioning.

“I’m really interested in how the whole brain works, and how it relates to behavior,” Converse says, and so far, he has used the new tool to pinpoint regions in the brain where specific activity is recorded during PET scans.

“It’s just so cool that with PET we can do this dynamic modeling and watch these radiotracers that have really exquisite biochemical specificity,” says Converse, referring to the slightly radioactive materials that the PET scanners track.

The new tool has both geographical and functional uses, Converse says, depending on how it’s employed. But it may also provide insights into the functional connectivity of the brain, enabling researchers to investigate how rhesus neurochemistry interacts with brain activity visible by functional MRI (fMRI).

Rhesus brains are approximately 15 times smaller than human brains, Converse says, but “the lay of the land is similar, so these different regions that we are interested in have a lot of homologues between the two species.”

The atlas is composed of regions of interest that have already been widely studied, Converse says, and he and his colleagues – hailing from Canada, Germany, and the Netherlands – made their National Institutes of Health-funded study data open source; the set of 200 brain regions is available for anyone to download.

The map was created using an existing set of digital slices of rhesus brains used by a wide variety of researchers and considered to be the gold standard anatomical reference. That set, called the Paxinos atlas, used 45 micron-thick slices – smaller than the width of a human hair – of the entire rhesus brain at half-millimeter intervals to develop digital versions of each slice.

Jeff Moirano, a graduate student in medical physics and lead author of the study, combined this highly-detailed anatomical Paxinos atlas with an MRI template. The template was created by Donald McLaren, who at the time was a graduate student in the lab of Sterling Johnson, Waisman Center affiliate and professor in the department of medicine. It combined 112 rhesus MRIs.

Moirano placed the slices one after another from front to back in a computer program, smoothed out any misalignments between neighboring slices, and used special algorithms to fill in any gaps that were left in the program.

He then performed the three-dimensional alignment by matching the gray matter regions of the rhesus brain – areas made up of mostly nerve cell bodies and dendrites –in the Paxinos slices to the gray matter regions in the MRI template.

The team used both qualitative and quantitative methods to measure the accuracy of the 3D map. Comparisons from the map to hand-drawn atlas sketches showed that the regions aligned well. Quantitatively, Converse tested the atlas against MRI and PET source datasets, again showing good alignment.

The product?

These colorized images of the brain reveal each individual region.

These colorized images of the brain reveal each individual region.

“This beautiful picture, this map with these multi-colored regions lined up with the right parts of the MRI,” says Converse. “Once you’ve got this 3D object, and you’re happy with it, then in the computer you can slice it any way you want.”

This work was primarily funded by the NIH grant R21EB004482, with additional support from R01AA012277, P50MH100031, and U54HD090256. It was also funded by JS McDonnell Collaborative Research Grant 220020255.

How the new UW buildings will transform campus https://uwmadscience.news.wisc.edu/technology/how-the-new-uw-buildings-will-transform-campus/ https://uwmadscience.news.wisc.edu/technology/how-the-new-uw-buildings-will-transform-campus/#comments Fri, 02 Nov 2018 17:51:04 +0000 https://uwmadscience.news.wisc.edu/?p=3228 No matter where you are, you can’t help but notice the new buildings slowly rising above the streets of University of Wisconsin-Madison’s campus. These new spaces are poised to enrich campus life for both students and faculty by providing new opportunities for education, culture and recreation to all on campus — and they wouldn’t be possible without cutting edge technology.

The Meat Science and Animal Biologics Discovery Building will provide new meat processing and education opportunities to many on campus. Photo courtesy of the department of meat sciences.

Meat Science and Animal Biologics Discovery Building:

Situated between the Veterinary Medicine building and the Natatorium, the new home for UW–Madison’s Meat Science program seeks to vastly improve the meat processing and teaching facilities currently on campus.

“This is the most complex building that the state has ever built,” says Jeff Sindelar, associate professor in the Department of Animal Sciences.

Using new technologies like blast freezing and pass-through smokehouse ovens, the building is designed to operate under Federal (USDA) meat processing requirements. Students can observe and learn about the process in the specially-designed lecture halls.

The two lecture halls face each other with a demonstration cooler in the center between them, allowing for demos ranging from carcass evaluation to sausage making to be performed. Large glass panes allow observers a view into the cooler, which is equipped with an AV system so students in the hall can speak with the lecturer inside. Rolling camera carts will be used to display images and video of the demonstrations to students.

Housing a meat processing plant with meat processing and teaching components in a single building can create significant sanitation challenges, which is why the building is sectioned into spaces with varying degrees of access. To maintain food safety practices, only certain individuals will have access to meat processing areas. Even the building’s air-handling system is designed to push air from the cleanest areas of the building to the dirtiest, ensuring that airborne pathogens cannot spread outward from the animal processing areas.

The Meat Science program works with many schools and departments to provide research materials, and at any stage of the process, researchers can collect biomaterial samples.

The second floor contains a shared research lab, and a new retail store will be opened called Bucky’s Varsity Meats, which will sell various fresh and processed meat products like steaks and sausages.

The building is scheduled for occupancy in early March 2019 with a grand opening on April 12th.

The Hamel Music Center will elevate music performance events for UW-Madison’s school of music. Photos courtesy of the Mead Witter School of Music.

Hamel Music Center:

Live music seems to be surging in popularity among Madisonians these days. New venues like the Sylvee and existing ones like the Orpheum and Majestic theaters bring in brilliant acts every year. And now, a new kind of performance center is under construction on campus, one specifically designed for the needs of UW–Madison’s Mead Witter School of Music. Located at the corner of University Avenue and Lake Street, the new Hamel Music Center is designed with three acoustically-isolated performance areas, each serving a different function.

The primary concert hall holds over 600 listeners and is designed with unique circular insets in the walls to aid in sound deflection. Some of the circular cutouts actually pass the sound into reverberation chambers that flank both sides of the concert hall. These chambers are designed to increase sound reverberation for listeners, which creates a wider soundstage and better listening experience for patrons.

The large number of surfaces the sound can reflect off lets listeners hear sound coming from all directions of the hall, creating an enveloping experience which draws the audience into the music.

Also featured in the Hamel Music Center is the Collins Recital Hall, which has over 300 seats and is suitable for slightly smaller performances. Finally, a large-ensemble rehearsal hall and recording room is situated on the southwest corner of the building, which features a large corner window that allows sidewalk-goers to view the music performance inside.

The primary concert hall contains 641 seats and features large circular cutouts in the walls to aid in sound dispersion.

Having three music halls within one building not only creates a spatial challenge but also a sonic one — the architect and acoustician wanted to ensure each performance room was acoustically isolated from the others. This is done by essentially constructing three buildings in one, and ensuring that no hard surfaces — which could conduct vibrations to other parts of the buildings — exist between them. The walls are separated using an acoustic joint, which is a two-inch gap surrounding each hall to isolate them.

“Having no rigid connections between rooms is incredibly important for a building like this,” says Brian Heller, the facilities director for UW–Madison’s music school.

And how do you go about creating a performance hall that’s built on one of the noisiest intersections on campus?

The answer revolves around the massive concrete, accordion-like walls that surround parts of the building. These walls are 10 to 12 inches thick and are key for repelling the roaring engines and blaring sirens passing outside.

The Hamel Music Center is funded entirely through donors and is scheduled for opening in Spring–Summer 2019.

The Nicholas Recreation Center features abundant natural light and vastly expanded fitness areas. Photos courtesy of RecSports.

Nicholas Recreation Center:

When the university put out a 2014 referendum to student voters on whether they approved of replacing the old SERF, it passed with overwhelming support. Students wanted updated and expanded workout spaces — and their input was crucial to the architects of the new building.

“Students are used to technology at this point, and they’ll expect that when they come into the new building,” says John Horn, director of RecSports. “Everything we are doing has a technology-first theme to it.”

Each piece of cardio equipment will be equipped with TV screens, and the building will provide opportunities for users to track their workouts with technology within the facility.

The Nicholas Recreation Center is built on the site of the old SERF building, and increasing the recreation area by six times on the same footprint presented a challenge to the designers.

“Given that we only had the same city block of space, our goal was to build up,” says Horn.

With five levels of activities, the designers had to maximize the available vertical space. Directly above the Olympic-sized swimming pool and separated by an acoustic ceiling sit six full-sized basketball courts, to accompany two more courts on the ground level.

The Nicholas Recreation Center contains five levels of recreation and competition spaces.

To help add even more available space, one-third of the main pool is equipped with a movable floor.

“If we want extra space for a fitness group we can raise the floor out of the water, and if we’re doing a youth swimming lesson we can raise the floor to 12 inches or a couple feet,” says Horn.

The builders are aiming for a late fall 2019 opening, and it will likely become one of the most prominent buildings of the southeast neighborhood of campus. And according to Chancellor Rebecca Blank, it will enhance student life for the next generation of students.

“It’s difficult to imagine a project with more of an impact across campus. To our students, the Nick is going to be a place to form healthy habits that we hope will last them for a lifetime, as well as to meet new friends, cross paths with people they might not otherwise know, and learn some new skills,” said Chancellor Blank at the groundbreaking ceremony. “All of those things are vital for preparing them for healthy and fulfilling lives.”

Header photo by Bryce Richter/UW-Madison. 

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As a new semester starts, UW faculty discuss a common college menace: mono https://uwmadscience.news.wisc.edu/health/as-a-new-semester-starts-uw-faculty-discuss-a-common-college-menace-mono/ Mon, 01 Oct 2018 08:00:01 +0000 https://uwmadscience.news.wisc.edu/?p=3217 This summer, I started running. Partly because it seemed healthier than lifting, but also because summer gym memberships are expensive. However, being an inexperienced runner, and balancing multiple jobs, I often went for runs at odd times, like at night or on days where the heat index topped 100 degrees.

I once went for a run on a day so hot that I came down with heat exhaustion — leaving me in an extremely weakened state. In addition to this weakness, I quickly began to show symptoms of mono in the following days, and my symptoms persisted for close to four weeks. To learn more about my illness, I spoke with Eric Johannsen, a University of Wisconsin–Madison professor of medicine that studies the Epstein-Barr virus behind the symptoms of mono.

Infectious mononucleosis, better known as mono, is an extremely common disease that overwhelmingly infects adolescents and college-aged adults. With a new semester — and new opportunities for mono to spread — upon us, Johannsen shares some insight into this scourge of college campuses.

“The most important thing to keep in mind with Epstein-Barr is it’s a herpes virus, so they do establish lifelong infections,” says Johannsen. “They’re able to do that because they enter the nucleus of the cell and establish themselves as episomes.”

Episomes are strings of foreign, circular DNA that replicate independently inside of a host cell. EBV can trick the host cell into replicating its episome and then hitch a ride on the host chromosome when the cell divides.

Since EBV is a member of the herpes virus family, it shares common elements with its notorious kin. Not only does the virus remain within the host for their entire life after infection, but it can also reactivate, just as the chickenpox virus can later reactivate to cause shingles. And like other herpes viruses, EBV is one of the most common infections around the world.

Mono infection is most commonly transmitted through saliva — mostly through kissing but also through shared glasses or intense coughing— which is partly what makes it so common among college students.

But what does mono typically look like in patients? According to UW–Madison Chief Health Officer William Kinsey, students commonly see headaches, sore throat, and a fever that gradually gets worse over time.

“Unfortunately there are students that are sick for two, three or even four weeks when they get mono,” says Kinsey.

When looking to prevent the disease, he advised that students focus on washing their hands, adding that “it really works to prevent the spread of viral diseases.”

And EBV infection is an incredibly common disease, with up to 95 percent of adults carrying the virus, according to Johannsen. In fact, all herpes viruses are widespread — the chickenpox (varicella) virus reached a peak of four million people per year before the vaccine was released in 1995. Since then, varicella incidences have declined by 79 percent.

For the herpes virus family, vaccines are only available for chickenpox. Researchers are working to develop an EBV vaccine but have to contend with possible side effects.

“The problem with EBV is there is a very low chance it can cause lymphomas, and its associated Hodgkin’s disease,” says Johannsen. Since the virus is technically a carcinogen in its live form, Johannsen explains that “no one is going to make a vaccine with a live attenuated virus,” for concern it might trigger cancer.

Eric Johannsen MD is a Virology Program Member at the Carbone Cancer Center.

Eric Johannsen, M.D. is a Virology Program Member at the Carbone Cancer Center. Photo by the McCardle Laboratory for Cancer Research.

If you think you may have mono, it is important to get tested to confirm its presence, as the symptoms involved with the disease are similar to other health complications like strep throat, HIV infection, and other herpes viruses.

There are a few different ways to test for mono. The most common test used is the mono spot test, though it isn’t perfect.

“If the mono spot test is positive, we’re done, and we can say you have mono,” says Johannsen. “But if its negative, we’re not done — you can’t rule out having the disease.”

Because of this imperfection, the United States Center for Disease Control does not recommend the spot test for general use. Another test commonly used is a blood antibody test, in which a blood sample tested for the presence of antibodies against EBV.

Testing often isn’t done until after a week or two of symptoms are seen, so it’s important to be prepared in case you do end up missing considerable amounts of work or school.

“It’s reasonable to let professors know ahead of time if you’re experiencing symptoms,” says Kinsey.

When I first began showing symptoms, my doctor thought it was strep throat. At the time this was the only symptom I was showing, but things quickly worsened and before long I had every symptom in the book: exhaustion, chills, high fever, swollen lymph nodes, and a lack of appetite. I ended up losing close to 20 pounds just from having mono, and my doctor told me my experience was fairly typical.

Johannsen adds that a vaccine that limits the symptoms of mono could be useful.

“I think the bigger challenge is that because EBV-associated cancers are so rare, if you can give a vaccine that allows you to handle primary infection better, that’s probably a legitimate reason to make the vaccine,” he says. “We think it could also further reduce the rate of cancer.”

Header photo by Creative Commons.