Adapted from original story by Brita Larson, Center for Healthy Minds:
We can feel stress in the body through common sensations: sweaty palms, racing heart and shallow breathing.
Some people cope with signs of stress in their lives by ignoring it. Some may not recognize these as signs of stress. What if the key to well-being during stressful periods in our lives involved syncing our physical and mental experiences of stress?
“This study suggests that it’s good to tune into your emotions and your body because it seems like the more those two things track together, the better off you are,” says Sasha Sommerfeldt, a graduate student at the Center and lead researcher on the project. “In other words, it’s not just whether someone experiences more stress or less stress, or whether their heart rate increases a lot or a little under stress. Rather, it is a person’s awareness of his or her stress levels and how consistent that is with heart rate that is linked to psychological and physical well-being.”
The team analyzed data from 1,065 participants in the Midlife in the United States (MIDUS) study, a longitudinal effort looking at well-being as adults age. Participants completed a series of stressful computer tasks, including a mental math task and a color identification task.
Before, during and after the tasks, researchers measured participants’ heart rate and asked them to rate their stress on a scale of one to 10.
After the participants completed the stress tests, researchers compared each person’s heart rate to the stress levels they reported and found that some people’s stress levels aligned with their heart rate better than others.
To examine the link between stress-heart rate coherence and people’s emotional well-being, researchers used psychological questionnaires focused on well-being, depression, anxiety and coping as well as blood samples measuring inflammation markers. Researchers found that people with greater stress-heart rate coherence had fewer symptoms of anxiety and depression, greater overall psychological well-being, and lower levels of inflammation.
Sommerfeldt says it’s unclear which comes first: good stress regulation or high stress-heart rate coherence.
“If people can recognize that they’re stressed and have a good relationship between their bodies and stress levels, then maybe it’s less likely that their stress will spill over and affect their mood and behavior,” says Sommerfeldt. “At the same time, if you have higher levels of emotional well-being, then you’re probably better at regulating your emotions. For example, you might say: ‘Yes, I’m stressed, but I know what to do with it and I can accept my stress.’ You use less denial in coping with it.”
Sommerfeldt says teaching coherence could begin with helping a person recognize their emotions, which might be an important part of the therapeutic process. Future research may explore whether coherence might be enhanced by interventions or practices like mindfulness or cognitive behavioral therapy. She says that for now, researchers do not know whether these findings can be applied to other emotions, since the team focused only on stress.
Richard Davidson, the senior author of the study and director of the Center for Healthy Minds, is excited about these new findings.
“The data support the potentially beneficial role of awareness in psychological well-being and physical health,” Davidson says. “And since we know that awareness can be enhanced through training, it raises the possibility that stress-heart rate coherence can be learned.”
This work was supported by the John D. and Catherine T. MacArthur Foundation Research Network, the National Institute on Aging (P01-AG020166, U19-AG051426), the NIH National Center for Advancing Translational Sciences (NCATS) Clinical and Translational Science Award (CTSA) program (UL1TR001409 [Georgetown], UL1TR001881 [UCLA], 1UL1RR025011 [UW]). Sommerfeldt was also supported by a University of Wisconsin – Madison University Fellowship, and a Pre-Doctoral Fellowship through the Training Program in Emotion Research (NIH T32MH018931-28).
Imagine you’re a plucky, golf ball-sized squid swimming in the clear blue ocean on a moonlit night. Your round shape means a distinctive shadow casts on the ocean floor thanks to the light of the moon, and predators are looking for prey by night. How do you, a small piece of prey without a protective shell, hide yourself in a sea full of predators?
If you were a Hawaiian bobtail squid, you’d employ a process called counter-illumination to create a natural camouflage in moonlit waters. The light — produced by the mutualistic bacteria Vibrio fischeri within the squid — is cast downward to eliminate the shadow and prevent predators from seeing a silhouette of the squid when looking up.
University of Wisconsin–Madison Professor of Medical Microbiology and Immunology Mark Mandel studies the genetic relationship between the bacteria and their squid hosts. But he didn’t start his scientific career studying bacterial camouflage. When he was working toward his doctorate, Mandel examined genetic regulation in E. coli before deciding to dive further into the relationships microbes develop with other organisms.
“The bobtail squid is special because it has just one bacterium that colonizes in a dedicated organ in the animal, so that allows us to look at the natural processes that occur,” Mandel says. “Our main approach is to mutate the bacteria and look at what changes in the colonization. If it does change, it’s likely the gene we interrupted was important for colonization.”
Bobtail squid in the wild depend on these bacteria for survival. The bacteria in turn receive nutrition and protection from the squid, as well as an opportunity to reproduce.
At dawn, most of the bacteria in the squid’s specialized organ are expelled into the seawater, in a process called venting. This sounds unfortunate for the microbes — but it allows them to be picked up by squid hatchlings and start reproducing inside their new host.
This venting process saturates squids’ nearby waters with these microbes, so the environments in which they live will contain higher concentrations of bacteria than other, squid-free waters.
The few bacteria that remain in the nocturnal squid reproduce during the day so that by nightfall the bacteria are ready to provide light again. The next morning, the cycle starts over.
One key mechanism that Mandel’s lab examines is a population-sensing process called quorum sensing, which many microbes, including Vibrio fischeri, use to determine when the bacteria have reached a certain population.
Once the Vibrio fischeri reach a high-enough density within the squid, they collectively turn on their light all at once, Mandel explains. This population-sensing process was first discovered in Vibrio fischeri in the 1970s, but also occurs in pathogenic microbes like Pseudomonas aeruginosa, which often infect the lungs of people with cystic fibrosis. When these pathogens reach a certain density, they begin attacking the immune system of their hosts.
Most research into the squid-Vibrio mutualistic relationship has focused on a single strain of Vibrio, but Mandel’s most recent work has evaluated several strains of the bacteria to further understand genetic differences and regulation.
In a recent paper, Mandel’s lab examined how the bacteria form a biofilm, which is a mass of bacterial cells that gives protection from toxic substances released by the squid.
“We showed that the biofilm can be regulated in three different ways in different strains,” says Mandel. “One strain doesn’t have the regulator gene and another strain has the regulator but it doesn’t work because of a mutation.”
The biofilm regulator gene RscS controls biofilm formation. In the lab, this activation can be artificially stimulated using a process called overexpression – where the gene is highly active and creates a greater number of proteins than it normally would. Alternatively, the researchers can remove the bacteria’s ability to form a biofilm and see what happens.
“We now understand the necessity of the biofilm in bacteria, because when we mutate them and they don’t form this biofilm, they don’t colonize very well,” Mandel explains.
Another application for Vibrio fischeri involves biomaterial for the military: the luminescent bacteria contain reflectin proteins that allow them to direct light in a specific direction, and the military is looking at using these specialized proteins for use in alternative camouflage materials.
The study of Hawaiian bobtail squid and its bacterial companions involves a great deal of genetic research. Vibrio fischeri’s similarities to how other bacteria colonize their hosts have led to a wide range of other findings.
Thanks in part to Mandel’s lab, we now understand how this unlikely partnership helps these little round squid hide from predators. Without protective shells, these spotted cephalopods could easily struggle out in the vast ocean ecosystem – but they get by with a little help from their bioluminescent friends.
More and more bacteria are becoming resistant to traditional antibiotics, and this resistance has become a focal point of research at many universities. Common infections like pneumonia, tuberculosis and salmonellosis are becoming harder to treat with today’s antibiotic medicines – creating an urgent need for new antibiotics.
Tiny Earth was launched in June of 2018 to address this problem. Jo Handelsman created the program at Yale University and soon brought it to the University of Wisconsin–Madison when she returned to direct the Wisconsin Institute for Discovery.
“The program’s goals are intertwined because it is participating in addressing a global health problem that is so inspiring to the students,” says Handelsman.
The mission of Tiny Earth is twofold: to address the antibiotic crisis and to counter the shortage of professionals in science, technology, engineering and math, or STEM, disciplines. To accomplish this, the initiative offers a class to undergraduate students that allows them to gain substantial laboratory experience while exploring their scientific interests.
“Not only are students learning scientific research practices, they’re also actually working toward solving a major health crisis,” says Josh Pultorak, WID researcher and instructor for the undergraduate Tiny Earth course. “Recruiting students to focus on the issue is a way to collect a lot more data useful for compound discovery while also being educationally beneficial.”
In the course at UW-Madison, students are encouraged to develop their own ideas for finding which variables influence antibiotic production in bacteria. The students form small groups and choose a variable to study. One group in this semester’s class decided to manipulate the temperature at which the bacteria are cultured, while others introduced stimuli like caffeine to investigate how bacteria react.
One student group decided to manipulate the temperature in which the bacteria were cultured. Photo by Tyler Fox.
At each biweekly meeting, the students return to their bacterial cultures and note any new developments. Their findings will be combined into their final research paper and poster report, which is displayed at the Introductory Biology research symposium at the end of the semester.
The course, which is offered and supported by the Departments of Integrative Biology and Plant Pathology under Professor Doug Rouse, is composed of freshmen and sophomores, and it satisfies their Independent Project requirement for Introductory Biology (Bio 152). For many of the students, the class presents a unique opportunity to explore their interests in research and the medical field early in their college path.
“It’s a great foot in the door for medical school, and it’d be cool to make a notable finding while in this class,” says Alec Brenner, a sophomore in the spring semester class.
Many of the students were enthusiastic about how the class is arranged, sharing their excitement about the chance to choose their own area to focus on and gain hands-on experience in that topic. This type of instruction, referred to as Course-based Undergraduate Research Experiences (CUREs), has proven to be more effective for teaching science than traditional lectures.
“Rather than sitting and listening passively to a lecturer, the students are actively participating and having opportunities to try new things, fail and try again,” says Pultorak. “The students are getting more comfortable learning around their peers and asking questions.”
Josh Pultorak, instructor for the course, is a WID researcher and thoroughly enjoys teaching students critical thinking and laboratory skills. Photo by Emma Byers.
Pultorak adds that the CURE model has been successful in encouraging students to pursue additional research opportunities and careers after they complete their coursework.
“I’m hoping this class can propel me into more research on campus,” says Jessica Dable, a sophomore. “I’m on the pre-health track, and the skills I’m learning are diverse and applicable to many other areas of science.”
Ultimately, the exploratory research of the students contributes reams of data to the Tiny Earth project, and the students gain valuable lab experience which they can take into their future careers as scientists and STEM professionals.
“All the institutions that are implementing Tiny Earth are doing antibiotic discovery research, but here at UW–Madison, we’re taking it one step further in that the students are asking research questions and making their own discoveries,” says Pultorak. “And there’s a growing number of students that have completed the course and reported that they really enjoyed it, so we’re seeing some pretty positive word-of-mouth feedback too.”
Give most kids a basic microscope and a leaf or a drop of pond water, and they are in awe of the, well, microscopic patterns and organisms they can now see. Give a cell biologist a transmission electron microscope (TEM), and they can understand how structures within cells are organized – and how changes in the structures contribute to diseases.
Now, thanks to the efforts of several University of Wisconsin–Madison researchers and funding from the Howard Hughes Medical Institute (HHMI), UW–Madison scientists will soon have a cutting-edge new TEM. It will augment an older version of the technology currently housed in the Materials Science Center that lacks some of the new features that are helping to revolutionize biological electron microscopy.
“What we were missing was more capability for 3D TEM for people imaging tissues or organs, which for biomedical research is essential to understand the cellular basis of disease,” explains Marisa Otegui, UW-Madison professor of botany and genetics.
Microscopy access on the University of Wisconsin-Madison campus is certainly not lacking. Between powerful light microscopes that allow researchers to monitor living samples and the new Cryo-electron microscopy (CryoEM) initiative that allows researchers to see the three-dimensional (3D) architecture of molecules down to individual atoms, a microscope exists to answer nearly any research question.
For example, Otegui’s group studies how signaling factor proteins on the surfaces of plant cells are degraded inside the cell when it is time to turn the proteins off. The cells have protein escorts (no really, they are named the ESCRT proteins) that help internalize the surface proteins and send them to a sorting compartment called an endosome. This process is carefully regulated by plant and animal cells. When it goes wrong in people, it can lead to diseases such as cancer or neurodegenerative diseases.
TEM shows structures that would not be visible at the resolution of light microscopy. Using TEM, Otegui and her lab group, in collaboration with Ahlquist’s group, found that endosomes in plant cells string together, rather than exist separately. From Buono et al, Journal of Cell Biology, 2017
“Just last year, we used electron microscopy to get three-dimensional information and show that these endosomes are completely different than we expected,” Otegui says. “We had the completely wrong idea of what these endosomes looked like, so just having the basic level of understanding their structure helped us understand the endosome and the cellular machinery.”
But the $1.3 million price tag for a new TEM was more than any individual lab on campus could afford. This is where HHMI comes in.
By stacking TEM images from sections of the plant cell, a 3D rendering is generated.
In 2016, the organization announced funding for “transformative technologies,” for which any of its members could apply and use toward purchasing cutting-edge instrumentation. Three HHMI investigators on campus – neuroscience professor Ed Chapman and Morgridge Investigators Paul Ahlquist and Phil Newmark – wanted to apply for the funds, but they were not sure on what, exactly.
“Ed asked a group of people on campus: ‘What do we want to request? What instrument will be a game changer for our labs and for campus?’ And we decided to request a new 3D TEM,” Otegui recalls. “Ed, Phil and Paul agreed to support the instrument that the group has identified as our priority. It was such a generous way to recognize not only what they needed individually but also what the campus needs.”
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)
“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.
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
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.
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. (Photo by Bryce Richter /UW-Madison)
Liesch delivers some more bad news: “Ticks overwinter down amongst leaf litter, meaning that they should be well insulated at this point.”
Lone Star Tick female (Amblyomma americanum) - Vimeo
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.
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 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.
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.
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 1900s. 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. 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 diseased branches and infected bark is burned. Chemical fungicides can also be applied to 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 with help of Japanese scientists, 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 elm clones. 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 Asian 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.
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.
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.
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 wold 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.