UWMadScience https://uwmadscience.news.wisc.edu Behind the science & research that makes the news at UW–Madison Fri, 31 Jan 2020 19:51:01 +0000 en-US hourly 1 https://wordpress.org/?v=5.3.2 Laser focused on Alpha Centauri https://uwmadscience.news.wisc.edu/curiosities/laser-focused-on-alpha-centauri/ Fri, 31 Jan 2020 19:50:33 +0000 https://uwmadscience.news.wisc.edu/?p=3472 Shine a laser pointer at a cat, and the cat may see and try to catch the light, but it certainly won’t feel it.

What if that light were not a milliwatt laser, but one hundred trillion times stronger — and the cat were essentially weightless, floating in space?

“Normally, optical forces are zero — you don’t feel light pushing on you. But with a very strong laser on a very light object, the forces start to be measurable and significant, and we are interested in studying those forces,” says Victor Brar, assistant professor of physics at the University of Wisconsin–Madison. “A new idea called laser sailing is one area where these optical forces become relevant.”

Laser sails are a proposed type of spacecraft that could take us to new stars, including our closest neighboring star system, Alpha Centauri, and then send images back to Earth. But Alpha Centauri is four lightyears (nearly 24 trillion miles) away. A conventional spacecraft would take around 100,000 years to reach it. Laser sailing could reduce travel time to as little as 20 years.

a cartoon of the 3D donut laser, looking a bit like a volcano, is shown pointed toward the disc-like laser sail. In three panels, the sail is shown moving outside the exact center of the beam, or tilting so as to not be perfectly perpendicular to the beam.

The laser sail in space (grey circles) is propelled by the optical force of a laser pointed toward Alpha Centauri from Earth, (color gradient volcano-like structure). The center, completely opaque to the laser, contains the camera and equipment to transmit photos back to Earth. The outer ring is comprised of a ‘metasurface’ that can self-correct to remain in the laser beam, even when it shifts to the side (middle image) or tilts (right image). Modified from Siegel et al., ACS Photonics

By aiming 100 gigawatts of laser power at our neighboring star system, then placing an ultralight, four-by-four meter laser sail in the beam’s path, the optical forces would be strong enough to propel the spacecraft at one-fifth the speed of light.

“That’s one of the problems: there is no way to steer the spacecraft. Once it’s going, it’s going,” says Joel Siegel, a physics graduate student in Brar’s group. “We were inspired by recent interest in laser sailing to design something that traps itself in the beam.”

So Brar, Siegel and colleagues set out to design a “metasurface:” a nearly two-dimensional array of tiny silicon unit cells that are positioned across the sail so that they reflect light in a way that allows it to remain in the laser’s trajectory. When the laser loses focus — about as far away as Mars — the sail is traveling along the correct path at nearly one-fifth the speed of light.

In a study published last year in ACS Photonics, Siegel and his colleagues conducted two main sets of computational simulations to design a stable, self-correcting sail.

A schematic of the 2D sail, looking from the side,

A view from the side of the sail, with a cross-section of the laser beam. The “inverted cateye” means that the center of the sail is non-transmissive, and light that hits it perpendicular to the sail surface reflects straight back, pushing the center of the sail straight forward. The outer ring of the sail is the metasurface. Depending on the layout of the individual silicon units, light reflects at an angle. Modified from Siegel et al., ACS Photonics

In the first, Siegel used what he calls a perfect optical model: without worrying about if the metasurface could be constructed, he first wanted to find which sail parameters and laser beam configurations could combine to construct a stable sail.

“This first part was all done with a simple MATLAB program: you just calculate at each point what the optical forces are, you sum them up, you get a net force, and then you can time evolve the system using equations of motion,” Siegel says.

The calculations suggested that the best design was an “inverted cat-eye” sail deign with a “doughnut” laser (the most intense light is a circle, with intensity dissipating inside and outside the circle). Siegel could then continue to play around with beam configurations, eventually landing on conditions that produce the stability and velocity the sail needs.

“From there, we can ask, ‘If we have this specific design with these beam parameters, what gets us the best structure?’” Siegel explains. “I know exactly what the reflection profile looks like, now how do I actually make the metasurface?”

two graphs of sail simulation results of distance as a function of time are shown, with 4 lines in each graph representing the sail's location in the simulation.. The top graph looks at distance from center, the bottom graph looks at tilt angle. In both situations, some sail designs immediately fly out of the beam, but some are able to withstand slight perturbations and self-correct.

In the first set of computer simulations, different sails, represented by the different colored lines, were measured for their location with respect to the center of the laser beam (top graph) or the angle they tilted from horizontal (bottom). In both situations, some sail designs immediately fly out of the beam, but some are able to withstand slight perturbations and self-correct. Modified from Siegel et al., ACS Photonics

Siegel and his colleagues next virtually designed the metasurface, arranging those tiny silicon unit cells in various arrangements and simulated how the laser light would reflect and apply force to the sail. When they compared this metasurface to the perfect optical model, they found they were in close agreement. In other words, the self-stabilizing sail is technically achievable.

Of course, technically achievable in computer simulations is not the same as achievable in the real world. Brar and Siegel next want to construct a scaled-down version of their sail and test it in an ultrahigh vacuum chamber in the lab that mimics conditions in space. The sail also needs to be designed to not fold on itself, and to dissipate the heat from the powerful laser.

But with a good start to the sail design, and a mere 20-year travel time (plus around four years to transmit the images back to earth), it is not out of the question that Brar, Siegel, and many people alive today will see close-up images of our nearest star system in their lifetimes.

UW–Madison associate professor of electrical and computer engineering, Mikhail Kats, and research assistant Anthony Wang were co-authors of the study.

Watch Mercury transit the Sun on Monday, Nov. 11! https://uwmadscience.news.wisc.edu/astronomy/watch-mercury-transit-the-sun-on-monday-nov-11/ Fri, 08 Nov 2019 21:02:13 +0000 https://uwmadscience.news.wisc.edu/?p=3440 This is a guest post by Jim Lattis, the director of UW Space Place

Drop by the Washburn Observatory on the University of Wisconsin–Madison campus from 6:30 a.m. to noon on Monday, Nov. 11, to get a safe, rare glimpse of Mercury as it crosses the face of the Sun. This free event is hosted by the Astronomy Department and is weather permitting.

The Washburn Observatory, 1401 Observatory Dr., is located at the peak of a hill overlooking Lake Mendota. Public parking is limited. Visit the parking website to find a nearby lot or the Metro Transit website to find a convenient bus route.

In 2004 and 2012, we saw our neighboring planet Venus transit the bright disk of the Sun in the form of a small, black disk crossing the star’s face. Transits of Venus are rare, and there won’t be another until December 2117. These events are analogous to a solar eclipse, in which the Moon crosses the face of the Sun. But while the Moon can completely block the sun — creating the unique effects of a total solar eclipse — no planet’s disk can do the same.

A Mercury transit is similar to a Venus transit, but Mercury makes a much smaller disk on the face of the Sun, because it is both smaller than Venus and farther away from Earth. Another difference is that Mercury transits are much more common than Venus transits, happening 13 or 14 times per century compared to over a century between pairs of Venus transits.

Mercury transits typically occur in pairs: one in May followed by one in November, about three and a half years apart. The May transit is often skipped. The most recent transit of Mercury was in May, 2016. After this year’s event, the next Mercury transit will occur on Nov. 13, 2032.

Seen against the solar disk, Mercury’s disk is so small that a telescope is required to make it visible. In fact, it would take over 190 Mercury disks to span a solar diameter! In contrast, Venus’ disk could be seen on the Sun without magnification. The diagram shows the path that Mercury’s disk will take across the face of the Sun and gives times local to Madison.

So come out Monday to take in this special event. In case of extensive cloud cover, this event will be canceled.

We want to remind you that  aiming a telescope or binoculars at the Sun is a dangerous operation, requiring special equipment and techniques, and therefore best left to experienced observers. At the Washburn Observatory event, we’ll be able to view the transit safely.

Diagram showing the times of the 2019 Mercury transit

The 2019 Mercury transit across the Sun will start just before sunrise and end around noon on Monday, Nov. 11.


Helping doctors keep their patients strong enough to recover https://uwmadscience.news.wisc.edu/health/helping-doctors-keep-their-patients-strong-enough-to-recover/ Thu, 12 Sep 2019 15:39:39 +0000 https://uwmadscience.news.wisc.edu/?p=3427 This guest post comes to us from Jevin Lortie, a graduate research assistant in the Department of Nutritional Sciences at UW–Madison.

Just before Christmas last year, Grandma Barbara, or Ba as we affectionately call her, had finally decided to let us admit her to the hospital. She had come down with what she thought was pneumonia six months ago. She was weak, coughing and had fluid in her lungs. She had been getting progressively worse: her legs were swollen, and she had lost a lot of weight. These symptoms told us that she was actually suffering from heart failure, which is often confused with pneumonia.

By the time we got to the hospital, the concerned nurses scolded us for not calling an ambulance and whisked her to the emergency room. She was given a barrage of tests, many of which required fasting, so it was hard for her to get enough to eat during the day. I had recently joined a lab studying nutrition, and I started to worry about how her body was going to recover without enough food.

After a few days in the hospital, Ba was struggling to breathe on her own. The doctors decided she needed a breathing tube and to be put in a medically-induced coma. While unconscious, she could have been fed by either a feeding tube or IV, but it took several days for this to start. These both carry some risks and are currently only given if absolutely necessary. Yet science has begun to demonstrate that the benefits of immediate nutrition by tube-feeding may outweigh the risks. Hospitalized patients lose 1 to 2 percent of muscle per day. Therefore, a patient in the hospital for a month can lose over half of their muscle.

Nutrition does not get the attention it deserves in medical training, which makes problems like malnutrition — a lack of adequate nutrients — hard to spot. A 2006 study in the American Journal of Clinical Nutrition found that medical schools on average spend just 24 hours on nutrition, and only 30 percent have a separate nutrition course. Doctor and author Rupy Aujla says, “I’m often met with disbelief when I describe the mere 10 hours of lectures on the subject that I received during my five-year medicine degree.” A 2016 study by Marigold Castilo found that fourth-year medical interns answered only half of a series of basic nutrition questions correctly.

My new lab, led by Adam Kuchnia at the University of Wisconsin–Madison, is investigating new imaging techniques to help doctors assess nutrition earlier and more accurately so they can provide the best care for patients like Ba. Kuchnia believes this problem can be solved by modifying a technology that has been in use for years: ultrasound. “It’s an ideal modality for all patients, no matter what their condition is,” Kuchnia says.

Ultrasound works by using sound waves to create an image, which in our case shows the thickness of a muscle and if it has more fluid or fat than it should. Research is beginning to show that before there is a change in muscle mass, this fat and fluid buildup may be signs the muscle is beginning to break down. These early signs could allow us to identify muscle loss much sooner than it can be detected by physical inspection.

An ultrasound image showing the composition of a quadriceps muscle.

An ultrasound image showing the composition of a quadriceps muscle.

Identifying signs of malnutrition could help doctors evaluate whether to ask a patient to fast for another test or wait and eat dinner instead. Kuchnia wants to help clinicians with this decision, and our lab focuses on identifying and preventing malnutrition. Malnutrition is especially important during illness, as additional protein is needed to repair damaged tissues and fight infection. If adequate nutrition is not available, the body will use what is available— fat, muscle, and as a last resort, organ tissue. While stored fat can provide energy, it lacks the amino acids, the building blocks of protein, we need to build and repair cells. Therefore, if we aren’t eating protein, muscles must be broken down to help the body recover. “There are several definitions of malnutrition, but at the core of each one is loss of muscle, which is particularly bad for patients,” says Kuchnia.

Our lab’s next goal is to investigate ways to help patients when we see early muscle loss, such as more immediate tube or IV feeding or additional protein supplementation. Kuchnia says that this research “can be extended to benefit anyone. Through nutritional intervention we are hoping to maintain muscle health in order to lengthen years of quality life.”

In Ba’s case, she made an amazing recovery. But after being bedridden for a month, and a week of that spent fasting in a coma, she needed to re-learn how to do everything — including walking, dressing, and feeding herself. However, her recovery could have been helped by nutritional intervention that allowed her to maintain the muscle she had, instead of being broken down to help her body repair itself. Research from the Kuchnia lab may help implement changes in nutritional interventions, resulting in better patient success and quicker recovery times, preventing others from the same difficult recovery as Ba.

Ba at the author's wedding after recovering from her hospitalization.

Ba at the author’s wedding after recovering from her hospitalization.

CBD: what researchers and medical professionals do and don’t know https://uwmadscience.news.wisc.edu/health/cbd-what-researchers-and-medical-professionals-do-and-dont-know/ Fri, 14 Jun 2019 14:32:38 +0000 https://uwmadscience.news.wisc.edu/?p=3408 This post comes to us from departing science writing intern Tyler Fox, who graduated in May. Congrats, Tyler! And thanks for a year of great stories.

Cannabidiol, better known as CBD, is everywhere. Walgreens and CVS now offer lotions and snacks containing CBD. Local restaurants sell cocktails with CBD infusions. Brewers are adding it to their beers. The maker of Oreo and Chips Ahoy cookies is looking into incorporating it into their products.

As these products become more accessible, consumer interest continues to grow.

CBD is being credited with curing a wide range of ailments from chronic pain, post-traumatic stress disorder, insomnia, and even acne. But with all this excitement about this seemingly miraculous new health trend, how much do we really know about CBD’s effects?

“There’s a lot of claims made about CBD’s effects with low amounts of research to back them up,” says Dipesh Navsaria, a UW Health pediatrician at American Family Children’s Hospital. “What’s really important to remember about these products is that they’re entirely unregulated, which means these products don’t need proof that they do anything.”

These CBD products are now more readily available since the 2018 Farm Bill and state legislatures have allowed for wider agricultural production of hemp. Hemp is a strain of cannabis plant that contains a higher concentration of CBD but lower amounts of THC, an active ingredient in marijuana that causes its characteristic high.

CBD is a chemical compound naturally derived from the plant, which is perhaps more often associated with marijuana. But CBD is unique in how it acts on endocannabinoid receptors in humans to affect certain physiological processes. These receptors contribute to our appetite, pain sensation, mood and memory, which is why CBD products have a wide range of effects.

Only recently has the FDA specifically approved a medication containing CBD, which is used to treat rare epilepsy disorders. Beyond that, there is still too little evidence to confirm its touted effects. And with its connection to THC and marijuana production, the FDA has not yet classified CBD as a food or as a drug, so it isn’t regulated as such.

This means that supplement shops are making their own recommendations on what and how much consumers should use.

“Asking someone who sells CBD oils about how much to take can be a dangerous thing,” says Navsaria. “And we don’t have clinical trials on dosages, so it’s difficult to discuss with patients.”

Early research indicates that CBD is relatively safe, explains Natalie Schmitz, a UW–Madison School of Pharmacy researcher and former medical cannabis pharmacist at the University of Minnesota.

“It’s always better to start low and go slow with dosages, but right now the most common reported side effect with increased dosages is diarrhea,” says Schmitz.

However, without regulations, there is no guarantee that the labels of CBD products accurately represent the amount of CBD they claim. A 2017 article in the Journal of the American Medical Association found that of the 84 CBD products they tested, 26 percent contained less CBD than the label stated. And while most CBD products claim not to contain any THC, 21 percent of the products tested positive for the psychoactive THC compound.

This means that athletes who may be interested in using CBD in sports medicine applications should be very cautious in which products they choose.

With these concerns, Schmitz advises patients that are interested in trying CBD to do so cautiously and with frequent check-ins and communication with their healthcare providers.

Research confirms that long-term exposure to THC can affect memory and cognition, but these long-term studies haven’t yet been performed with CBD, which makes it more difficult for medical professionals to recommend its use.

While the FDA works to more closely regulate CBD products, it’s important to remember that there is no miracle drug. With wide and untested claims made about the compound, history reminds us that there is no cure-all. With every medication there are limitations and for CBD, we just don’t know them yet.

“Prescription medications cost what they do because we know what they’ll do,” says Navsaria. “I hope people wait to see how the research clarifies what CBD actually does.”

Greater well-being when awareness of stress aligns with the heart https://uwmadscience.news.wisc.edu/neuroscience/greater-well-being-when-awareness-of-stress-aligns-with-the-heart/ https://uwmadscience.news.wisc.edu/neuroscience/greater-well-being-when-awareness-of-stress-aligns-with-the-heart/#comments Fri, 10 May 2019 21:18:09 +0000 https://uwmadscience.news.wisc.edu/?p=3400

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?

For the first time, a study from researchers at the Center for Healthy Minds published in Psychological Science suggests that people whose reported stress levels aligned more with their heart rate — called “stress-heart rate coherence”— also had higher levels of psychological well-being and lower levels of inflammation.

Sasha Sommerfeldt2

“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).

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How charming squid and glowing bacteria make a match in Hawaiian waters https://uwmadscience.news.wisc.edu/animals/how-charming-squid-and-glowing-bacteria-make-a-match-in-hawaiian-waters/ Wed, 01 May 2019 19:53:36 +0000 https://uwmadscience.news.wisc.edu/?p=3392 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.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.

Header photo by Chris Frazee. 

Tiny Earth: Advancing antibiotic discoveries through undergraduate research https://uwmadscience.news.wisc.edu/biology/tiny-earth-advancing-antibiotic-discoveries-through-undergraduate-research/ https://uwmadscience.news.wisc.edu/biology/tiny-earth-advancing-antibiotic-discoveries-through-undergraduate-research/#comments Wed, 27 Mar 2019 18:33:41 +0000 https://uwmadscience.news.wisc.edu/?p=3382 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.

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 laboratory skills. Photo by Emma Byers.

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.”

Header photo by Kim Leadholm. 

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Seeing things more clearly, thanks to campus-wide microscopy effort https://uwmadscience.news.wisc.edu/uncategorized/seeing-things-more-clearly-thanks-to-campus-wide-microscopy-effort/ Wed, 20 Feb 2019 22:46:59 +0000 https://uwmadscience.news.wisc.edu/?p=3336 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.

four panels of TEM images are shown from plant cells. Vesicles are circular, and have bridges between them, showing they are connected

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.

A 3D image is shown of the circular vesicles and how they are connected

By stacking TEM images from sections of the plant cell, a 3D rendering is generated.

The organization recently 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.”

Crucial to securing the money from HHMI was an additional $700,000 in contributions from campus partners to cover the installation and upkeep of the microscope. These include: The Morgridge Institute for Research, the Office of the Vice Chancellor for Research and Graduate Education, the School of Medicine and Public Health, the UW Carbone Cancer Center, the College of Letters & Sciences, the Department of Biomolecular Chemistry, and the Laboratory of Cell and Molecular Biology. Otegui and colleagues on campus secured the campus funding and submitted the HHMI proposal in under a month — an impressively quick turnaround time for a multi-million dollar grant.

“HHMI only selected those proposals that had very strong support from the institutions; without that money, we wouldn’t have the HHMI funding,” Otegui says.

The new microscope will be installed in the Laboratory of Cell & Molecular Biology in Bock Labs and will be available to all researchers on campus.

“Acquiring this microscope is a great example of trust and collaboration across campus,” Otegui says.

A greyscale TEM image of plant cellular structures is shown on the left; a false-color cartoon-like image of the greyscale image is shown on the right.

The raw TEM image, in greyscale, left, can be used to render a false-color image depicting cellular features, right. From Reyes et al, Journal of Biological Chemistry, 2011


Disaster watch: Meet the meteorologist who keeps campus safe https://uwmadscience.news.wisc.edu/climate/disaster-watch-meet-the-meteorologist-who-keeps-campus-safe/ 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. “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 a winter weather watch or warning is issued for the campus.

“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.

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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