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How leafcutter ants cultivate a fungal garden to degrade plants and provide insights into future biofuels

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How leafcutter ants cultivate a fungal garden to degrade plants and provide insights into future biofuels


Scientists have spent decades finding ways to efficiently and affordably degrade plant materials so that they can be converted into useful bioproducts that benefit everyday life.

Bio-based fuels, detergents, nutritional supplements, and even plastics are the result of this work. And while scientists have found ways to degrade plants to the extent needed to produce a range of products, certain polymers such as lignin, which is a primary ingredient in the cell wall of plants, remain incredibly difficult to affordably break down without adding pollutants back into the environment. These polymers can be left behind as waste products with no further use.

A specialized microbial community composed of fungus, leafcutter ants, and bacteria is known to naturally degrade plants, turning them into nutrients and other components that are absorbed and used by surrounding organisms and systems. But identifying all components and biochemical reactions needed for the process remained a significant challenge — until now.

As part of her Department of Energy (DOE) Early Career award, Kristin Burnum-Johnson, science group leader for Functional and Systems Biology at Pacific Northwest National Laboratory (PNNL), and a team of fellow PNNL researchers, developed an imaging method called metabolome informed proteome imaging (MIPI). This method allows scientists to peer deep down to the molecular level and view exactly what base components are part of the plant degradation process, as well as what, when, and where important biochemical reactions occur that make it possible.

Using this method, the team revealed important metabolites and enzymes that spur different biochemical reactions that are vital in the degradation process. They also revealed the purpose of resident bacteria in the system — which is to make the process even more efficient. These insights can be applied to future biofuels and bioproducts development.

The team’s research was recently published in Nature Chemical Biology.

Symbiotic relationship between leafcutter ants and fungus reveal key to success in plant degradation

For its research, the team studied a type of fungus known for its symbiotic relationship with a species of leafcutter ants — a fungus known as Leucoagaricus gongylophorus. The ants use the fungus to cultivate a fungal garden that degrades plant polymers and other material. Remnant components from this degradation process are used and consumed by a variety of organisms in the garden, allowing all to thrive.

The ants accomplish this process by cultivating fungus on fresh leaves in specialized underground structures. These structures ultimately become the fungal gardens that consume the material. Resident bacterial members help with the degradation by producing amino acids and vitamins that support the overall garden ecosystem.

“Environmental systems have evolved over millions of years to be perfect symbiotic systems,” Burnum-Johnson said. “How can we better learn from these systems than by observing how they accomplish these tasks naturally?”

But what makes this fungal community so difficult to study is its complexity. While the plants, fungus, ants, and bacteria are all active components in the plant degradation process, none of them focus on one task or reside in one location. Factor in the small-scale size of the biochemical reactions occurring at the molecular level, and an incredibly difficult puzzle presents itself. But the new MIPI imaging method developed at PNNL allows scientists to see exactly what is going on throughout the degradation process.

“We now have the tools to fully understand the intricacies of these systems and visualize them as a whole for the first time,” Burnum-Johnson said.

Revealing important components in a complex system

Using a high-powered laser, the team took scans across 12-micron-thick sections of a fungal garden — the approximate width of plastic cling film. This process helped determine locations of metabolites in the samples, which are remnant products of plant degradation. This technique also helped identify the location and abundance of plant polymers such as cellulose, xylan, and lignin, as well as other molecules in specific regions. The combined locations of these components indicated hot spots where plant material had been broken down.

From there, the team homed in on those regions to see enzymes, which are used to kick start biochemical reactions in a living system. Knowing the type and location of these enzymes allowed them to determine which microbes were a part of that process.

All of these components together helped affirm the fungus as the primary degrader of the plant material in the system. Additionally, the team determined that the bacteria present in the system transformed previously digested plant polymers into metabolites that are used as vitamins and amino acids in the system. These vitamins and amino acids benefit the entire ecosystem by accelerating fungal growth and plant degradation.

Burnum-Johnson said if scientists had used other, more traditional methods that take bulk measurements of primary components in a system, such as metabolites, enzymes, and other molecules, they would simply get an average of those materials, creating more noise and masking information.

“It dilutes the important chemical reactions of interest, often making these processes undetectable,” she said. “To analyze the complex environmental ecosystems of these fungal communities, we need to know those fine detail interactions. These conclusions can then be taken back into a lab setting and used to create biofuels and bioproducts that are important in our everyday life.”

Using knowledge of complex systems for future fungal research

Marija Velickovic, a chemist and lead author of the paper, said she initially became interested in studying the fungal garden and how it degrades lignin based on the difficulty of the project.

“Fungal gardens are the most interesting because they are one of the most complex ecosystems composed of multiple members that effectively work together,” she said. “I really wanted to map activities at the microscale level to better understand the role of each member in this complex ecosystem.”

Velickovic performed all the hands-on experiments in the lab, collecting material for the slides, scanning the samples to view and identify metabolites in each of the sections, and identifying hot spots of lignocellulose degradation.

Both Velickovic and Burnum-Johnson said they are ecstatic about their team’s success.

“We actually accomplished what we set out for,” Burnum-Johnson said. “Especially in science, that isn’t guaranteed.”

The team plans to use its findings for further research, with specific plans to study how fungal communities respond and protect themselves amid disturbances and other perturbations.

“We now have an understanding of how these natural systems degrade plant material very well,” Burnum-Johnson said. “By looking at complex environmental systems at this level, we can understand how they are performing that activity and capitalize on it to make biofuels and bioproducts.”

The work was funded by DOE’s Office of Science. Additionally, researchers accessed mass spectrometry imaging and computing and proteomics resources at the Environmental Molecular Sciences Laboratory, an Office of Science user facility located at PNNL.



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New understanding of fly behavior has potential application in robotics, public safety

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How leafcutter ants cultivate a fungal garden to degrade plants and provide insights into future biofuels


Why do flies buzz around in circles when the air is still? And why does it matter?

In a paper published online July 26, 2024 by the scientific journal Current Biology, University of Nevada, Reno Assistant Professor Floris van Breugel and Postdoctoral Researcher S. David Stupski respond to this up-until-now unanswered question. And that answer could hold a key to public safety — specifically, how to better train robotic systems to track chemical leaks.

“We don’t currently have robotic systems to track odor or chemical plumes,” van Breugel said. “We don’t know how to efficiently find the source of a wind-borne chemical. But insects are remarkably good at tracking chemical plumes, and if we really understood how they do it, maybe we could train inexpensive drones to use a similar process to find the source of chemicals and chemical leaks.”

A fundamental challenge in understanding how insects track chemical plumes — basically, how does the fly find the banana in your kitchen? — is that wind and odors can’t be independently manipulated.

To address this challenge, van Breugel and Stupski used a new approach that makes it possible to remotely control neurons — specifically the “smell” neurons — on the antennae of flying fruit flies by genetically introducing light-sensitive proteins, an approach called optogenetics. These experiments, part of a $450,000 project funded through the Air Force Office of Scientific Research, made it possible to give flies identical virtual smell experiences in different wind conditions.

What van Breugel and Stupski wanted to know: how do flies find an odor when there’s no wind to carry it? This is, after all, likely the wind experience of a fly looking for a banana in your kitchen. The answer is in the Current Biology article, “Wind Gates Olfaction Driven Search States in Free Flight.” The print version will appear in the Sept. 9 issue.

Flies use environmental cues to detect and respond to air currents and wind direction to find their food sources, according to van Breugel. In the presence of wind, those cues trigger an automatic “cast and surge” behavior, in which the fly surges into the wind after encountering a chemical plume (indicating food) and then casts — moves side to side — when it loses the scent. Cast-and-surge behavior long has been understood by scientists but, according to van Breugel, it was fundamentally unknown how insects searched for a scent in still air.

Through their work, van Breugel and Stupski uncovered another automatic behavior, sink and circle, which involves lowering altitude and repetitive, rapid turns in a consistent direction. Flies perform this innate movement consistently and repetitively, even more so than cast-and-surge behavior.

According to van Breugel, the most exciting aspect of this discovery is that it shows flying flies are clearly able to assess the conditions of the wind — its presence, and direction — before deploying a strategy that works well under these conditions. The fact that they can do this is actually quite surprising — can you tell if there is a gentle breeze if you stick your head out of the window of a moving car? Flies aren’t just reacting to an odor with the same preprogrammed response every time like a simple robot, they are responding in context-appropriate manner. This knowledge potentially could be applied to train more sophisticated algorithms for scent-detecting drones to find the source of chemical leaks.

So, the next time you try to swat a fly in your home, consider the fact that flies might actually be a little more aware of some of their natural surroundings than you are. And maybe just open a window to let it out.



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New drug shows promise in clearing HIV from brain

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How leafcutter ants cultivate a fungal garden to degrade plants and provide insights into future biofuels


An experimental drug originally developed to treat cancer may help clear HIV from infected cells in the brain, according to a new Tulane University study.

For the first time, researchers at Tulane National Primate Research Center found that a cancer drug significantly reduced levels of SIV, the nonhuman primate equivalent of HIV, in the brain by targeting and depleting certain immune cells that harbor the virus.

Published in the journal Brain, this discovery marks a significant step toward eliminating HIV from hard-to-reach reservoirs where the virus evades otherwise effective treatment.

“This research is an important step in tackling brain-related issues caused by HIV, which still affect people even when they are on effective HIV medication,” said lead study author Woong-Ki Kim, PhD, associate director for research at Tulane National Primate Research Center. “By specifically targeting the infected cells in the brain, we may be able to clear the virus from these hidden areas, which has been a major challenge in HIV treatment.”

Antiretroviral therapy (ART) is an essential component of successful HIV treatment, maintaining the virus at undetectable levels in the blood and transforming HIV from a terminal illness into a manageable condition. However, ART does not completely eradicate HIV, necessitating lifelong treatment. The virus persists in “viral reservoirs” in the brain, liver, and lymph nodes, where it remains out of reach of ART.

The brain has been a particularly challenging area for treatment due to the blood-brain barrier — a protective membrane that shields it from harmful substances but also blocks treatments, allowing the virus to persist. In addition, cells in the brain known as macrophages are extremely long-lived, making them difficult to eradicate once they become infected.

Infection of macrophages is thought to contribute to neurocognitive dysfunction, experienced by nearly half of those living with HIV. Eradicating the virus from the brain is critical for comprehensive HIV treatment and could significantly improve the quality of life for those with HIV-related neurocognitive problems.

Researchers focused on macrophages, a type of white blood cell that harbors HIV in the brain. By using a small molecule inhibitor to block a receptor that increases in HIV-infected macrophages, the team successfully reduced the viral load in the brain. This approach essentially cleared the virus from brain tissue, providing a potential new treatment avenue for HIV.

The small molecule inhibitor used, BLZ945, has previously been studied for therapeutic use in amyotrophic lateral sclerosis (ALS) and brain cancer, but never before in the context of clearing HIV from the brain.

The study, which took place at the Tulane National Primate Research Center, utilized three groups to model human HIV infection and treatment: an untreated control group, and two groups treated with either a low or high dose of the small molecule inhibitor for 30 days. The high-dose treatment lead to a notable reduction in cells expressing HIV receptor sites, as well as a 95-99% decrease in viral DNA loads in the brain .

In addition to reducing viral loads, the treatment did not significantly impact microglia, the brain’s resident immune cells, which are essential for maintaining a healthy neuroimmune environment. It also did not show signs of liver toxicity at the doses tested.

The next step for the research team is to test this therapy in conjunction with ART to assess its efficacy in a combined treatment approach. This could pave the way for more comprehensive strategies to eradicate HIV from the body entirely.

This research was funded by the National Institutes of Health, including grants from the National Institute of Mental Health and the National Institute of Neurological Disorders and Stroke, and was supported with resources from the Tulane National Primate Research Center base grant of the National Institutes of Health, P51 OD011104.



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Chemical analyses find hidden elements from renaissance astronomer Tycho Brahe’s alchemy laboratory

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How leafcutter ants cultivate a fungal garden to degrade plants and provide insights into future biofuels


In the Middle Ages, alchemists were notoriously secretive and didn’t share their knowledge with others. Danish Tycho Brahe was no exception. Consequently, we don’t know precisely what he did in the alchemical laboratory located beneath his combined residence and observatory, Uraniborg, on the now Swedish island of Ven.

Only a few of his alchemical recipes have survived, and today, there are very few remnants of his laboratory. Uraniborg was demolished after his death in 1601, and the building materials were scattered for reuse.

However, during an excavation in 1988-1990, some pottery and glass shards were found in Uraniborg’s old garden. These shards were believed to originate from the basement’s alchemical laboratory. Five of these shards — four glass and one ceramic — have now undergone chemical analyses to determine which elements the original glass and ceramic containers came into contact with.

The chemical analyses were conducted by Professor Emeritus and expert in archaeometry, Kaare Lund Rasmussen from the Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark. Senior researcher and museum curator Poul Grinder-Hansen from the National Museum of Denmark oversaw the insertion of the analyses into historical context.

Enriched levels of trace elements were found on four of them, while one glass shard showed no specific enrichments. The study has been published in the journal Heritage Science.

“Most intriguing are the elements found in higher concentrations than expected — indicating enrichment and providing insight into the substances used in Tycho Brahe’s alchemical laboratory,” said Kaare Lund Rasmussen.

The enriched elements are nickel, copper, zinc, tin, antimony, tungsten, gold, mercury, and lead, and they have been found on either the inside or outside of the shards.

Most of them are not surprising for an alchemist’s laboratory. Gold and mercury were — at least among the upper echelons of society — commonly known and used against a wide range of diseases.

“But tungsten is very mysterious. Tungsten had not even been described at that time, so what should we infer from its presence on a shard from Tycho Brahe’s alchemy workshop?,” said Kaare Lund Rasmussen.

Tungsten was first described and produced in pure form more than 180 years later by the Swedish chemist Carl Wilhelm Scheele. Tungsten occurs naturally in certain minerals, and perhaps the element found its way to Tycho Brahe’s laboratory through one of these minerals. In the laboratory, the mineral might have undergone some processing that separated the tungsten, without Tycho Brahe ever realizing it.

However, there is also another possibility that Professor Kaare Lund Rasmussen emphasizes has no evidence whatsoever — but which could be plausible.

Already in the first half of the 1500s, the German mineralogist Georgius Agricola described something strange in tin ore from Saxony, which caused problems when he tried to smelt tin. Agricola called this strange substance in the tin ore “Wolfram” (German for Wolf’s froth, later renamed to tungsten in English).

“Maybe Tycho Brahe had heard about this and thus knew of tungsten’s existence. But this is not something we know or can say based on the analyses I have done. It is merely a possible theoretical explanation for why we find tungsten in the samples,” said Kaare Lund Rasmussen.

Tycho Brahe belonged to the branch of alchemists who, inspired by the German physician Paracelsus, tried to develop medicine for various diseases of the time: plague, syphilis, leprosy, fever, stomach aches, etc. But he distanced himself from the branch that tried to create gold from less valuable minerals and metals.

In line with the other medical alchemists of the time, he kept his recipes close to his chest and shared them only with a few selected individuals, such as his patron, Emperor Rudolph II, who allegedly received Tycho Brahe’s prescriptions for plague medicine.

We know that Tycho Brahe’s plague medicine was complicated to produce. It contained theriac, which was one of the standard remedies for almost everything at the time and could have up to 60 ingredients, including snake flesh and opium. It also contained copper or iron vitriol (sulphates), various oils, and herbs.

After various filtrations and distillations, the first of Brahe’s three recipes against plague was obtained. This could be made even more potent by adding tinctures of, for example, coral, sapphires, hyacinths, or potable gold.

“It may seem strange that Tycho Brahe was involved in both astronomy and alchemy, but when one understands his worldview, it makes sense. He believed that there were obvious connections between the heavenly bodies, earthly substances, and the body’s organs. Thus, the Sun, gold, and the heart were connected, and the same applied to the Moon, silver, and the brain; Jupiter, tin, and the liver; Venus, copper, and the kidneys; Saturn, lead, and the spleen; Mars, iron, and the gallbladder; and Mercury, mercury, and the lungs. Minerals and gemstones could also be linked to this system, so emeralds, for example, belonged to Mercury,” explained Poul Grinder-Hansen.

Kaare Lund Rasmussen has previously analyzed hair and bones from Tycho Brahe and found, among other elements, gold. This could indicate that Tycho Brahe himself had taken medicine that contained potable gold.



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