Bacteria produce chemicals called bacteriocins to kill microbial competitors. These chemicals can serve as natural preservatives by killing potentially dangerous pathogens in food. Lanthipeptides, a class of bacteriocins with especially potent antimicrobial properties, are widely used by the food industry and have become known as “lantibiotics” (a scientific portmanteau of lanthipeptide and antibiotics).

Despite their widespread use, however, little is known about how these lantibiotics affect the gut microbiomes of people who consume them in food. Microbes in the gut live in a delicate balance, and commensal bacteria provide important benefits to the body by breaking down nutrients, producing metabolites, and — importantly — protecting against pathogens. If too many commensals are indiscriminately killed off by antimicrobial food preservatives, opportunistic pathogenic bacteria might take their place and wreak havoc — a result no better than eating contaminated food in the first place.

Effects on good and bad bacteria

A new study published in ACS Chemical Biology by scientists from the University of Chicago found that one of the most common classes of lantibiotics has potent effects both against pathogens and against the commensal gut bacteria that keep us healthy.

Nisin is a popular lantibiotic used in everything from beer and sausage to cheese and dipping sauces. It is produced by bacteria that live in the mammary glands of cows, but microbes in the human gut produce similar lantibiotics too. Zhenrun “Jerry” Zhang, PhD, a postdoctoral scholar in the lab of Eric Pamer, MD, the Donald F. Steiner Professor of Medicine and Director of the Duchossois Family Institute at UChicago, wanted to study the impact of such naturally-produced lantibiotics on commensal gut bacteria.

“Nisin is, in essence, an antibiotic that has been added to our food for a long time, but how it might impact our gut microbes is not well studied,” Zhang said. “Even though it might be very effective in preventing food contamination, it might also have a greater impact on our human gut microbes.”

He and his colleagues mined a public database of human gut bacteria genomes and identified genes for producing six different gut-derived lantibiotics that closely resemble nisin, four of which were new. Then, in collaboration with Wilfred A. van der Donk, PhD, the Richard E. Heckert Endowed Chair in Chemistry at the University of Illinois Urbana-Champaign, they produced versions of these lantibiotics to test their effects on both pathogens and commensal gut bacteria. The researchers found that while the different lantibiotics had varying effects, they killed pathogens and commensal bacteria alike.

“This study is one of the first to show that gut commensals are susceptible to lantibiotics, and are sometimes more sensitive than pathogens,” Zhang said. “With the levels of lantibiotics currently present in food, it’s very probable that they might impact our gut health as well.”

Harnessing the power of lantibiotics

Zhang and his team also studied the structure of peptides in the lantibiotics to better understand their activity, in the interest of learning how to use their antimicrobial properties for good. For example, in another study, the Pamer lab showed that a consortium of four microbes, including one that produces lantibiotics, help protect mice against antibiotic-resistant Enterococcus infections. They are also studying the prevalence of lantibiotic-resistant genes across different populations of people to better understand how such bacteria can colonize the gut under different conditions and diets.

“It seems that lantibiotics and lantibiotic-producing bacteria are not always good for health, so we are looking for ways to counter the potential bad influence while taking advantage of their more beneficial antimicrobial properties,” Zhang said.

The study, “Activity of Gut-derived Nisin-like Lantibiotics Against Human Gut Pathogens and Commensals,” was supported by the GI Research Foundation, the Howard Hughes Medical Institute, the National Institutes of Health (grants R01AI095706, P01 CA023766, U01 AI124275, and R01 AI042135) and the Duchossois Family Institute at UChicago. Additional authors include Chunyu Wu, Ryan Moreira, and Darian Dorantes from the Univeristy of Illinois Urbana-Champaign, and Téa Pappas, Anitha Sundararajan, and Huaiying Lin from UChicago.

Seeing that structure snap open and shut in mere millionths of a second is giving Duke Human Vaccine Institute (DHVI) investigators a new handle on the surface of the virus that could lead to broadly neutralizing antibodies for an AIDS vaccine. Their findings appear Feb. 2 in Science Advances.

Being able to attach an antibody specifically to this little structure that would prevent it from popping open would be key. Their findings appear Feb. 2 in Science Advances.

The moving part is a structure called envelope glycoprotein, and AIDS researchers have been trying to figure it out for years because it is a key part of the virus’ ability to dock on a T-cell receptor known as CD4. Many parts of the envelope are constantly moving to evade the immune system, but vaccine immunogens are designed to stay relatively stable.

“Everything that everybody’s done to try to stabilize this (structure) won’t work, because of what we learned,” said lead author Rory Henderson, a structural biologist who is an associate professor of medicine in DHVI. “It’s not that they did something wrong; it’s just that we didn’t know it moves this way.”

Postdoctoral researcher and study co-author Ashley Bennett offers a play-by-play: As the virus feels for its best attachment point on a human T-cell, the host cell’s CD4 receptor is the first thing it latches onto. That connection is what then triggers the envelope structure to pop open, which in turn, exposes a co-receptor binding site “and that’s the event that actually matters.”

Once both molecules of the virus are bound to the cell membrane, the process of injecting viral RNA can begin. “If it gets inside the cell, your infection is now permanent,” Henderson said.

“If you get infected, you’ve already lost the game because it’s a retrovirus,” Bennett agrees.

The moving structure they found protects the sensitive co-receptor binding site on the virus. “It’s also a latch to keep it from springing until it’s ready to spring,” Henderson said. Keeping it latched with a specific antibody would stop the process of infection.

To see the viral parts in various states of open, closed and in-between, Bennett and Henderson used an electron accelerator at the Argonne National Laboratory outside Chicago that produces X-rays in wavelengths that can resolve something as small as a single atom. But this expensive, shared equipment is in high demand. The AIDS researchers were awarded three 120-hour blocks of time with the synchrotron to try to get as much data as they could in marathon sessions. “Basically, you just go until you can’t anymore,” Bennett said.

Earlier research elsewhere had argued that antibodies were being designed for the wrong shapes on the virus and this work shows that was probably correct.

“The question has been ‘why, when we immunize, are we getting antibodies to places that are supposed to be blocked?'” Henderson said. Part of the answer should lie in this particular structure and its shape-shifting.

“It’s the interplay between the antibody binding and what this shape is that’s really critical about the work that we did,” Henderson said. “And that led us to design an immunogen the day we got back from the first experiment. We think we know how this works.”

This research was supported by the National Institutes of Health (UM1AI14437, R01AI145687, U54AI170752, P30 GM124169, S10OD018483), the Department of Energy (DE-AC02-06CH11357) and the DOE Office of Biological and Environmental Research.

Drylands make up 40 percent of the Earth’s landmass and are places where water is the limiting resource for life. They often display a characteristic clustering of vegetation surrounded by bare soil — patterns that are easy to spot in aerial images. The new study, led by SFI External Professor Sonia Kéfi, who is a researcher at CNRS in France, finds that not only are these spatial patterns caused by the stressful environmental conditions of drylands, but they are also a critical adaptation that allows drylands to function in changing conditions. When a dryland ecosystem tips into a degraded state, the spatial patterns disappear.

“Many people have the idea that ‘interesting’ ecosystems are places like the Amazon, and that drylands are poor in some way,” says SFI External Professor Ricard Solé (Pompeu Fabra University), a co-author on the paper. “But they can be very rich. They are responsible for managing how water is being retained or not in these habitats, and are important for CO2 exchange.” Beyond their ecological importance, drylands are also home to one-third of the world’s human population, making them important economically and culturally.

In healthy dryland ecosystems, islands of vegetation create oases where conditions are a bit better than the rest of the landscape. There’s more water, more nutrients, and more shade. If an ecosystem’s climate becomes drier, those clusters tend to move further apart.

And this, says Kéfi, is a double-edged sword. While improving local conditions, these clusters also create spaces without vegetation — harsh places where a single plant would not survive on its own. If conditions become too harsh, the ecosystem can reach a tipping point into desertification.

Kéfi and her colleagues wondered if aerial images, and their evidence of changes in spatial patterns, could themselves indicate the health or level of degradation in a given plot of land.

“In theory, we could tell something about the ecosystem from the sky — that’s what the models predict, in very broad terms,” says Kéfi. To test this, the team paired aerial images with soil and vegetation data gathered from 115 dryland ecosystems across 13 different countries. “This on-the-ground data shows us where one ecosystem is healthier or functioning better than other ecosystems.” Using the two types of data, the team could test the predictions of the model against real-world observations.

“Our results represent a significant advance in the development of tools for the management and preservation of dryland ecosystems in a warmer, drier world,” says Kéfi. “More specifically, changes in spatial vegetation patterns (or the lack thereof) could be used as indicators of degradation.”

According to Solé, the study offers, for the first time, real validation that the model correctly predicts the nonlinear dynamics of what has been unfolding in dryland ecosystems. “The beauty of this work is that it reveals something that goes beyond the pattern-forming problem. You can talk about ecosystem health in ways that are not metaphoric, and it opens new interesting questions about how to address the future of these ecosystems,” he says.

The authors hope their work will make it easier to spot degrading systems that might be approaching a tipping point. And, because vegetation patterning seems to also be key in other natural systems, such as microbial communities or coastal wetlands, their results could have implications for systems beyond arid zones.

3D surface imaging is a common tool used in smartphone facial recognition, as well as in computer vision and autonomous driving. These systems typically consist of a dot projector that contains multiple components: a laser, lenses, a light guide and a diffractive optical element (DOE). The DOE is a special kind of lens that breaks the laser beam into an array of about 32,000 infrared dots. So, when a person looks at a locked screen, the facial recognition system projects an array of dots onto most of their face, and the device’s camera reads the pattern created to confirm the identity. However, dot projector systems are relatively large for small devices such as smartphones. So, Yu-Heng Hong, Hao-Chung Kuo, Yao-Wei Huang and colleagues set out to develop a more compact facial recognition system that would be nearly flat and require less energy to operate.

To do this, the researchers replaced a traditional dot projector with a low-power laser and a flat gallium arsenide surface, significantly reducing the imaging device’s size and power consumption. They etched the top of this thin metallic surface with a nanopillar pattern, which creates a metasurface that scatters light as it passes through the material. In this prototype, the low-powered laser light scatters into 45,700 infrared dots that are projected onto an object or face positioned in front of the light source. Like the dot projector system, the new system incorporates a camera to read the patterns that the infrared dots created.

In tests of the prototype, the system accurately identified a 3D replica of Michelangelo’s David by comparing the infrared dot patterns to online photos of the famous statue. Notably, it accomplished this using five to 10 times less power and on a platform with a surface area about 230 times smaller than a common dot-projector system. The researchers say their prototype demonstrates the usefulness of metasurfaces for effective small-scale low-power imaging solutions for facial recognition, robotics and extended reality.

The authors acknowledge funding from Hon Hai Precision Industry, the National Science and Technology Council in Taiwan, and the Ministry of Education in Taiwan.

In recent years, the functional and mechanical properties of low-dimensional metals, including nanoparticles, nanotubes and nanosheets, have garnered attention for their potential applications in small-scale devices, such as sensors, nano-robots and metamaterials. However, most metals are electrochemically active and susceptible to oxidation in ambient environments, which often degrades their properties and functionalities.

“Metallic nanomaterials have a high surface-to-volume ratio, which can be up to 10⁸m^-1. So in principle, they are expected to be particularly prone to oxidation,” said Professor Yang Yong, in the Department of Mechanical Engineering at CityU, who led the research team together with his collaborators. “To use low-dimensional metals to develop next-generation devices and metamaterial, we must thoroughly understand the adverse effects of oxidation on the properties of these nanometals and then find a way to overcome them.”

Therefore, Professor Yang and his team investigated oxidation in nanometals, and in sharp contrast to their expectation, they found that severely oxidized metallic glass nanotubes and nanosheets can attain an ultrahigh recoverable elastic strain of up to about 14% at room temperature, which outperforms bulk metallic glasses, metallic glass nanowires, and many other super-elastic metals.

They made metallic glass nanotubes with an average wall thickness of just 20nm, and fabricated nanosheets from different substrates, such as sodium chloride, polyvinyl alcohol and conventional photoresist substrates, with different levels of oxygen concentration.

They then conducted 3D atom probe tomography (APT) and electron energy loss spectroscopy measurements. In both the results, oxides were dispersed within the metallic glass nanotubes and nanosheets, unlike conventional bulk metals, in which a solid oxide layer forms on the surface. As the oxygen concentration in the samples increased owing to metal-substrate reactions, connected and percolating oxide networks were formed inside the nanotubes and nanosheets.

In-situ microcompression measurements also revealed that the severely oxidized metallic glass nanotubes and nanosheets exhibited a recoverable strain of 10-20%, which was several times more than that of most conventional superelastic metals, such as shape memory alloys and gum metals. The nanotubes also had an ultra-low elastic modulus of about 20-30 GPa.

To understand the mechanism behind this, the team conducted atomistic simulations, which indicated that the superelasticity originates from severe oxidation in the nanotubes and can be attributed to the formation of a damage-tolerant percolation network of nano-oxides in the amorphous structure. These oxide networks not only restrict atomic-scale plastic events during loading, but also lead to the recovery of elastic rigidity on unloading in metallic glass nanotubes.

“Our research introduces a nano-oxide engineering approach for low-dimensional metallic glasses. The morphology of nano-oxides within metallic-glass nanotubes and nanosheets can be manipulated by adjusting the oxide concentration, ranging from isolated dispersions to a connected network,” said Professor Yang.

“With this approach, we can develop a class of heterogeneous nanostructured ceramic-metal composites by blending metals with oxides at the nanoscale. Such composites have great potential for various future commercial applications and nanodevices working in harsh environments, such as sensors, medical devices, micro- and nano-robots, springs and actuators,” he added.