Tag Archives: UC Riverside

Could this discovery end global amphibian pandemic?

Caption: Panamanian golden frog is nearing extinction. Credit: Brian Gratwicke/U.S. Fish & Wildlife Service

An April 3, 2024 University of California at Riverside (also on EurekAlert) by Jules Bernstein describes the possibility of using a virus to infect a fungus that kills frogs worldwide, Note: A link has been removed,

A fungus devastating frogs and toads on nearly every continent may have an Achilles heel. Scientists have discovered a virus that infects the fungus, and that could be engineered to save the amphibians.

The fungus, Batrachochytrium dendrobatidis or Bd, ravages the skin of frogs and toads, and eventually causes heart failure. To date it has contributed to the decline of over 500 amphibian species, and 90 possible extinctions including yellow-legged mountain frogs in the Sierras and the Panamanian golden frog. 

A new paper in the journal Current Biology documents the discovery of a virus that infects Bd, and which could be engineered to control the fungal disease.

The UC Riverside researchers who found the virus are excited about the implications of their discovery. In addition to helping them learn about how fungal pathogens rise and spread, it offers the hope of ending what they call a global amphibian pandemic. 

“Frogs control bad insects, crop pests, and mosquitoes. If their populations all over the world collapse, it could be devastating,” said UCR microbiology doctoral student and paper author Mark Yacoub. 

“They’re also the canary in the coal mine of climate change. As temperatures get warmer, UV light gets stronger, and water quality gets worse, frogs respond to that. If they get wiped out, we lose an important environmental signal,” Yacoub said. 

Bd was not prevalent before the late 1990s, but then, “all of a sudden frogs started dying,” Yacoub said.

When they found the Bd-infecting virus, Yacoub and UCR microbiology professor Jason Stajich had been working on the population genetics of Bd, hoping to gain a better understanding about where it came from and how it is mutating. 

“We wanted to see how different strains of fungus differ in places like Africa, Brazil, and the U.S., just like people study different strains of COVID-19,” Stajich said. To do this, the researchers used DNA sequencing technology. As they examined the data, they noticed some sequences that did not match the DNA of the fungus. 

“We realized these extra sequences, when put together, had the hallmarks of a viral genome,” Stajich said. 

Previously, researchers have looked for Bd viruses but did not find them. The fungus itself is hard to study because complex procedures are required to keep it alive in a laboratory. 

“It is also a hard fungus to keep track of because they have a life stage where they’re motile, they have a flagellus, which resembles a sperm tail, and they swim around,” Stajich said. 

Additionally, the virus that infects Bd was hard to find because most known viruses that infect fungi, called mycoviruses, are RNA viruses. However, this virus is a single-stranded DNA virus. By studying the DNA, the researchers could see the virus stuck in the genome of the fungus. 

It appears that only some strains of the fungus have the virus in their genome. But the infected ones seem to behave differently than the ones that don’t. “When these strains possess the virus they produce fewer spores, so it spreads more slowly. But they also might become more virulent, killing frogs faster,” Stajich said. 

Right now, the virus is essentially trapped inside the fungal genome. The researchers would eventually like to clone the virus and see if a manually infected strain of Bd also produces fewer spores.

“Because some strains of the fungus are infected and some are not, this underscores the importance of studying multiple strains of a fungal species,” Yacoub said. 

Moving forward, the researchers are looking for insights into the ways that the virus operates. “We don’t know how the virus infects the fungus, how it gets into the cells,” Yacoub said. “If we’re going to engineer the virus to help amphibians, we need answers to questions like these.”

In some places, it appears there are a few amphibian species acquiring resistance to Bd. “Like with COVID, there is a slow buildup of immunity. We are hoping to assist nature in taking its course,” Yacoub said. 

Here’s a link to and a citation for the paper,

An endogenous DNA virus in an amphibian-killing fungus associated with pathogen genotype and virulence by Rebecca A. Clemons, Mark N. Yacoub, Evelyn Faust, L. Felipe Toledo, Thomas S. Jenkinson, Tamilie Carvalho, D. Rabern Simmons, Erik Kalinka, Lillian K. Fritz-Laylin, Timothy Y. James, Jason E. Stajich. Current Biology Volume 34, ISSUE 7, P1469-1478.e6, April 08, 2024 DOI: https://doi.org/10.1016/j.cub.2024.02.062 Published online: March 14, 2024

This paper is open access.

Electron quantum materials, a new field in nanotechnology?

Physicists name and codify new field in nanotechnology: ‘electron quantum metamaterials’

UC Riverside’s Nathaniel Gabor and colleague formulate a vision for the field in a perspective article

Courtesy: University of California at Riverside

Bravo to whomever put the image of a field together together with a subhead that includes the phrases ‘vision for a field’ and ‘perspective article’. It’s even better if you go to the November 5, 2018 University of California at Riverside (UCR) news release (also on EurekAlert) by Iqbal Pittalwala to see the original format,

When two atomically thin two-dimensional layers are stacked on top of each other and one layer is made to rotate against the second layer, they begin to produce patterns — the familiar moiré patterns — that neither layer can generate on its own and that facilitate the passage of light and electrons, allowing for materials that exhibit unusual phenomena. For example, when two graphene layers are overlaid and the angle between them is 1.1 degrees, the material becomes a superconductor.

“It’s a bit like driving past a vineyard and looking out the window at the vineyard rows. Every now and then, you see no rows because you’re looking directly along a row,” said Nathaniel Gabor, an associate professor in the Department of Physics and Astronomy at the University of California, Riverside. “This is akin to what happens when two atomic layers are stacked on top of each other. At certain angles of twist, everything is energetically allowed. It adds up just right to allow for interesting possibilities of energy transfer.”

This is the future of new materials being synthesized by twisting and stacking atomically thin layers, and is still in the “alchemy” stage, Gabor added. To bring it all under one roof, he and physicist Justin C. W. Song of Nanyang Technological University, Singapore, have proposed this field of research be called “electron quantum metamaterials” and have just published a perspective article in Nature Nanotechnology.

“We highlight the potential of engineering synthetic periodic arrays with feature sizes below the wavelength of an electron. Such engineering allows the electrons to be manipulated in unusual ways, resulting in a new range of synthetic quantum metamaterials with unconventional responses,” Gabor said.

Metamaterials are a class of material engineered to produce properties that do not occur naturally. Examples include optical cloaking devices and super-lenses akin to the Fresnel lens that lighthouses use. Nature, too, has adopted such techniques – for example, in the unique coloring of butterfly wings – to manipulate photons as they move through nanoscale structures.

“Unlike photons that scarcely interact with each other, however, electrons in subwavelength structured metamaterials are charged, and they strongly interact,” Gabor said. “The result is an enormous variety of emergent phenomena and radically new classes of interacting quantum metamaterials.”

Gabor and Song were invited by Nature Nanotechnology to write a review paper. But the pair chose to delve deeper and lay out the fundamental physics that may explain much of the research in electron quantum metamaterials. They wrote a perspective paper instead that envisions the current status of the field and discusses its future.

“Researchers, including in our own labs, were exploring a variety of metamaterials but no one had given the field even a name,” said Gabor, who directs the Quantum Materials Optoelectronics lab at UCR. “That was our intent in writing the perspective. We are the first to codify the underlying physics. In a way, we are expressing the periodic table of this new and exciting field. It has been a herculean task to codify all the work that has been done so far and to present a unifying picture. The ideas and experiments have matured, and the literature shows there has been rapid progress in creating quantum materials for electrons. It was time to rein it all in under one umbrella and offer a road map to researchers for categorizing future work.”

In the perspective, Gabor and Song collect early examples in electron metamaterials and distil emerging design strategies for electronic control from them. They write that one of the most promising aspects of the new field occurs when electrons in subwavelength-structure samples interact to exhibit unexpected emergent behavior.

“The behavior of superconductivity in twisted bilayer graphene that emerged was a surprise,” Gabor said. “It shows, remarkably, how electron interactions and subwavelength features could be made to work together in quantum metamaterials to produce radically new phenomena. It is examples like this that paint an exciting future for electronic metamaterials. Thus far, we have only set the stage for a lot of new work to come.”

Gabor, a recipient of a Cottrell Scholar Award and a Canadian Institute for Advanced Research Azrieli Global Scholar Award, was supported by the Air Force Office of Scientific Research Young Investigator Program and a National Science Foundation Division of Materials Research CAREER award.

There is a video illustrating the ideas which is embedded in a November 5, 2018 news item on phys.oirg,

Here’s a link to and a citation for the ‘perspective’ paper,

Electron quantum metamaterials in van der Waals heterostructures by Justin C. W. Song & Nathaniel M. Gabor. Nature Nanotechnology, volume 13, pages986–993 (2018) DOI: https://doi.org/10.1038/s41565-018-0294-9 Published: 05 November 2018

This paper is behind a paywall.

Anyone have a spare portabella (also known as, portobello) mushroom? I need for my phone

Scientists as the University of California at Riverside (UCR) have developed a type of lithium-ion battery with portabella mushrooms, from a Sept. 29, 2015 news item on ScienceDaily,

Can portabella mushrooms stop cell phone batteries from degrading over time?

Researchers at the University of California, Riverside Bourns College of Engineering think so.

They have created a new type of lithium-ion battery anode using portabella mushrooms, which are inexpensive, environmentally friendly and easy to produce. The current industry standard for rechargeable lithium-ion battery anodes is synthetic graphite, which comes with a high cost of manufacturing because it requires tedious purification and preparation processes that are also harmful to the environment.

A Sept. 29, 2015 UCR news release (also on EurekAlert) by Sean Nealon, which originated the news item, expands on the theme,

With the anticipated increase in batteries needed for electric vehicles and electronics, a cheaper and sustainable source to replace graphite is needed. Using biomass, a biological material from living or recently living organisms, as a replacement for graphite, has drawn recent attention because of its high carbon content, low cost and environmental friendliness.

UC Riverside engineers were drawn to using mushrooms as a form of biomass because past research has established they are highly porous, meaning they have a lot of small spaces for liquid or air to pass through. That porosity is important for batteries because it creates more space for the storage and transfer of energy, a critical component to improving battery performance.

In addition, the high potassium salt concentration in mushrooms allows for increased electrolyte-active material over time by activating more pores, gradually increasing its capacity.

A conventional anode allows lithium to fully access most of the material during the first few cycles and capacity fades from electrode damage occurs from that point on. The mushroom carbon anode technology could, with optimization, replace graphite anodes. It also provides a binderless and current-collector free approach to anode fabrication.

“With battery materials like this, future cell phones may see an increase in run time after many uses, rather than a decrease, due to apparent activation of blind pores within the carbon architectures as the cell charges and discharges over time,” said Brennan Campbell, a graduate student in the Materials Science and Engineering program at UC Riverside.

Nanocarbon architectures derived from biological materials such as mushrooms can be considered a green and sustainable alternative to graphite-based anodes, said Cengiz Ozkan, a professor of mechanical engineering and materials science and engineering.

The nano-ribbon-like architectures transform upon heat treatment into an interconnected porous network architecture which is important for battery electrodes because such architectures possess a very large surface area for the storage of energy, a critical component to improving battery performance.

One of the problems with conventional carbons, such as graphite, is that they are typically prepared with chemicals such as acids and activated by bases that are not environmentally friendly, said Mihri Ozkan, a professor of electrical and computer engineering. Therefore, the UC Riverside team is focused on naturally-derived carbons, such as the skin of the caps of portabella mushrooms, for making batteries.

It is expected that nearly 900,000 tons of natural raw graphite would be needed for anode fabrication for nearly six million electric vehicle forecast to be built by 2020. This requires that the graphite be treated with harsh chemicals, including hydrofluoric and sulfuric acids, a process that creates large quantities of hazardous waste. The European Union projects this process will be unsustainable in the future.

Here’s link to and a citation for the paper,

Hierarchically Porous Carbon Anodes for Li-ion Batteries by Brennan Campbell, Robert Ionescu, Zachary Favors, Cengiz S. Ozkan, & Mihrimah Ozkan. [Nature] Scientific Reports 5, Article number: 14575 (2015)  doi:10.1038/srep14575 Published online: 29 September 2015

This is an open access paper

Copper nanoparticles, toxicity research, colons, zebrafish, and septic tanks

Alicia Taylor, a graduate student at UC Riverside, surrounded by buckets of effluent from the septic tank system she used for her research. Courtesy: University of California at Riverside

Alicia Taylor, a graduate student at UC Riverside, surrounded by buckets of effluent from the septic tank system she used for her research. Courtesy: University of California at Riverside

Those buckets of efflluent are strangely compelling. I think it’s the abundance of orange. More seriously, a March 2, 2015 news item on Nanowerk poses a question about copper nanoparticles,

What do a human colon, septic tank, copper nanoparticles and zebrafish have in common?

They were the key components used by researchers at the University of California, Riverside and UCLA [University of California at Los Angeles] to study the impact copper nanoparticles, which are found in everything from paint to cosmetics, have on organisms inadvertently exposed to them.

The researchers found that the copper nanoparticles, when studied outside the septic tank, impacted zebrafish embryo hatching rates at concentrations as low as 0.5 parts per million. However, when the copper nanoparticles were released into the replica septic tank, which included liquids that simulated human digested food and household wastewater, they were not bioavailable and didn’t impact hatching rates.

A March 2, 2015 University of California at Riverside (UCR) news release (also on EurekAlert), which originated the news item, provides more detail about the research,

“The results are encouraging because they show with a properly functioning septic tank we can eliminate the toxicity of these nanoparticles,” said Alicia Taylor, a graduate student working in the lab of Sharon Walker, a professor of chemical and environmental engineering at the University of California, Riverside’s Bourns College of Engineering.

The research comes at a time when products with nanoparticles are increasingly entering the marketplace. While the safety of workers and consumers exposed to nanoparticles has been studied, much less is known about the environmental implications of nanoparticles. The Environmental Protection Agency is currently accessing the possible effects of nanomaterials, including those made of copper, have on human health and ecosystem health.

The UC Riverside and UCLA [University of California at Los Angeles] researchers dosed the septic tank with micro copper and nano copper, which are elemental forms of copper but encompass different sizes and uses in products, and CuPRO, a nano copper-based material used as an antifungal agent to spray agricultural crops and lawns.

While these copper-based materials have beneficial purposes, inadvertent exposure to organisms such as fish or fish embryos has not received sufficient attention because it is difficult to model complicated exposure environments.

The UC Riverside researchers solved that problem by creating a unique experimental system that consists of the replica human colon and a replica two-compartment septic tank, which was originally an acyclic septic tank. The model colon is made of a custom-built 20-inch-long glass tube with a 2-inch diameter with a rubber stopper at both ends and a tube-shaped membrane typically used for dialysis treatments within the glass tube.

To simulate human feeding, 100 milliliters of a 20-ingredient mixture that replicated digested food was pumped into the dialysis tube at 9 a.m., 3 p.m. and 9 p.m. for five-day-long experiments over nine months.

The septic tank was filled with waste from the colon along with synthetic greywater, which is meant to simulate wastewater from sources such as sinks and bathtubs, and the copper nanoparticles. The researchers built a septic tank because 20 to 30 percent of American households rely on them for sewage treatment. Moreover, research has shown up to 40 percent of septic tanks don’t function properly. This is a concern if the copper materials are disrupting the function of the septic system, which would lead to untreated waste entering the soil and groundwater.

Once the primary chamber of the septic system was full, liquid began to enter the second chamber. Once a week, the effluent was drained from the secondary chamber and it was placed into sealed five-gallon containers. The effluent was then used in combination with zebrafish embryos in a high content screening process using multiwall plates to access hatching rates.

The remaining effluent has been saved and sits in 30 five-gallon buckets in a closet at UC Riverside because some collaborators have requested samples of the liquid for their experiments.

Here’s a link to and a citation for the paper,

Understanding the Transformation, Speciation, and Hazard Potential of Copper Particles in a Model Septic Tank System Using Zebrafish to Monitor the Effluent* by Sijie Lin, Alicia A. Taylor, Zhaoxia Ji, Chong Hyun Chang, Nichola M. Kinsinger, William Ueng, Sharon L. Walker, and André E. Nel. ACS Nano, 2015, 9 (2), pp 2038–2048 DOI: 10.1021/nn507216f
Publication Date (Web): January 27, 2015

Copyright © 2015 American Chemical Society

This paper is behind a paywall.

* Link added March 10, 2015.