Ink flows to meet surging demand for national security research

Student interns are introduced to Sandia National Laboratories’ superfuge by test operations engineer Orlando Abeyta during a tour. Several new agreements signed this year are expected to increase the numbers of students and faculty partnering with Sandia to support its growing national security workload.
Photo credit: Craig Fritz

The nation’s largest national laboratory is embarking on a major expansion of its network of academic partners to meet the surging demand for national security science and engineering.

This year, Sandia National Laboratories inked memoranda of understanding with Texas A&M University; the University of California, Berkeley; North Carolina State University and the University of Texas at El Paso. It is finalizing agreements with Arizona State University and the University of Washington. When those are signed, Sandia will have formal ties with 27 universities, including 13 minority serving institutions.

Work at Sandia, which is performed almost entirely for federal agencies, has been rising steadily. From fiscal year 2015 to fiscal year 2021, the Labs’ budget increased more than 50%, from $2.9 billion to $4.5 billion. Over the same period, the Labs increased its workforce by more than 25%, from 11,700 to 15,000.

But Sandia won’t meet its obligations just by hiring staff.

“Partnering with universities keeps Sandia science at the state of the art and enables us to do more research for our national security mission than we can on our sites alone,” said Diane Peebles, Sandia’s senior manager of academic programs.

Deformation fingerprints will help researchers identify and design better metallic materials

Materials science and engineering professors Jean-Charles Stinville and Marie Charpagne captured nanoscale deformation events at the origin of metal failure that can help researchers design new materials for medical, transportation, safety, energy and environmental applications. 
Photo credit: Fred Zwicky

Engineers can now capture and predict the strength of metallic materials subjected to cycling loading, or fatigue strength, in a matter of hours – not the months or years it takes using current methods.

In a new study, researchers from the University of Illinois Urbana-Champaign report that automated high-resolution electron imaging can capture the nanoscale deformation events that lead to metal failure and breakage at the origin of metal failure. The new method helps scientists to rapidly predict the fatigue strength of any alloy, and design new materials for engineering systems subject to repeated loading for medical, transportation, safety, energy and environmental applications.

The findings of the study, led by materials science and engineering professors Jean-Charles Stinville and Marie Charpagne, are published in the journal Science.

Fatigue of metals and alloys – such as the repeated bending of a metal paperclip that leads to its fracture – is the root cause of failure in many engineering systems, Stinville said. Defining the relationship between fatigue strength and the microstructure is challenging because metallic materials display complex structures with features ranging from the nanometer to the centimeter scale.

Ural Scientists Develop Technology to Correct Genetic Defects

According to Mikhail Bolkov, a regulatory framework is also needed for genetic intervention therapy. Photo credit: Ilya Safarov

Scientists at the Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences and UrFU develop methods for genetic diagnosis and therapy of diseases caused by primary immunodeficiency. This is a congenital malfunction of one or more parts of the immune system that predisposes to the development of frequent, prolonged, hard-to-treat diseases, not only infectious but also autoimmune, autoinflammatory and oncological diseases. For example, systemic lupus erythematosus, various vasculitis, chronic pneumonia, and even hair loss.

Today, primary immunodeficiencies are treated with replacement therapy and hematopoietic stem cell transplantation. However, the treatment of such diseases promises to become more effective by replacing genetic defects in human DNA. Mikhail Bolkov, a Senior Researcher at the Department of Immunochemistry of Ural Federal University and the Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, spoke about this on the air of Radio "Komsomolskaya Pravda".

More than 10 million children were affected by COVID-19-associated parental and caregiver deaths

According to a new modeling study, published in JAMA Pediatrics, the number of children estimated to have experienced the death of a parent or caregiver as a result of the COVID-19 pandemic has climbed to more than 10.5 million globally as of May 1, 2022.

The new study, involving the University of Oxford, Imperial College, the African Institute for Mathematical Sciences, the Centers for Disease Control and Prevention (CDC), and the World Health Organization (WHO), builds on the best available and most conservative data recently published by WHO on excess COVID-19 deaths (14.9 million as of Dec 31, 2021), to establish estimates of orphaned children in every country. This is the first-time availability of these comprehensive data on excess deaths for every country, and it enabled the data modelers to update global minimum estimates of pandemic orphanhood and caregiver death among children based on these excess deaths.

Excess deaths are typically defined as the difference between the observed numbers of deaths in specific time periods and expected numbers of deaths in the same time periods. Estimates of excess deaths can provide information about the burden of mortality potentially related to the COVID-19 pandemic, including deaths that are directly or indirectly attributed to COVID-19.

In this study, authors analyzed country-level deaths, fertility rates, and national excess mortality data provided by the WHO, the Economist, and the Institute for Health Metrics and Evaluation, and used mathematical modelling to develop global estimates based on the WHO estimates, which were the most conservative.

Using science to solve ancient Chinese art mystery

UC assistant professor Pietro Strobbia consulted with the Cincinnati Art Museum to solve a mystery about one of its ancient Chinese masterpieces.
Photo credit: Andrew Higley/University of Cincinnati

The Cincinnati Art Museum turned to a scientist at the University of Cincinnati for help solving a mystery 1,300 years in the making.

The museum’s Chinese dancing horse sculpture is so realistic that the fiery steed seems ready to gallop off its pedestal. But East Asian art curator Hou-mei Sung questioned the authenticity of a decorative tassel on the terracotta horse’s forehead that resembles the horn of a mythological unicorn.

The museum reached out to UC College of Arts and Sciences assistant professor of chemistry Pietro Strobbia for help to determine if the tassel was original to the work.

“Many museums have a conservator but not necessarily scientific facilities needed to do this kind of examination,” Strobbia said. “The forehead tassel looks original, but the museum asked us to determine what materials it was made from.”

Strobbia and his collaborators wrote about the project for a paper published in the journal Heritage Science.

Scientists Grow Lead-Free Solar Material With a Built-In Switch

Light microscopy image of nanowires, 100 to 1,000 nanometers in diameter, grown from cesium germanium tribromide (CGB) on a mica substrate. The CGB nanowires are samples of a new lead-free halide perovskite solar material that is also ferroelectric.
Credit: Peidong Yang and Ye Zhang/Berkeley Lab

Solar panels, also known as photovoltaics, rely on semiconductor devices, or solar cells, to convert energy from the sun into electricity.

To generate electricity, solar cells need an electric field to separate positive charges from negative charges. To get this field, manufacturers typically dope the solar cell with chemicals so that one layer of the device bears a positive charge and another layer a negative charge. This multilayered design ensures that electrons flow from the negative side of a device to the positive side – a key factor in device stability and performance. But chemical doping and layered synthesis also add extra costly steps in solar cell manufacturing.

Now, a research team led by scientists at DOE’s Lawrence Berkeley National Laboratory (Berkeley Lab), in collaboration with UC Berkeley, has demonstrated a unique workaround that offers a simpler approach to solar cell manufacturing: A crystalline solar material with a built-in electric field – a property enabled by what scientists call “ferroelectricity.” The material was reported earlier this year in the journal Science Advances.

Genome Editing Terminology Is Standardized in NIST-Led Effort

These words are included in the new Genome Editing Vocabulary. 
Credit: N. Hanacek/NIST

Genome editing can cure diseases, boost food production and open vast new fields of scientific discovery. But to realize its full potential, scientists need to precisely describe the details of their genome editing attempts to one another and the wider world.

For instance, if a company is developing a new gene therapy for use in the United States, it needs to tell the U.S. Food and Drug Administration (FDA) what the product does and demonstrate that it is safe and effective. Scientists could do that more precisely if they had a standard set of terms and definitions.

As of recently, they have one. In November 2021 the International Organization for Standardization (ISO) published the Genome Editing Vocabulary — an internationally agreed-upon list of 42 precisely defined terms that will help scientists from all over the world avoid errors of communication. (The word “genome” refers to all the inherited DNA in an organism.)

This effort was spearheaded by the National Institute of Standards and Technology (NIST) Genome Editing Consortium — an international group of industry, academic and government scientists who work in this field. NIST first convened the consortium in 2018 so that experts and organizations that often compete with one another would have a venue for collaborating on standards that advance the field for all. The FDA joined the consortium last year.

Altered gene helps plants absorb more carbon dioxide, produce more useful compounds

Hiroshi Maeda

Every day, plants around the world perform an invisible miracle. They take carbon dioxide from the air and, with the help of sunlight, turn it into countless chemicals essential to both plants and humans.

Some of these chemicals, known as aromatic compounds, are the starting material for a wealth of useful medications, such as aspirin and morphine. Yet, many of these chemicals come from fossil fuels because it’s hard to get plants to make enough of them to harvest economically. Others are essential human nutrients and can only be obtained through our food since our bodies are unable to make them.

In new work, scientists at the University of Wisconsin–Madison identified a way to release the brakes on plants’ production of aromatic amino acids by changing, or mutating, one set of genes. The genetic change also caused the plants to absorb 30% more carbon dioxide than normal, without any ill effect on the plants.

If scientists could add a trait like this to crops or drug-producing plants, it could help them produce more chemicals naturally while reducing greenhouse gases in the atmosphere.

“We’ve long been interested in this aromatic amino acid pathway because it’s one of the major plant pathways that transform carbon fixed by photosynthesis into medicines, food, fuels, and materials,” says Hiroshi Maeda, a UW–Madison professor of botany who led the new research. “Now for the first time, we’ve discovered how to regulate the key control knob plants use to turn up production of this pathway.”

Real-time, accurate virus detection method could help fight the next pandemic

Scanning electron microscopy image showing carbon nanotubes (purple) effectively trapping Influenza viruses (light purple round objects). These trapped viruses are then analyzed by Raman spectroscopy and machine learning and they can be identified with accuracies >95%.
Credit: Elizabeth Floresgomez and Yin-Ting Yeh.

A method of highly accurate and sensitive virus identification using Raman spectroscopy, a portable virus capture device and machine learning could enable real-time virus detection and identification to help battle future pandemics, according to a team of researchers led by Penn State.

“This virus detection method is label-free and not aimed at any specific virus, thus enabling us to identify potential new strains of viruses,” said Shengxi Huang, assistant professor of electrical engineering and biomedical engineering and co-author of the study that appeared today (June 2) in the Proceedings of the National Academy of Sciences. “It is also rapid, so suitable for fast screening in crowded public spaces. In addition, the rich Raman features together with machine learning analysis enable a deeper understanding of the virus structures.”

Raman spectroscopy detects unique vibrations in molecules by picking up shifts when a laser light beam induces these vibrations. To capture the viruses, a tool known as a microfluidic device would be used to trap viruses between forests of aligned carbon nanotubes.

Microfluidic devices use very small amounts of body fluids on a microchip to do medical and laboratory tests. Such a device could use virus cultures, saliva, nasal washes, or even exhaled breath, including samples gathered on-site during an outbreak. The carbon nanotubes forests would filter out any foreign substance or background molecules from the host or surrounding air that could make it more difficult to get an accurate reading.

Blocking enzyme could hold the key to preventing, treating severe COVID-19

Amal Amer

The sickest COVID-19 patients develop acute respiratory distress syndrome resulting from the combination of high levels of pro-inflammatory proteins called cytokines, fluid accumulation in air sacs that seeps into lung tissue and blood clots, or thrombosis, caused by damage to cells lining vessel walls. In a series of experiments in infected mice, the research team found that inhibiting caspase 11 reduced the intensity of multiple effects.

Blocking an immune response-related enzyme holds promise in preventing or treating severe COVID-19 symptoms by reducing inflammation, tissue injury and blood clots in the lungs, new research in mice suggests.

Scientists who have long studied this molecule’s functions in bacterial infections traced the development of extensive lung damage in infected mice to heightened levels of the enzyme triggered by the invading SARS-CoV-2 virus.

Versions of this enzyme exist and have similar functions in both mice and humans – they’re called caspase 11 and caspase 4, respectively. After finding that the molecule is an attractive therapeutic target, researchers are exploring compounds that could safely and effectively block its activation.

“The whole idea is if this molecule is not there, the mouse will do better, which means if you target this molecule, then humans should do better,” said co-senior study author Amal Amer, professor of microbial infection and immunity in The Ohio State University College of Medicine.

The research was published online recently in Proceedings of the National Academy of Sciences.

Shark antibodies may have the teeth to stop COVID-19

Nurse sharks have a surprisingly effective adaptive immune system that may help shape novel COVID-19 therapies

Fossil evidence suggests sharks first existed 420 million years ago, predating humanity, Mount Everest and even trees. Over the course of time, sharks and other fish with cartilage skeletons developed what is now believed to be the oldest adaptive immune system in the animal kingdom.

According to a recent study published in Nature Communications, these ancient predators and their prehistoric immune systems may also be key to developing effective COVID-19 treatments.

“The shark antibodies neutralized the proteins in ways we weren’t expecting.” — 

Surajit Banerjee, Cornell University/NE-CAT

Professors Aaron LeBeau of the University of Wisconsin and Hideki Aihara of the University of Minnesota used the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory, to look at nurse shark antibodies. With exquisite resolution, the APS’s extremely bright X-ray beams showed that variable new antigen receptors (VNARs), the smallest unit of a shark antibody, can stop SARS-CoV-2, the virus that causes COVID-19 and its variants.

Scientists Synthesize Material for Fuel Cells

Natalia Tarasova notes that the new material is harmless to the environment.
Credit: Ilya Safarov

Scientists at Ural Federal University and the Institute of High Temperature Electrochemistry, Ural Branch of the Russian Academy of Sciences have synthesized a proton conductor, a solid electrolyte in which positively charged hydrogen (proton) particles are current carriers. It has a high level of electrical conductivity and could become the basis for a solid oxide fuel cell (SOFC). Such cells are an environmentally friendly alternative to hydrocarbon energy sources. The results of the study are published in the International Journal of Hydrogen Energy, an international journal dedicated to hydrogen energy.

Solid oxide fuel cells are instruments that convert fuel energy into electrical energy through a chemical reaction. SOFC is used in hydrogen power, they can replace fossil fuel sources and reduce their impact on climate change and air pollution. Such cells can be used in car engines or the space industry to reduce hydrocarbon emissions into the environment. Fuel cells based on the new material developed by scientists are potentially cost-effective to produce and can exhibit higher electrical conductivity than other solid-state conductors for SOFC.

"The transition to clean hydrogen energy is one of the possible ways to solve the problem of fossil fuel pollution. Proton-ceramic fuel cells are a promising alternative to hydrocarbon engines, because they combine high efficiency, flexibility in various operating conditions, and excellent performance. In our work we obtained a new energy-efficient material in which the proton concentration is doubled and the electrical conductivity becomes two times higher. It is important to note that the material shows such results at a temperature that is twice as low as the currently most studied solid-state oxygen-ion conductors. Lowering the temperature increases the economic efficiency of the final electrochemical device," explains the study's co-author Natalia Tarasova, Associate Professor at the Department of Physical Chemistry at UrFU.

Quest for elusive monolayers just got a lot simpler

Researchers can process 100 images covering 1 centimeter x 1 centimeter-sized samples like this one in around nine minutes using a new system that greatly simplifies the often-tedious search for monolayers in the lab.
Credit: University of Rochester photo / J. Adam Fenster

One of the most tedious, daunting tasks for undergraduate assistants in university research labs involves looking for hours on end through a microscope at samples of material, trying to find monolayers.

These two-dimensional materials—less than 1/100,000th the width of a human hair—are highly sought for use in electronics, photonics, and optoelectronic devices because of their unique properties.

“Research labs hire armies of undergraduates to do nothing but look for monolayers,” says Jaime Cardenas, an assistant professor of optics at the University of Rochester. “It’s very tedious, and if you get tired, you might miss some of the monolayers or you might start making misidentifications.”

Even after all that work, the labs then must doublecheck the materials with expensive Raman spectroscopy or atomic force microscopy.

Jesús Sánchez Juárez, a PhD student in the Cardenas Lab, has made life a whole lot easier for those undergraduates, their research labs, and companies that encounter similar difficulties in detecting monolayers.

Discovery offers starting point for better gene-editing tools

CRISPR has ushered in the era of genomic medicine. A line of powerful tools has been developed from the popular CRISPR-Cas9 to cure genetic diseases. However, there is a last-mile problem – these tools need to be effectively delivered into every cell of the patient, and most Cas9s are too big to be fitted into popular genome therapy vectors, such as the adenovirus-associated virus (AAV).

In new research, Cornell scientists provide an explanation for how this problem is solved by nature: they define with atomic precision how a transposon-derived system edits DNA in RNA-guided fashion. Transposons are mobile genetic elements inside bacteria. A lineage of transposon encodes IscB, which is less than half the size of Cas9 but equally capable of DNA editing. Replacing Cas9 with IscB would definitively solve the size problem.

The researchers’ paper, “Structural Basis for RNA-Guided DNA Cleavage by IscB-ωRNA and Mechanistic Comparison with Cas9,” published May 26 in Science.

The researchers used cryo-electron microscopy (Cryo-EM) to visualize the IscB-ωRNA molecule from a transposon system in high resolution. They were able to capture snapshots of the system in different conformational states. They were even able to engineer slimmer IscB variants, by removing nonessential parts from IscB.

“Next-generation fancy applications require the gene editor to be fused with other enzymes and activities and most Cas9s are already too big for viral delivery. We are facing a traffic jam at the delivery end,” said corresponding author Ailong Ke, professor of molecular biology and genetics in the College of Arts and Sciences. “If Cas9s can be packaged into viral vectors that have been used for decades in the gene therapy field, like AAV, then we can be confident they can be delivered and we can focus research exclusively on the efficacy of the editing tool itself.”

Silk layer improves function of surgical masks

UC researchers studied the effectiveness of surgical masks in combination with a silk face mask. Biology student Adam Parlin, now with SUNY-ESF, examined the properties of silk in a UC biology lab.
Photo/Joseph Fuqua II/UC Creative + Brand

University of Cincinnati researchers found that a double layer of silk in combination with a surgical mask can enhance its ability to prevent the spread of viruses like COVID-19.

UC biologist Patrick Guerra, UC biologist Theresa Culley, UC postdoctoral researcher Adam Parlin, now at SUNY-ESF, and UC graduate student Samuel Stratton, now at the University of Michigan, began investigating silk as an alternative face mask material at the start of the COVID-19 pandemic in 2020 when personal protective equipment such as the N95 face mask was in short supply.

UC researchers found that double masking with a silk face mask also helps prolong the life of surgical masks without impeding a person's ability to breathe comfortably.

The study was published in the journal Aerosol and Air Quality Research.

Does herpes simplex virus change during transmission?

A new study offers clues as to how herpes simplex virus (HSV) genetic diversity is shared between transmission partners. The authors used viral genome sequencing to follow oral and genital samples of HSV, collected over a year of each partner's infection. Often, the same viral variants were observed in both partners within a transmission pair. Occasionally these variants developed into viral genome differences between partners. This is the first study to compare HSV-1 genomes between adult sexual transmission partners. Image created with BioRender.com.
Credit: Moriah Szpara, Penn State / Penn State

A new study helps explain how the virus that causes herpes might change during transmission between partners and over time during a long-term infection within a human host, which could have implications for future treatment strategies. The study, by a team of researchers from Penn State and the University of Washington, is the first to track genetic differences of the herpes simplex virus (HSV-1) as it moves between adult sexual transmission partners. Their findings revealed that viral population movement between partners has a strong impact on whether genetic differences appear at the start of new infections.

A paper describing this work appears online in the journal PLoS Pathogens.

“Hundreds of minor differences in the genome of HSV-1 have been documented around the world, and many of these differences — called variants — can be detected within a single human host,” said Molly Rathbun, graduate student in biochemistry and molecular biology at Penn State and the lead author of the paper. “How often these variants are transmitted and how quickly they evolve within a person has remained elusive until now. Improving our understanding of these processes might help us understand why individuals vary so much in the severity and frequency of their symptoms.”

PFAS chemicals do not last forever

Once dubbed “forever chemicals,” per-and polyfluoroalkyl substances, or PFAS, might be in the market for a new nickname.

That’s because adding iodide to a water treatment reactor that uses ultraviolet (UV) light and sulfite destroys up to 90% of carbon-fluorine atoms in PFAS forever chemicals in just a few hours, reports a new study led by environmental engineering researchers at UC Riverside. The addition of iodide accelerates the speed of the reaction up to four times, saving energy and chemicals.

“Iodide is really doing some substantial work,” said corresponding author Jinyong Liu, an assistant professor of chemical and environmental engineering. “Not only does it speed up the reaction but it also allows the treatment of a ten times higher concentrations of PFAS, even some very recalcitrant structures.”

Liu’s lab has been working on ways to destroy PFAS through photochemical reactions since 2017. The new method has already attracted interest from industry and Liu’s group is partnering with companies to conduct pilot tests.

Synthetic chemicals known as PFAS contain multiple very strong carbon-fluorine bonds. Widespread use of these nonbiodegradable compounds in countless products since the 1940s has contaminated water supplies across America, with various negative health effects on humans and animals. Because the carbon-fluorine bond is very hard to break, PFAS pass through most water treatment systems unchanged.

Using Light and Sound to Reveal Rapid Brain Activity in Unprecedented Detail

The image shows the vasculature of the brain, and the colors illuminate how capillaries experience varying levels of oxygenation as the brain undergoes hypoxia.
Credit: Duke University

Duke researchers use a combination of hardware innovations and machine learning algorithms to create the fastest photoacoustic imaging tool available

Biomedical engineers at Duke University have developed a method to scan and image the blood flow and oxygen levels inside a mouse brain in real-time with enough resolution to view the activity of both individual vessels and the entire brain at once.

This new imaging approach breaks long-standing speed and resolution barriers in brain imaging technologies and could uncover new insights into neurovascular diseases like stroke, dementia and even acute brain injury.

The research appeared in the Nature journal Light: Science & Applications.

Imaging the brain is a balancing act. Tools need to be fast enough to capture rapid events, like a neuron firing or blood flowing through a capillary, and they need to show activity at different scales, whether it’s across the entire brain or at the level of a single artery.

Research breakthrough means warp speed ‘Unruh effect’ can finally be tested in lab settings

SFLORG Stock image

A major hurdle for work at the forefront of fundamental physics is the inability to test cutting-edge theories in a laboratory setting. But a recent discovery opens the door for scientists to see ideas in action that were previously only understood in theory or represented in science fiction.

One such theory is on the Unruh effect. When astronauts in a spacecraft undergo super strong acceleration and see the light of stars stream by, then the Unruh effect is an additional warm glow on top of the streaming light. First predicted by Canadian physicist Bill Unruh, this effect is closely related to the glow from black holes predicted by Stephen Hawking. This is because black holes strongly accelerate everything towards them.

“Black holes are believed to be not entirely black,” says Barbara Šoda, a PhD student in physics at the University of Waterloo. “Instead, as Stephen Hawking discovered, black holes should emit radiation. This is because, while nothing else can escape a black hole, quantum fluctuations of radiation can.”

Similar to how the Hawking effect needs a black hole, the Unruh effect requires enormous accelerations to produce a significant glow. The Unruh effect was therefore thought to be so weak that it would be impossible to measure with the acceleration that can be achieved in experiments with current technology.

Hidden Distortions Trigger Promising Thermoelectric Property

Brookhaven Lab members of the research team: Simon Billinge, Milinda Abeykoon, and Emil Bozin adjust instruments for data collection at the Pair Distribution Function beamline of the National Synchrotron Light Source II. In this setup, a stream of hot air heats samples with degree-by-degree precision as x-rays collect data on how the material changes.
Credit: Brookhaven National Laboratory

In a world of materials that normally expand upon heating, one that shrinks along one 3D axis while expanding along another stands out. That’s especially true when the unusual shrinkage is linked to a property important for thermoelectric devices, which convert heat to electricity or electricity to heat.

In a paper just published in the journal Advanced Materials, a team of scientists from Northwestern University and the U.S. Department of Energy’s Brookhaven National Laboratory describe the previously hidden sub-nanoscale origins of both the unusual shrinkage and the exceptional thermoelectric properties in this material, silver gallium telluride (AgGaTe2). The discovery reveals a quantum mechanical twist on what drives the emergence of these properties—and opens up a completely new direction for searching for new high-performance thermoelectrics.