FSU researchers capture high-resolution images of magnesium ions interacting with CRISPR gene-editing enzyme

Hong Li, professor in the Department of Chemistry and Biochemistry and director of the Institute of Molecular Biophysics.
Photo Credit: Devin Bittner/FSU College of Arts and Sciences

The gene-editing technology known as CRISPR has led to revolutionary changes in agriculture, health research and more.

In research published in Nature Catalysis, scientists at Florida State University produced the first high-resolution, time-lapsed images showing magnesium ions interacting with the CRISPR-Cas9 enzyme while it cut strands of DNA, providing clear evidence that magnesium plays a role in both chemical bond breakage and near-simultaneous DNA cutting.

“If you are cutting genes, you don’t want to have only one strand of DNA broken, because the cell can repair it easily without editing. You want both strands to be broken,” said Hong Li, professor in the Department of Chemistry and Biochemistry and director of the Institute of Molecular Biophysics. “You need two cuts firing close together. Magnesium plays a role in that, and we saw exactly how that works.”

Illuminating the dance of RNA with ultrabright X-rays

Researchers demonstrated the ability to observe fine details, right down to angstrom-scale features in RNA at SLAC’s Linac Coherent Light Source (LCLS).   
Photo Credit: Olivier Bonin/SLAC National Accelerator Laboratory

DNA, RNA, and proteins are three pillars of molecular biology. While DNA holds genetic instructions and proteins put these plans to action, RNA serves as the messenger and interpreter. DNA is transcribed to RNA, which then decodes those instructions to synthesize proteins. But large portions of RNA don't proceed to produce proteins, with a vast majority remaining just as RNA. What these molecules do or why they exist in such a state is still not fully understood.

Now, scientists have developed a promising method to uncover RNA’s secrets. Using X-ray free-electron laser sources such as the Linac Coherent Light Source at the Department of Energy’s SLAC National Accelerator Laboratory, researchers can now observe fine details, right down to angstrom-scale features, in RNA that is freely dispersed in solution so that large scale structural changes can occur – just as they would in our bodies. Not only does this research shed light on RNA's behavior, but the techniques developed can also be applied to other biological molecules. The implications are far-reaching, from better understanding diseases to designing new therapeutics. The results were published last week in Science Advances.

Scorpius images to test nuclear stockpile simulations

Two cathode inductive voltage-adder cells on the electrical test stand are aligned at Sandia National Laboratories. After thousands of tests, each holding 50 kilovolts across the insulating gap, they are ready to be mounted on seven-cell modules.
Photo Credit: Craig Fritz

One thousand feet below the ground, three national defense labs and a remote test site are building Scorpius — a machine as long as a football field — to create images of plutonium as it is compressed with high explosives, creating conditions that exist just prior to a nuclear explosion.

These nanosecond portraits will be compared with visuals of the same events generated by supercomputer codes to check how accurately the computed images replicate the real thing.

“It’s clear we need to know that the stockpile will work if required,” said Jon Custer, Sandia National Laboratories project lead. “Before President Bush’s testing moratorium in 1992, we knew it did since we were physically testing. Now we have computer codes. How well do they predict what really happens? Do we have accurate data we put into the codes? To answer these questions with higher fidelity, we need better experimental tools, and Scorpius is a major new experimental tool.”

The $1.8 billion project, combining the expertise of researchers from Sandia, Los Alamos and Lawrence Livermore national labs with support from the Nevada National Security Site — a test area bigger than the state of Rhode Island — is expected to be up and running by late 2027.

Small but mighty new gene editor

Structural analysis and deep mutational scanning (DMS) of AsCas12f. The team used cryogenic electron microscopy, a method to look at the structure of biological molecules in high-resolution, to analyze AsCas12f and engineer their new version. The DMS “heatmap” illustrates how all single mutations affected genome-editing activity. Blue squares indicate an undesirable mutation, while red ones represent desirable changes. The darker the color, the greater the effect.
Illustration Credit: © Hino et al. 2023

A new CRISPR-based gene-editing tool has been developed which could lead to better treatments for patients with genetic disorders. The tool is an enzyme, AsCas12f, which has been modified to offer the same effectiveness but at one-third the size of the Cas9 enzyme commonly used for gene editing. The compact size means that more of it can be packed into carrier viruses and delivered into living cells, making it more efficient. Researchers created a library of possible AsCas12f mutations and then combined selected ones to engineer an AsCas12f enzyme with 10 times more editing ability than the original unmutated type. This engineered AsCas12f has already been successfully tested in mice and has the potential to be used for new, more effective treatments for patients in the future.

By now you have probably heard of CRISPR, the gene-editing tool which enables researchers to replace and alter segments of DNA. Like genetic tailors, scientists have been experimenting with “snipping away” the genes that make mosquitoes malaria carriers, altering food crops to be more nutritious and delicious, and in recent years begun human trials to overcome some of the most challenging diseases and genetic disorders. The potential of CRISPR to improve our lives is so phenomenal that in 2020, researchers Jennifer Doudna and Emmanuelle Charpentier, who developed the most precise version of the tool named CRISPR-Cas9, were awarded the Nobel Prize in chemistry.

Revolutionary X-ray microscope unveils sound waves deep within crystals

Scientists developed a groundbreaking technology that allows them to see sound waves and microscopic defects inside crystals, promising insights that connect ultrafast atomic motion to large-scale macroscopic behaviors.
Photo Credit: Olivier Bonin/SLAC National Accelerator Laboratory

Scientists developed a groundbreaking technology that allows them to see sound waves and microscopic defects inside crystals, promising insights that connect ultrafast atomic motion to large-scale macroscopic behaviors.

Researchers at the Department of Energy’s SLAC National Accelerator Laboratory. Stanford University, and Denmark Technical University have designed a cutting-edge X-ray microscope capable of directly observing sound waves at the tiniest of scales – the lattice level within a crystal. These findings, published last week in Proceedings of the National Academy of Sciences, could change the way scientists study ultrafast changes in materials and the resulting properties.

“The atomic structure of crystalline materials gives rise to their properties and associated ‘use-case’ for an application,” said one of the researchers, Leora Dresselhaus-Marais, an assistant professor at Stanford and SLAC. “The crystalline defects and atomic scale displacements describe why some materials strengthen while others shatter in response to the same force. Blacksmiths and semiconductor manufacturing have perfected our ability to control some types of defects, however, few techniques today can image these dynamics in real-time at the appropriate scales to resolve how those the distortions connect to the bulk properties.”

Physicists Have Presented a New Way to Control Wheat Quality

Russia is one of the world's largest grain producers
Photo Credit: Andriy Nestruiev

A team of scientists from the Ural Federal University and the Ural Branch of the Russian Academy of Sciences has tested a new method that can be used to verify whether wheat has been irradiated and how safe the consequences are for consumers. Without documentation and sophisticated equipment, it is difficult to determine whether grain has been treated. Currently, there are methods for testing irradiated products, but they are more expensive and not as accurate, physicists say. The method of verification proposed by the scientists can make the analysis easier and cheaper, because the products themselves will act as an alternative to the detector in the radiation treatment. The study was supported by the Russian Foundation for Basic Research (project № 20-58-26002). The experimental results were published in the journal Radiation Physics and Chemistry.

Ionizing radiation of agricultural products is an effective method of disinfecting and neutralizing harmful microorganisms. This method is widely used in many countries and is approved by international organizations such as the World Health Organization, the Food and Agriculture Organization, and the International Atomic Energy Agency. After irradiation, the product is safe and does not lose its beneficial properties. Moreover, the destruction of harmful microorganisms (for example, mold) can increase the safety of the same wheat for further planting. In Russia, radiation treatment of agricultural products is allowed by law. There are several facilities in the country that use this type of decontamination. However, this type of food decontamination is not as widespread as, for example, in the United States or China.

CRISPR/Cas9-Based Gene Drive Could Suppress Agricultural Pests

NC State researchers used a florescent protein to mark the genetic changes to spotted-wing Drosophila.
Photo Credit: Courtesy of the researchers / North Carolina State University

Researchers have developed a “homing gene drive system” based on CRISPR/Cas9 that could be used to suppress populations of Drosophila suzukii vinegar flies – so-called “spotted-wing Drosophila” that devastate soft-skinned fruit in North America, Europe and parts of South America – according to new research from North Carolina State University.

The NC State researchers developed dual CRISPR gene drive systems that targeted a specific D. suzukii gene called doublesex, which is important for sexual development in the flies. CRISPR stands for “clustered regularly interspaced short palindromic repeats” and Cas9 is an enzyme that performs like molecular scissors to cut DNA. CRISPR systems are derived from bacterial immune systems that recognize and destroy viruses and other invaders, and are being developed as solutions to problems in human, plant and animal health, among other uses.

Targeting the doublesex gene resulted in female sterility in numerous experiments as females were unable to lay eggs, says Max Scott, an NC State entomologist who is the corresponding author of a paper in Proceedings of the National Academy of Sciences that describes the research.

“This is the first so-called homing gene drive in an agricultural pest that potentially could be used for suppression,” Scott said.

New therapy helps immune system eradicate brain tumors

Professor Anna Dimberg.
Photo Credit: Mikael Wallerstedt

Researchers from Uppsala University have developed a method that helps immune cells exit from blood vessels into the tumor and kill cancer cells. The aim is to improve the treatment of aggressive brain tumors. The study has been published in the journal Cancer Cell.

Glioblastoma is an aggressive brain tumor that lacks efficient treatment. This is in part due to the ability of the tumor to suppress or evade the body´s natural anti-cancer immune response. Immunotherapy, using checkpoint inhibitors, aims to reactivate our immune system against cancer. However, for this type of treatment to be effective, specific immune cells known as killer T cells are required to be present within the tumor.

Unfortunately, blood vessels in brain cancer are dysfunctional and act as a barrier, preventing killer T cells from reaching the tumor. As a result, this form of immunotherapy, which is effective against many forms of cancer, is ineffective against brain cancers.

Help the killer T cells

In the new study, the Uppsala researchers have developed a method to help the killer T cells reach the tumors and fight cancer cells. They used a viral vector that specifically infected the blood vessels in the brain and enabled them to produce a factor called LIGHT. This altered the function of the tumor vessels, increasing their ability to transport T cells from the blood into the tumor tissue.

Australian fruit holds the key to citrus disease resistance

Upuli Nakandala and Prof Robert Henry with a native Finger lime.
Photo Credit: Megan Pope

A comprehensive map of the genome of a native lime species that is resistant to a devastating citrus disease could be the key to preventing that disease entering Australia.

Researchers from The University of Queensland have sequenced the genome of the Australian round lime, also known as the Gympie lime, and are now looking at five other native citrus species including the finger lime.

PhD candidate Upuli Nakandala said the work aimed to identify a gene which provides resistance to Huanglongbing (HLB), also known as 'citrus greening', that could be incorporated into commercial citrus varieties.

“The species citrus australis is recognized as HLB-resistant so we put it first on our list,” Ms. Nakandala said.

How hallucinogenic substance in psilocybin mushrooms works on the molecular level

Once it was hot research. Then it was banned. Now, research on psychedelic substances is both hot and legal. There is a revival in psilocybin research in labs and clinics all over the world, including at SDU.
Photo Credit: Artur Kornakov

Psilocybin is a hallucinogenic compound found in about 200 mushroom species, including the liberty cap (Psilocybe semilanceata). For millennia, our ancestors have known and used this substance, and in recent years, it has received renewed interest from scientific researchers and therapists.

The substance has the potential to revolutionize the way we treat conditions such as severe depression and substance addiction, according to many. This is also the opinion of SDU researchers Himanshu Khandelia and Ali Asghar Hakami Zanjani from the Department of Physics, Chemistry and Pharmacy.

The two researchers have recently published the scientific paper The Molecular Basis of the Antidepressant Action of the Magic Mushroom extract, Psilocin. The article is the third in a series on the same topic from the two researchers (Interaction of psychedelic tryptamine derivatives with a lipid bilayer and Magic mushroom extracts in lipid membranes). The newest study's co-authors are Teresa Quynh Tram Nguyen and Luise Jacobsen. 

Exercise Increases the Number of Cancer-Destroying Immune Cells in Cancer Patients

Two new Finnish studies show that short bouts of light or moderate exercise can increase the number of immune cells in the bloodstream of cancer patients.
Photo Credit: Zen Chung

Exercise decreases the risk of cancer and reduces side effects of cancer treatments. In addition, it improves patients’ quality of life and the prognosis of cancer patients.

 “It was previously thought that cancer patients should just rest after a cancer diagnosis. Today, we have more and more researched information that exercise can even improve the prognosis of cancer. However, it is not yet fully known how exercise controls cancer,” explains Research Assistant Tiia Koivula.

Previous preclinical studies have found that exercise affects the functioning of the immune system so that more immune cells are transferred to the tumor site and they become more active in destroying cancer cells. Two studies conducted at the Turku PET Centre of the University of Turku in Finland aimed to find out whether a short exercise bout affects the mobilization of immune cells in cancer patients.

Genetically Modified Plants Grow Better in Arid and Saline Conditions

Tobacco is one of the most well-studied plants by scientists.
Photo Credit: Rodion Narudinov

Russian scientists have modified tobacco. They added the AtGSTF11 gene and improved the plant's resistance to adverse conditions. These adverse conditions include low temperatures, drought and salty soil. Model plants with the new gene used in the experiments showed increased vitality. The scientists have published a description of their experiments in the Russian Journal of Plant Physiology.

Plant stress (caused by a variety of factors - drought, temperature, contaminated soil, etc.) ends at the cellular level with oxidative stress: reactive oxygen species are formed in the cell. They destroy proteins, disrupt the structure of DNA and lead to cell death or interfere with vital functions, the scientists add. There are cellular mechanisms that prevent the development of oxidative stress - low-molecular antioxidant compounds, proteins (antioxidant enzymes), glutathione.

"Glutathione is a short sulfur-containing peptide that plays an important role in protecting plants from stress. It is formed, then cycled into oxidized and reduced forms, and so on. This is the glutathione cycle. In this process, reactive oxygen species are eliminated and plant cells do not die. A number of genes are involved in this cycle. We added another gene, glutathione S-transferase, and got a more viable plant," says Bulat Kuluev, Head of the Plant Genomics Laboratory at the Institute of Biochemistry and Genetics (Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences).

Even as temperatures rise, this hydrogel material keeps absorbing moisture

MIT engineers have found that a common hydrogel has unique, super-soaking abilities. Even as temperatures climb, the transparent material continues to absorb moisture, and could serve to harvest water in desert regions, and passively regulate humidity in tropical climates.
Photo Credit: Felice Frankel

The vast majority of absorbent materials will lose their ability to retain water as temperatures rise. This is why our skin starts to sweat and why plants dry out in the heat. Even materials that are designed to soak up moisture, such as the silica gel packs in consumer packaging, will lose their sponge-like properties as their environment heats up.

But one material appears to uniquely resist heat’s drying effects. MIT engineers have now found that polyethylene glycol (PEG) — a hydrogel commonly used in cosmetic creams, industrial coatings, and pharmaceutical capsules — can absorb moisture from the atmosphere even as temperatures climb.

The material doubles its water absorption as temperatures climb from 25 to 50 degrees Celsius (77 to 122 degrees Fahrenheit), the team reports.

PEG’s resilience stems from a heat-triggering transformation. As its surroundings heat up, the hydrogel’s microstructure morphs from a crystal to a less organized “amorphous” phase, which enhances the material’s ability to capture water.

Researchers develop carbon-negative concrete

Graduate student Zhipeng Li and Professor Xianming Shi.
Photo Credit: Courtesy of Washington State University

A viable formula for a carbon-negative, environmentally friendly concrete that is nearly as strong as regular concrete has been developed at Washington State University.  

In a proof-of-concept work, the researchers infused regular cement with environmentally friendly biochar, a type of charcoal made from organic waste, that had been strengthened beforehand with concrete wastewater. The biochar was able to suck up to 23% of its weight in carbon dioxide from the air while still reaching a strength comparable to ordinary cement.   

The research could significantly reduce carbon emissions of the concrete industry, which is one of the most energy- and carbon-intensive of all manufacturing industries. The work, led by doctoral student Zhipeng Li, is reported in the journal Materials Letters.

“We’re very excited that this will contribute to the mission of zero-carbon built environment,” said Xianming Shi, professor in the WSU Department of Civil and Environmental Engineering and the corresponding author on the paper.

Testing coatings to conserve canisters against corrosion

Video Credit: Ruth Frank

As anyone who has lived near the ocean can attest, metal and sea mist are a recipe for corrosion. A nuisance of coastal life, the consequences of these common chemical reactions become far more serious when it is taking aim at the stainless-steel canisters that contain spent nuclear fuel.

To shield steel from the corrosive threats posed by sea air, Sandia National Laboratories researchers tested a variety of nickel mixtures as protective coatings on stainless steel. The researchers found that the specific material applied, and the specific application process used, impacted the properties of the coating, including how protective it was against corrosion. Their results were published recently in the scientific journal Frontiers in Metals and Alloys.

Spent nuclear fuel is stored in quite a few coastal areas, where sea breezes can buffet canisters and deposit corrosive chloride salts such as sodium chloride, or more commonly known as table salt. Given enough time, the brine formed by these salts can corrode and pit stainless-steel canisters.

“Through our research, it became clear that it would not be easy to completely eliminate the possibility of a type of corrosion known as stress corrosion cracking,” said Charles Bryan, an expert on the storage of spent nuclear fuel and co-lead on the project. “Stress corrosion cracking is likely to eventually occur at some interim storage sites. It might take hundreds of years, but it could happen, so people started thinking about mitigation and repair technologies. We started looking at cold spray, which is a technique industry is very interested in, and at corrosion-resistant polymer coatings.”

Neutrons for better vaccines against multidrug resistant germs

Dr. Jia-Jheng Kang prepares measurements for the vaccines at the KWS-2 sample site.
Photo Credit: Bernhard Ludewig, FRM II / TUM

Neutrons from the Research Neutron Source Heinz Maier-Leibnitz (FRM II) can be used to explore the structure of biomolecules. The most recent success: the precise analysis of a promising vaccine against multidrug resistant germs.

Bacteria which are resistant to all conventional antibiotics cause more than a million deaths each year. Consequently, researchers around the world are searching for new therapeutic approaches to combat these pathogens. Two years ago, an international team in Grenoble identified an active ingredient suitable for the production of a vaccine against multidrug resistant bacteria Pseudomonas aeruginosa. The vaccine has in the meantime been successfully tested on mice.

"As with many new vaccines, in this case the active ingredient is embedded in liposomes. The exact characterization and understanding of these nanoscopic biomolecules is a key factor in the development and optimization of future vaccines," says Dr. Marco Maccarini, biophysicist at the French National Centre for Scientific Research (CNRS). Together with experts at the TIMC laboratory of the Université Grenoble Alpes (UGA) and at the FRM II he has successfully analyzed the structure of the candidate vaccine against Pseudomonas aeruginosa.

How football-shaped molecules occur in the universe

Graphic Credit: Shane Goettl/Ralf I. Kaiser

For a long time, it has been suspected that fullerene and its derivatives could form naturally in the universe. These are large carbon molecules shaped like a football, salad bowl or nanotube. An international team of researchers using the Swiss SLS synchrotron light source at PSI has shown how this reaction works. The results have just been published in the journal Nature Communications.

“We are stardust, we are golden. We are billion-year-old carbon.” In the song they performed at Woodstock, the US group Crosby, Stills, Nash & Young summarized what humans are essentially made of: star dust. Anyone with a little knowledge of astronomy can confirm the words of the cult American band – both the planets and we humans are actually made up of dust from burnt-out supernovae and carbon compounds billions of years old. The universe is a giant reactor and understanding these reactions means understanding the origins and development of the universe – and where humans come from.

In the past, the formation of fullerenes and their derivatives in the universe has been a puzzle. These carbon molecules, in the shape of a football, bowl or small tube, were first created in the laboratory in the 1980s. In 2010 the infrared space telescope Spitzer discovered the C60 molecules with the characteristic shape of a soccer ball, known as buckyballs, in the planetary nebula Tc 1. They are therefore the biggest molecules to have been discovered to date known to exist in the universe beyond our solar system.

Purifying water with the power of the sun

A Notre Dame researcher’s invention could improve access to clean water for some of the world’s most vulnerable people.

 “Today, the big challenges are information technology and energy,” says László Forró, the Aurora and Thomas Marquez Professor of Physics of Complex Quantum Matter in the University of Notre Dame's Department of Physics and Astronomy. “But tomorrow, the big challenge will be water.”

The World Health Organization reports that today nearly 2 billion people regularly consume contaminated water. It estimates that by 2025 half of the world’s population could be facing water scarcity. Many of those affected are in rural areas that lack the infrastructure required to run modern water purifiers, while many others are in areas affected by war, natural disasters or pollution. There is a greater need than ever for innovative ways to extend water access to those living without power, sanitation and transportation networks.

Recently, Forró's lab developed just such a solution. They created a water purifier, described in the Nature partner journal Clean Water, that is powered by a resource nearly all of the world’s most vulnerable people have access to: the sun.

Forensic Study Sheds Light on the Remains of Infants, Children

Photo Credit: Kat Wilcox

A new forensic science study sheds light on how the bones of infants and juveniles decay. The findings will help forensic scientists determine how long a young person’s remains were at a particular location, as well as which bones are best suited for collecting DNA and other tissue samples that can help identify the deceased.

“Crimes against children are truly awful, and all too common,” says Ann Ross, co-author of the study and a professor of biological sciences at North Carolina State University. “It is important to be able to identify their remains and, when possible, understand what happened to them. However, there is not much research on how the bones of infants and children break down over time. Our work here is a significant contribution that will help the medical legal community bring some closure to these young people and, hopefully, a measure of justice.”

For this study, the researchers used the remains of domestic pigs, which are widely used as an analogue for human remains in forensic research. Specifically, the researchers used the remains of 31 pigs, ranging in size from 1.8 kilograms (4 pounds) to 22.7 kilograms (50 pounds). The smaller remains served as surrogates for infant humans, up to one year old. The larger remains served as surrogates for children between the ages of one and nine.

Ural Scientists Design Plastics That Resist Radiation from Technology

Aleksey Korotkov tests the material for electrodynamic properties in an anechoic chamber.
Photo Credit: Rodion Narudinov

The team of scientists from the Institute of Technical Chemistry of the Ural Branch of the Russian Academy of Sciences (branch of the Perm Federal Research Centre of UB RAS) and the Ural Federal University created a composite polymer material. The new composite is made from recycled materials and has unique properties. It reflects electromagnetic waves. It is suitable for wireless systems, including radar and satellite communications systems. Such a composite (actually a plastic) can be used to make housing for devices such as smartphones. It will allow them to reduce their electromagnetic radiation. The description of the new material is published in the journal Diamond and Related Materials.

"It is extremely important that we have been able to create a new composite material from virtually recycled raw materials. The basis of the material is chopped carbon fibers, which we extracted from carbon plastics. In addition, the composition of the composite includes magnetite (it is the magnetic nanoparticles) synthesized in our laboratory. Our work can increase the attractiveness of carbon plastics processing due to the use of secondary extracted carbon fibers in the expensive technologies," says Svetlana Astafieva, the co-author of the development, the Head of the Laboratory of Structural-Chemical Modification of Polymers of the Institute of Technical Chemistry of UB RAS.