Scientists use quantum biology, AI to sharpen genome editing tool

ORNL scientists developed a method that improves the accuracy of the CRISPR Cas9 gene editing tool used to modify microbes for renewable fuels and chemicals production. This research draws on the lab’s expertise in quantum biology, artificial intelligence and synthetic biology.
Illustration Credit: Philip Gray/ORNL, U.S. Dept. of Energy

Scientific Frontline: Extended "At a Glance" Summary: Enhancing CRISPR Cas9 with Quantum Biology and AI

The Core Concept: Scientists have combined principles of quantum biology with explainable artificial intelligence (AI) to significantly improve the accuracy and efficiency of the CRISPR Cas9 genome editing tool for modifying microbes.

Key Distinction/Mechanism: While traditional CRISPR models were developed for mammalian or model species and often failed in microbes due to differing chromosomal structures, this new approach analyzes the quantum chemical properties of nucleotides (like electron distribution). An explainable AI model is then used to predict the most effective guide RNAs, ensuring the Cas9 enzyme binds successfully to the targeted microbial DNA.

Major Frameworks/Components: 

• CRISPR Cas9 Machinery: A powerful bioengineering tool that uses a unique guide RNA to direct an enzyme to cleave and modify specific genetic code.
• Quantum Biology: A field bridging molecular biology and quantum chemistry, used here to investigate how the electronic structures of nucleotides affect chemical reactivity and conformational stability.
• Explainable Artificial Intelligence (Iterative Random Forest): An interpretable AI model trained on roughly 50,000 guide RNAs targeting E. coli. Unlike "black box" algorithms, it reveals the specific molecular mechanisms and rules that dictate optimal cutting efficiency.
• Functional Genomics: The biological discipline of linking specific genetic codes (genotype) to physical traits (phenotype).

New strategy may halt tumors' aggressive response to glucose deprivation

The figure shows the expression of a differentiation marker in the tumors of mice treated with the glucose inhibitor, the epigenetic inhibitor, or both. Top left image is the placebo, top right is the glucose inhibitor, bottom left is the epigenetic inhibitor and bottom right is the glucose inhibitor and epigenetic inhibitor. The brown signal indicates the presence of the differentiation marker. The treatment with the glucose inhibitor (top right) reduces the brown signal, whereas the addition of the epigenetic inhibitor rescues the expression of the differentiation marker.
Image Credit: Dr. Claudio Scafoglio.

One of the hallmarks of cancer cell development is its dependence on sugar, especially glucose, to grow and divide. Scientists have long been studying how to restrict or block this process that promotes tumor growth, called glycolysis, from happening as a possible effective strategy against cancer.

Previously, researchers from the UCLA Health Jonsson Comprehensive Cancer Center identified a specific protein sodium glucose transporter 2, or SGLT2, as a mechanism that lung cancer cells can utilize to obtain glucose. Drugs that inhibit SGLT2 are already FDA approved for other conditions and the UCLA team found these drugs could also delay the development of lung cancer and improved survival when tested in mice, suggesting these drugs could be repurposed for lung cancer treatment.

However, while inhibiting glycolysis can slow down the growth of tumors, the researchers found it can also make cancer cells more aggressive, making the cancer harder to treat. This led the team to look at other mechanisms of resistance in the tumors that still grow while being treated with SGLT2 inhibition that may link glucose restriction to increases aggression.

‘Neglected’ Dinosaur Had Super Senses

A family of Thescelosaurus emerges from safety to forage in the forests of the Hell Creek Formation, 66 million years ago.
Illustration Credit: Anthony Hutchings.

A CT scan of an often-overlooked, plant-eating dinosaur’s skull reveals that while it may not have been all that “brainy,” it had a unique combination of traits associated with living animals that spend at least part of their time underground, including a super sense of smell and outstanding balance. The work is the first to link a specific sensory fingerprint with this behavior in extinct dinosaurs.

The dinosaur in question, Willo, is a specimen housed at the North Carolina Museum of Natural Sciences. Willo is a Thescelosaurus neglectus – a small (12 feet or 3.6 meters long) but heavy (750 pounds or 340 kilograms) herbivore that lived in what is now North America just before the end-Cretaceous mass extinction event, 66 million years ago.

Willo’s scientific name roughly translates to “wonderful, overlooked lizard.” But David Button, a former Brimley Postdoctoral Scholar at the North Carolina Museum of Natural Sciences and North Carolina State University, decided to look more closely at this “overlooked” dinosaur’s skull. Button is currently a research associate at the University of Bristol in the U.K.

The kids aren't alright: Saplings reveal how changing climate may undermine forests

A University of Arizona-led experiment exposed different species of trees to heat and drought to study how young trees respond to climate change. After 20 weeks of drought and a one-week heat wave, this Douglas fir sapling was dry and brittle.
Photo Credit: Alexandra Lalor

UArizona researchers studied how young trees respond to a hotter, drier climate. Their findings can help shape forest management policy and our understanding of how landscapes will change.

A University of Arizona-led experiment exposed different species of trees to heat and drought to study how young trees respond to climate change. After 20 weeks of drought and a one-week heat wave, this Douglas fir sapling was dry and brittle. Alexandra Lalor

As climate scientist Don Falk was hiking through a forest, the old, green pines stretched overhead. But he had the feeling that something was missing. Then his eyes found it: a seedling, brittle and brown, overlooked because of its lifelessness. Once Falk's eyes found one, the others quickly fell into his awareness. An entire generation of young trees had died.

Falk – a professor in the UArizona School of Natural Resources and the Environment, with joint appointments in the Laboratory of Tree-Ring Research and the Arizona Institute for Resilience – refers to this large-scale die-off of the younger generation of trees as a recruitment failure. This is particularly devastating for a population of trees because the youngest are essential for forest recovery following massive die-off events, such as severe wildfires and insect outbreaks, both of which will become more frequent as the climate continues to change, he said.

People with prior illness more likely to report longer symptoms after COVID-19 infection

Photo Credit: Kelly Sikkema

The study from King’s College London, which is published on the pre-print server MedRxiv and has not been peer-reviewed, shows that while two thirds of individuals with post-COVID illness were healthy before infection, individuals with long illness duration were significantly more likely to have similar symptoms 1-2 months before developing COVID-19.

Most people with COVID-19 recover completely within a few days or weeks. However, some report ongoing symptoms including fatigue, ‘brain fog’, sneezing, a runny nose and headache long after infection. For some individuals, this may manifest as long COVID.

In this study, researchers first analyzed data from over 23,000 ZOE Symptom Study app users, who reported their health (whether healthy or unhealthy) at least once weekly, both before and after they had COVID-19. They found that individuals who had symptoms before they caught SARS-CoV-2 infection were significantly more likely to have a longer illness duration.

The researchers then assessed 1350 adults who reported long-term symptoms after COVID-19 (at least eight weeks, with nearly a thousand having symptoms for more than 12 weeks), matched with 1350 individuals whose symptoms had resolved within four weeks.

Warmer, wetter winters bring risks to river insects

Professor Steve Ormerod, School of Biosciences
Photo Credit: Courtesy of Cardiff University

Research by Cardiff University has shown that the warmer, wetter winters in the UK caused by climate change are likely to impact the stability of insect populations in streams.

The research, spanning four decades, has demonstrated that stream insects are affected by warmer, wetter winters caused by fluctuating climate over the Atlantic Ocean. The consequences are felt by insect populations even in the smallest Welsh river sources.

“UK winters are becoming warmer and wetter on average, and we wanted to understand how this might impact our rivers. Streams and rivers are profoundly affected by climate through changes in global air temperatures and precipitation which affect flow patterns and water temperature.

“Over the years, we’ve noticed increasingly that changes in our rivers also track global climatic patterns over the Atlantic and these provide important clues about climate change” said Professor Steve Ormerod, the Water Research Institute at Cardiff University.

Predatory Bacteria

Predatory bacteria such as B. bacteriovorus attack and neutralize other types of bacteria.
Illustration Credit:: Benjamin Güdel

Antibiotic resistance is increasingly becoming a challenge for treating bacterial infections. Microbiologist Simona Huwiler is researching whether predatory bacteria — that is, bacteria that eat other bacteria — can be used as a new kind of antibiotic and whether this approach also leads to the development of resistance.

The spread of antibiotic-resistant bacteria is an enormous challenge for the healthcare system. It is almost impossible to stop the development of antimicrobial resistance, and there are almost no new kinds of antibiotics being developed that can be used against drug-resistant bacteria. Researchers are therefore looking to nature to find alternatives. They have set their sights on the natural enemies of pathogenic bacteria such as bacteriophages – viruses that kill bacteria – as well as predatory bacteria that attack, consume and eliminate other types of bacteria. Bdellovibrio bacteriovorus is one type of predatory bacteria that is of interest to researchers. It’s an ideal candidate because it likes to dine on gram-negative bacteria with antibiotic resistance. Experiments in the lab have shown that Bdellovibrio bacteriovorus is capable of killing and eating many kinds of pathogenic bacteria, including Escherichia coli, Enterobacter, Proteus, Serratia, Citrobacter, Yersinia, Shigellen, Salmonella and Vibrio. This varied meal plan is an advantage compared to bacteriophages, which usually prefer to eat one specific kind of bacteria.

Ural Scientists Have Modernized the Process of Nuclear Fuel Reprocessing

The uranium obtained after reprocessing spent nuclear fuel can be reused.
Photo Credit: Lukas Lehotsk

UrFU scientists have discovered that the use of gallium and indium can make the process of pyrochemical reprocessing of nuclear fuel cheaper while maintaining its efficiency. This technology uses molten salts and liquid gallium to separate components of spent nuclear fuel (SNF). To make the process cheaper, the physicists added indium: the technology remained as effective, but the cost of reprocessing itself decreased. The results of the study will help modernize current SNF reprocessing methods and make them more efficient. Full details of the study are published in Alloys.

"This method has many advantages, in particular it focuses on the reprocessing of high-activity, low-life nuclear fuel with a high burn-up depth, which cannot be achieved by other methods such as water technology. It is also environmentally safer, as the amount of radioactive waste after reprocessing is reduced. Gallium can be used in fuel reprocessing by this method, but we have found that by adding indium, the reprocessing efficiency remains as high, but the cost of the process is reduced," explains Alexander Dedyukhin, senior engineer at the Department of Rare Metals and Nanomaterials at UrFU.

World’s first smart breathing tube for mechanically ventilated patients set for human trials

Professor Steve Morgan
Photo Credit: Courtesy of University of Nottingham

The University of Nottingham has secured £1.1 million in funding from the Medical Research Council to undertake human trials for the world’s first optical fiber sensor-equipped endotracheal tube (iTraXS).

Seriously ill or anaesthetized patients are unable to breathe naturally, so clinicians often use endotracheal tubes (ETTs), which are placed in the trachea (windpipe) to maintain an open airway and allow the patient to breathe through a mechanical ventilator. To do this, the tube is placed into the airway and a cuff (balloon) is inflated at the trachea to create a gas seal that allows air to be delivered to the lungs effectively. However, incorrect cuff inflation pressure can cause two main problems.

If pressure is too low, it can risk fluid getting past the cuff and causing ventilator-associate pneumonia (VAP). VAP increases the likelihood of death, affecting up to 20% of people in intensive care, and costs the NHS between £10,000 and £20,000 per patient. Conversely, if pressure is too high it can cause a pressure injury in the trachea, ranging from moderate to severe sore throats through to permanent scarring and narrowing of the windpipe.

The fascinating relationship between mice and a plant that flowers once a century in terms of seed dispersal

Researchers revealed unexpected dispersal behavior of field mice, which influences the forest ecosystem.
Illustration Credit: Reiko Matsushita

Researchers at Nagoya University in Japan have revealed new insights into the interaction between mast seeding plants and the animals that eat their seeds. Hanami Suzuki and Professor Hisashi Kajimura examined the behavior of field mice using seeds from once-in-a-century flowering sasa bamboo plants in central Japan.

The researchers found that the seed use patterns of field mice differed by species (large Japanese field mouse Apodemus speciosus and small Japanese field mouse A. argenteus), the presence or absence of understory vegetation, forest tree species (broadleaf forest or coniferous forest), and season (summer or fall). Their findings underscore the importance of understanding the needs of both plants and animals to ensure the health of local ecosystems. They also overturn a previously held belief about how mice store seeds. 

Dwarf bamboo (Sasa borealis) exhibits masting behavior in wide areas. Masting behavior means a plant collectively flowers and seeds at regular intervals to overwhelm predators and maximize pollination rates. Masting events are rare, however, with intervals up to 120 years. But when they occur, the resulting abundance of seeds in the forest provides easily available food for various animals, especially rodents such as field mice.