. Scientific Frontline: November 2023

Sunday, November 12, 2023

Atomic dance gives rise to a magnet

Tong Lin (from left), Hanyu Zhu and Jiaming Luo at EQUAL lab.
Photo Credit: Jeff Fitlow/Rice University

Quantum materials hold the key to a future of lightning-speed, energy-efficient information systems. The problem with tapping their transformative potential is that, in solids, the vast number of atoms often drowns out the exotic quantum properties electrons carry.

Rice University researchers in the lab of quantum materials scientist Hanyu Zhu found that when they move in circles, atoms can also work wonders: When the atomic lattice in a rare-earth crystal becomes animated with a corkscrew-shaped vibration known as a chiral phonon, the crystal is transformed into a magnet.

According to a study published in Science, exposing cerium fluoride to ultrafast pulses of light sends its atoms into a dance that momentarily enlists the spins of electrons, causing them to align with the atomic rotation. This alignment would otherwise require a powerful magnetic field to activate, since cerium fluoride is naturally paramagnetic with randomly oriented spins even at zero temperature.

A closer look at rebel T cells

Video Credit: La Jolla Institute

Scientists at La Jolla Institute for Immunology (LJI) are investigating a talented type of T cell.

Most T cells only work in the person who made them. Your T cells fight threats by responding to molecular fragments that belong to a pathogen—but only when these molecules are bound with markers that come from your own tissues. Your influenza-fighting T cells can’t help your neighbor, and vice versa.

“However, we all have T cells that do not obey these rules,” says LJI Professor and President Emeritus Mitchell Kronenberg, Ph.D. “One of these cell types is mucosal-associated invariant T (MAIT) cells.”

Now Kronenberg and his LJI colleagues have uncovered another MAIT cell superpower: MAIT cells can recognize the same markers whether they come from humans or mice. Kronenberg calls this finding “astounding.” “Humans diverged from mice in evolution 60 million years ago,” he says.

This new research, published in Science Immunology, sheds light on the genes and nutrients that give MAIT cells their fighting power. The findings are an important step toward one day harnessing these cells to treat infectious diseases and improve cancer immunotherapies.

Researchers identify previously unknown step in cholesterol absorption in the gut

Illustration Credit: Scientific Frontline

UCLA researchers have described a previously unknown step in the complex process by which dietary cholesterol is processed in the intestines before being released into the bloodstream – potentially revealing a new pathway to target in cholesterol treatment.

Although an existing drug and statins impact part of the process, an experimental drug being studied in UCLA research labs appears to specifically target the newfound pathway, possibly adding a new approach to the cholesterol management toolbox.

“Our results show that certain proteins in the Aster family play a critical role in moving cholesterol through the absorption and uptake process,” said Dr. Peter Tontonoz, a UCLA professor and researcher in Pathology and Laboratory Medicine and Biological Chemistry, senior author of an article in Science. “The Aster pathway appears to be a potentially attractive target for limiting intestinal cholesterol absorption and reducing levels of plasma cholesterol.”

Cholesterol from food is absorbed by cells that line the inner surface of the intestines – enterocytes – where it is processed into droplets that eventually reach the bloodstream. But this journey involves a multistep process.

Thursday, November 9, 2023

Plastics treaty must tackle problem at source

The treaty should cover the entire lifecycle of plastics, including fossil fuel production.
Photo Credit Aaron M Sprecher / Greenpeace

The new Global Plastics Treaty must tackle the problem at source, researchers say.

An international negotiation meeting (INC-3) in Kenya begins on Monday, aiming to further develop a legally binding treaty on plastic pollution.

Writing in the journal Science, researchers say the treaty must priorities “upstream” issues: cutting total production and consumption of plastics, phasing out hazardous chemicals and tackling fossil fuel subsidies.

They highlight a “worrying” level of focus on downstream recycling and waste management – when the true solution must address the full life cycle of plastics.

They say the treaty must be holistic – with more focus on early interventions and the people, places and ecosystems most impacted by plastic pollution.

“Right now, simply too much attention and capital is focused ‘downstream’ – recycling and cleaning up plastic already in the environment, in many cases just after a single use” said Dr Mengjiao (Melissa) Wang, from Greenpeace Research Laboratories at the University of Exeter.

Antibodies to Cow’s Milk Linked to Increased Risk of Cardiovascular Death

Corinne Keet, MD, PhD, pediatric allergy and immunology professor in the UNC Department of Pediatrics
Photo Credit: Courtesy of University of North Carolina School of Medicine

Sensitivity to common food allergens such as cow’s milk and peanuts could be an important and previously unappreciated cause of heart disease, new research suggests – and the increased risk for cardiovascular death includes people without obvious food allergies.

In a paper published in The Journal of Allergy and Clinical Immunology that describes analyses led by Corinne Keet, MD, PhD, pediatric allergy and immunology professor in the UNC Department of Pediatrics of two longitudinal studies, the authors show that the people who produced IgE antibodies to cow’s milk and other foods were at significantly increased risk of cardiovascular mortality. This was true even when traditional risk factors for heart disease, such as smoking, high blood pressure, and diabetes were accounted for. The strongest link was for cow’s milk, but IgE to other allergens such as peanut and shrimp were also significant among those who eat the foods.

This troubling finding represents the first time that IgE antibodies to common foods have been linked to increased risk of cardiovascular mortality, the researchers report. The findings do not conclusively prove that food antibodies are causing the increased risk, but the work builds on previous studies connecting allergic inflammation and heart disease.

What’s the story behind ASMR clips?

Quiet noises such as touching a microphone with your fingertips trigger a pleasant feeling in some people.
Photo Credit: © RUB, Marquard

Researchers at Ruhr University Bochum have published the first systematic review of Autonomous Sensory Meridian Response (ASMR).

Millions of people watch content creators on YouTube and social media platforms such as TikTok as they whisper soothing words, perform simulated role plays such as a visit to the hairdresser, or interact with certain objects such as the keyboard of a computer in a specific rhythm. About 25 to 30 percent of the viewers experience the Autonomous Sensory Meridian Response (ASMR) associated with well-being, a characteristic tingling sensation on the scalp and neck. Tobias Lohaus of Ruhr University Bochum, Germany, together with Professor Patrizia Thoma (also Ruhr University) and Professor Silja Bellingrath (University of Duisburg-Essen), published the first systematic review on this topic. This systematic review reveals that, among other things, this phenomenon is associated with short-term positive effects on mental health. The research team published their findings in the journal Psychology of Consciousness: Theory, Research, and Practice.

General aviation sector grounded by red tape and sky-high costs

Dr Lucas Tisdall piloting his plane.
Photo Credit: Courtesy of University of South Australia

Red tape, over-regulation, spiraling costs and a vacuum of government policy are putting significant pressure on the general aviation sector in Australia, according to a survey of industry chiefs.

Ageing infrastructure, thin profit margins and conflicts over airspace allocation are all contributing to pessimism in the non-airline civil aviation sector that employs thousands of people.

In a new paper published this month in Case Studies on Transport Policy, aviation experts from Queensland and the University of South Australia (UniSA) outline the issues plaguing the industry, most of which come down to a lack of policy direction in aviation.

The sector includes training, aeromedical, emergency response and charter services in rural and remote communities.

Interviews conducted with the principals of 21 aviation organizations reveal that outside of regulation, the main concerns are the costs associated with operating premises and airport infrastructure.

Extracellular vesicles captured using sustainable wood cellulose-based nanofiber sheets may identify and improve cancer treatment

Researchers developed a technique using cellulose nanofiber (CNF) sheets to capture extracellular vesicles (EVs). Extracting and analyzing EVs using this technology has the potential to revolutionize early cancer diagnosis and open the door to personalized medicine.
Image Credit: Takao Yasui

A research team in Japan, led by Nagoya University’s Akira Yokoi, has developed an innovative technique using cellulose nanofiber (CNF) sheets derived from wood cellulose to capture extracellular vesicles (EVs) from fluid samples and even organs during surgery. EVs are small structures from cancerous cells that play a crucial role in cell-to-cell communication. Extracting and analyzing EVs using this new technology has the potential to revolutionize early cancer diagnosis and open the door to personalized medicine. The researchers published their findings in Nature Communications

Cancer is notorious for its poor prognosis and in many cases goes undetected until its advanced stages, leaving patients with limited treatment options. Detecting the cancer early using EVs and analyzing them provides vital information on disease status and its progression. This should assist physicians in monitoring and adjusting personalized cancer treatment plans. However, researchers have been limited in previous attempts to use EVs due to the lack of an effective isolation strategy. 

Wednesday, November 8, 2023

Scientists are taking major steps towards completing the world’s first synthetic yeast.

Photo Credit: Karyna Panchenko

A UK-based team of Scientists, led by experts from the University of Nottingham and Imperial College London, have completed construction of a synthetic chromosome as part of a major international project to build the world’s first synthetic yeast genome.

The work, which is published today in Cell Genomics, represents completion of one of the 16 chromosomes of the yeast genome by the UK team, which is part of the biggest project ever in synthetic biology; the international synthetic yeast genome collaboration.

The collaboration, known as 'Sc2.0' has been a 15-year project involving teams from around the world (UK, US, China, Singapore, UK, France and Australia), working together to make synthetic versions of all of yeast's chromosomes. Alongside this paper, another 9 publications are also released today from other teams describing their synthetic chromosomes. The final completion of the genome project - the largest synthetic genome ever - is expected next year.

New antifungal molecule kills fungi without toxicity in human cells, mice

The mechanism for a critical but highly toxic antifungal is revealed in high resolution. Self-assembled Amphotericin B sponges (depicted in light blue) rapidly extract sterols (depicted in orange and white) from cells. This atomic level understanding yielded a novel kidney-sparing antifungal agent. 
Illustration Credit: Jose Vazquez

A new antifungal molecule, devised by tweaking the structure of prominent antifungal drug Amphotericin B, has the potential to harness the drug’s power against fungal infections while doing away with its toxicity, researchers at the University of Illinois Urbana-Champaign and collaborators at the University of Wisconsin-Madison report in the journal Nature.

Amphotericin B, a naturally occurring small molecule produced by bacteria, is a drug used as a last resort to treat fungal infections. While AmB excels at killing fungi, it is reserved as a last line of defense because it also is toxic to the human patient – particularly the kidneys. 

Temperature increase triggers viral infection

Illustration of phage virus injecting its DNA into a cell
Illustration Credit: Alex Evilevitch and Ting Liu

Researchers at Lund University, together with colleagues at the NIST Synchrotron Facility in the USA, have mapped on an atomic level what happens in a virus particle when the temperature is raised.

"When the temperature rises, the virus's genetic material changes its form and density, becoming more fluid-like, which leads to its rapid injection into the cell," says Alex Evilevitch who led the study.

Viruses lack their own metabolism and the ability to replicate independently; they are entirely dependent on a host cell to multiply. Instead, the virus hijacks the internal machinery of the infected cell to produce new virus particles, which are then released and spread to infect other cells.

In most cases, the virus's genetic material, DNA, is enclosed within a protective protein shell called a capsid. A research group at Lund University is working to understand the process by which the virus ejects its genetic material from the capsid and into cells and what causes the virus's DNA to be released.

It all began with a study published in 2014, where the Lund University researchers observed that there seems to be a sudden change in the virus's genetic material when exposed to the infection temperature, around 37 degrees.

‘Alien’ wasps thriving in tropical forests, study finds

Dolichomitus
Photo Credit: Pjt56
(CC BY-SA 4.0 DEED)

Researchers say they have discovered high diversity of Darwin wasps in a tropical rainforest in Brazil, wasps which were previously thought to thrive more in cooler habitats.

The wasps, which survive by living off host insects and spiders until adult-sized, were discovered on a mountain in the Brazilian Atlantic Rainforest. The number of types found were similar to that previously found in the whole of the UK.

The latest findings adds to a growing body of evidence that debunks the widely held belief that the Darwin wasp does not thrive in tropical environments and points to the possibility of many wasp species unknown to researchers in the past.

Researchers say it also provides further evidence of the biodiversity of the Brazilian Atlantic Rainforest and the significance of protecting and restoring the land from the effects of climate change and damage caused by human activities.

Physicists trap electrons in a 3D crystal for the first time

The rare electronic state is thanks to a special cubic arrangement of atoms (pictured) that resembles the Japanese art of “kagome.” 
Image Credit: Courtesy of the researchers / MIT

Electrons move through a conducting material like commuters at the height of Manhattan rush hour. The charged particles may jostle and bump against each other, but for the most part they’re unconcerned with other electrons as they hurtle forward, each with their own energy.

But when a material’s electrons are trapped together, they can settle into the exact same energy state and start to behave as one. This collective, zombie-like state is what’s known in physics as an electronic “flat band,” and scientists predict that when electrons are in this state, they can start to feel the quantum effects of other electrons and act in coordinated, quantum ways. Then, exotic behavior such as superconductivity and unique forms of magnetism may emerge.

Now, physicists at MIT have successfully trapped electrons in a pure crystal. It is the first time that scientists have achieved an electronic flat band in a three-dimensional material. With some chemical manipulation, the researchers also showed they could transform the crystal into a superconductor — a material that conducts electricity with zero resistance.

Scientists engineer potent immune cells for ‘off-the-shelf’ cancer immunotherapy

Illustration Credit: Scientific Frontline

UCLA scientists have developed a new method to engineer more powerful immune cells that can potentially be used for “off-the-shelf” cell therapy to treat challenging cancers.

“Off-the-shelf” cell therapy, also known as allogenic therapy, uses immune cells derived from healthy donors instead of patients. The approach can bring cell therapies, like chimeric antigen receptor (CAR) T cell therapy, to more patients in a timelier manner, which is one of the major barriers in getting these life-saving treatments to patients.

“Time is often of the essence when it comes to treating people with advanced cancers,” said Lili Yang, associate professor of microbiology, immunology and molecular genetics and member of the UCLA Health Jonsson Comprehensive Cancer Center. “Currently, these types of therapies need to be tailored to the individual patient. We have to extract white blood cells from a patient, genetically engineer the cells and then re-infuse them back into the patient. This process can take weeks to months and can cost hundreds of thousands of dollars to treat each patient.”

Experts predict ‘catastrophic ecosystem collapse’ of UK forests within the next 50 years if action not taken

Photo Credit: Greg Larcombe

A team of experts from across Europe has produced a list of 15 overlooked and emerging issues that are likely to have a significant impact on UK forests over the next 50 years.

This is the first ‘horizon scanning’ exercise – a technique to identify relatively unknown threats, opportunities, and new trends – of UK forests. The aim is to help researchers, practitioners, policymakers, and society in general, better prepare for the future and address threats before they become critical.

Dr Eleanor Tew, first author, visiting researcher at Cambridge’s Department of Zoology and Head of Forest Planning at Forestry England said: “The next 50 years will bring huge changes to UK forests: the threats they face, the way that we manage them, and the benefits they deliver to society.”

Forestry England, a part of the Forestry Commission, collaborated with the University of Cambridge on the study, which was published today in the journal, Forestry.

TUM makes first daily current measurements of changes in the earth's rotation

The ring laser in Wettzell has been continuously improved since its commissioning.
Photo Credit: Astrid Eckert / TUM 

Researchers at the Technical University of Munich (TUM) have succeeded in measuring the earth's rotation more exactly than ever before. The ring laser at the Geodetic Observatory Wettzell can now be used to capture data at a quality level unsurpassed anywhere in the world. The measurements will be used in determining the earth's position in space, will benefit climate research and will make climate models more reliable.

Care to take a quick step down to the basement and see how fast the earth has been turning in the last few hours? Now you can at the Geodetic Observatory Wettzell. TUM researchers have improved the ring laser there so that it can provide daily current data, which until now has not been possible at comparable quality levels.

What exactly does the ring laser measure? On its journey through space the earth rotates on its axis at slightly varying speeds. In addition, the axis around which the planet spins is not completely static, it wobbles a bit. This is because our planet is not completely solid, but is made up of various component parts, some solid, some liquid. So, the insides of the earth itself are constantly in motion. These shifts in mass accelerate or brake the planet's rotation, differences which can be detected using measurement systems like the TUM ring laser.

Poison dart frogs: Personality determines reproductive strategies

The Allobates femoralis species of poison dart frogs follows different strategies during reproduction according to their behavioral type.
Photo Credit: Eva Ringler

Poison frogs of the species Allobates femoralis are common in the rainforests in South America. Their highly poisonous relatives, such as frogs of the genus Phyllobates, were frequently used by indigenous people of Colombia to extract toxins by rubbing the skin onto arrowheads for the purposes of hunting and fighting. Allobates femoralis frogs are not poisonous. Like many other animal species, however, they have distinct personality traits. Both the males and females, for example, may be particularly bold, aggressive, or eager to explore. Poison frogs mate with several partners over the course of a reproductive period and their character traits have a considerable influence on the reproductive strategies employed by individual animals. 

Most of the previous studies in other animal taxa have examined the effect of personality traits on a single measure of reproductive success. In two recently published studies, researchers in the Institute of Ecology and Evolution at the University of Bern have presented new results on the effects of different combinations of personality traits in both males and females on different components of reproductive success. They examined the influence of personality on mating success, the number of clutches produced, as well as the numbers of offspring that survive into adulthood. The researchers were able to show that certain personality traits are already present in poison dart frogs at tadpole stage and that they also persist after the subsequent metamorphosis. 

Ural Scientists Have Synthesized a New Substance for the Treatment of Alzheimer’s Disease


Scientists from the Ural Federal University, the Institute of Organic Synthesis of the Ural Branch of the Russian Academy of Sciences, together with colleagues from India have developed a method for creating safe and non-toxic substances that could become the basis for drugs for Alzheimer's disease. Using the new technology, they synthesized and tested several compounds of tacrine analogues, which toxicity is estimated to be from two to five times lower than that of the known drug. The description of the new method and the compounds obtained was published in the Journal of Heterocyclic Chemistry

"We believe that our technology will help to create safe substances that will become the basis for future drugs for Alzheimer's disease. Our studies have shown that the toxicity of the resulting substances is two to five times lower than that of tacrine. At the same time, they are effective as they help to increase the level of acetylcholine in the cerebral cortex, which slows down the destruction of neuronal connections. This allows patients to maintain their cognitive functions and lead an active and fulfilling life for as long as possible," explains Nibin Joy Muthipeedika, Senior Researcher at the UrFU Organic Synthesis Laboratory.

Why do climate models underestimate polar warming? ‘Invisible clouds’ could be the answer

Polar stratospheric clouds, also called nacreous or mother-of-pearl clouds, are not normally visible to the naked eye.
Photo Credit: Alan Light
(CC BY 4.0 DEED)

Stratospheric clouds over the Arctic may explain the differences seen between the polar warming calculated by climate models and actual recordings, find researchers from UNSW Sydney.  

The Earth’s average surface temperature has increased drastically since the start of the Industrial Revolution, but the warming effect seen at the poles is even more exaggerated. While existing climate models consider the increased heating in the Arctic and Antarctic poles, they often still underestimate the warming in these regions. This is especially true for climates millions of years ago, when greenhouse gas concentrations were very high. 

This is a problem because future climate projections are generated with these same models: if they do not produce enough warming for the past, we might underestimate polar warming – and therefore the associated risks, such as ice sheet or permafrost melting – for the future. 

This missing information caught the attention of scientists from the UNSW Climate Change Research Centre. 

How Mega-Floods can be Predicted

Flooding in Germany 2021
Photo Credit: Martin Seifert
Public Domain

When floods are predicted only on the basis of local data, there may be unpleasant surprises. A new method makes it possible to significantly improve predictions - using international data from hydrologically similar areas.

What can we expect in the worst-case scenario? In regions with a high risk of flooding, this is an important question: what extreme events should the protective measures be designed for? Often this is answered simply by looking at history: The worst flood events of the past decades or centuries are regarded as a realistic upper limit for what can be expected in the future.

However, this can be misleading, as so-called "mega-floods" have shown in recent years. Time and again, extreme flood events occur, extraordinary outliers that were not considered possible on the basis of local data. However, a major research project carried out under the leadership of TU Wien (Vienna) has now been able to demonstrate: If one considers the entire European continent, these local surprises are no longer surprising at all. If data from other regions with similar hydrological conditions is taken into account, the extent of these "mega-floods" suddenly becomes predictable. This has drastic consequences for the way in which flood protection must be dimensioned. The results have now been presented in the journal Nature Geoscience.

Tuesday, November 7, 2023

SwRI-led Lucy observes first-ever contact binary orbiting an asteroid

This image shows the asteroid Dinkinesh and its satellite as seen by the Lucy Long-Range Reconnaissance Imager (LORRI). As NASA's Lucy Spacecraft departed the system, the SwRI-led Lucy team captured this image at 1 p.m. EDT (1700 UTC) Nov. 1, 2023, about six minutes after closest approach. From a range of approximately 1,010 miles (1,630 km), the satellite is revealed to be a contact binary, the first time such an object has been seen orbiting another asteroid.
Image Credit: NASA/Goddard/SwRI/Johns Hopkins APL

After the Southwest Research Institute-led Lucy mission flew past the asteroid Dinkinesh, the team discovered that it is even more “marvelous” as its newly discovered satellite is now shown to be a double-lobed moonlet. As NASA’s Lucy spacecraft continued to return data acquired during its first asteroid encounter on Nov. 1, 2023, the team discovered that Dinkinesh’s surprise satellite is itself a contact binary, made of two smaller objects touching each other.

In the first image of Dinkinesh and its satellite taken at closest approach, the two lobes of the contact binary lined up, one behind the other, appearing to be one body from Lucy’s point of view. When the team downlinked additional images captured after the closest encounter, the data revealed that Dinkenesh has a double moonlet.

“Contact binaries seem to be fairly common in the solar system,” said John Spencer, Lucy deputy project scientist, of the Boulder, Colorado, branch of the San Antonio-based SwRI. “We haven’t seen many up close, and we’ve never seen one orbiting another asteroid. We’d been puzzling over odd variations in Dinkinesh’s brightness that we saw on approach, which gave us a hint that Dinkinesh might have a moon of some sort, but we never suspected anything so bizarre!”

Why are songbirds larger in colder climates?

A song-sparrow
Photo Credit: Anish Lakkapragada

Scientists have unlocked the genetic basis underlying the remarkable variation in body size observed in song sparrows, one of North America’s most familiar and beloved songbirds. This discovery also provides insights into this species’ capacity to adapt to the challenges of climate change.

The study, published today in Nature Communications, used genomic sequencing to successfully pinpoint eight genetic variants, or DNA mutations, largely responsible for the nearly threefold difference in body size observed across the song sparrow range from Mexico to Alaska. For instance, song sparrows that live year-round in the Aleutian Islands can be up to three times larger than their counterparts in the coastal marshes of California.

Katherine Carbeck, the study’s first author and a PhD candidate in the faculty of forestry, University of British Columbia, explains that body size varies predictably in many species that inhabit vastly different climatic conditions, aligning with “Bergmann’s rule” which states that organisms in cooler climates tend to be larger as an adaptation to regulate body temperature.

Under Pressure: Seeing the Squeeze in Living Organisms

Double emulsion droplet (pink and cyan) located in between cells (yellow) of a living zebrafish embryo. Monitoring the changes in droplet size allows scientists to measure the osmotic pressure in the tissue.
Image Credit: © PoL / Antoine Vian

In order to survive, organisms must control the pressure inside them, from the single-cell level to tissues and organs. Measuring these pressures in living cells and tissues in physiological conditions has been very challenging. Now, researchers from the Cluster of Excellence Physics of Life (PoL) at the Technical University in Dresden (TU Dresden), Germany, report in the journal Nature Communications a new technique to ‘visualize’ these pressures as organisms develop. These measurements can help understand how cells and tissues survive under pressure, and reveal how problems in regulating pressures lead to disease. 

When molecules dissolved in water are separated into different compartments, water has the tendency to flow from one compartment to another to equilibrate their concentrations, a process known as osmosis. If some molecules cannot cross compartments, a pressure imbalance, known as osmotic pressure, builds up across them. This principle is the basis for many technical applications, such as the desalination of seawater or the development of moisturizing creams. It turns out that maintaining a healthy functioning organism makes the list too. 

30-foot whale shark spotted off Kāneʻohe Bay by UH researchers


University of Hawaiʻi at Mānoa researchers spotted the world’s largest fish species, a 30-foot whale shark, a mile off Kāneʻohe Bay near Kualoa Ranch on November 2.

Researchers from the Hawaiʻi Institute of Marine Biology (HIMB) Shark Research Lab were returning from conducting field work when they spotted seabirds flying over what they suspected was a bait ball, where small fish swarm in a tightly packed spherical formation near the surface while being pursued and herded by predators below.

Mark Royer, a HIMB shark researcher, went into the water to see what sealife had gathered to feed and was surprised to see the whale shark.

“It is surprising,” said Royer. “[Whale sharks] are here more often than we think, however they are probably hard to come across, because I didn’t see this animal until I hopped in the water.”

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

Scientists at Oak Ridge National Laboratory used their expertise in quantum biology, artificial intelligence and bioengineering to improve how CRISPR Cas9 genome editing tools work on organisms like microbes that can be modified to produce renewable fuels and chemicals.

CRISPR is a powerful tool for bioengineering, used to modify genetic code to improve an organism’s performance or to correct mutations. The CRISPR Cas9 tool relies on a single, unique guide RNA that directs the Cas9 enzyme to bind with and cleave the corresponding targeted site in the genome. Existing models to computationally predict effective guide RNAs for CRISPR tools were built on data from only a few model species, with weak, inconsistent efficiency when applied to microbes.

“A lot of the CRISPR tools have been developed for mammalian cells, fruit flies or other model species. Few have been geared towards microbes where the chromosomal structures and sizes are very different,” said Carrie Eckert, leader of the Synthetic Biology group at ORNL. “We had observed that models for designing the CRISPR Cas9 machinery behave differently when working with microbes, and this research validates what we’d known anecdotally.”

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.  

Monday, November 6, 2023

Detecting nuclear materials using light

Sandia National Laboratories researcher Patrick Feng, left, and Former Sandian Joey Carlson, right, hold Organic Glass Scintillators they helped create to detect radioactive materials.
Photo Credit: Randy Wong

Blueshift Optics, owned by former Sandia employee Joey Carlson, is working to shift the way radioactive materials are detected, using technology that he helped create at Sandia National Laboratories.

Radiation detection has long been a critical aspect of national security and efforts to make the world safer.

“Agencies are trying to cast this wide net to catch nuclear smuggling, and this is one aspect of that effort,” said Sandia materials scientist Patrick Feng. “You could use this technology at a border crossing, in a handheld detector as someone enters a facility or fly it on a drone to map an area.”

However, the uses of this technology extend far beyond border security.

“It has the potential to provide us with better data from nuclear physics experiments, enhance national security applications both at home and abroad and has applications in fusion energy,” Carlson said.

Feng and Carlson collaborated to develop the state-of-the-art technology known as Organic Glass Scintillators for radiation detection. Sandia recently licensed the technology to Blueshift Optics, paving the way for potential commercial production.

European wildcats avoided introduced domestic cats for 2000 years

A wildcat which is part of the Saving Wildcats conservation breeding for release program which conducted the first release of wildcats to the Cairngorms National Park, Scotland in 2023
Photo Credit: Saving Wildcats

Domestic cats introduced from the Near East and wildcats native to Europe did not mix until the 1960s, despite being exposed to each other for two thousand years.

Two studies published today in Current Biology involving new archaeological and genetic evidence rewrites the history of cats in Europe.

The international team of researchers sequenced and analyzed both wildcats and domestic cats including 48 modern individuals and 258 ancient samples excavated from 85 archaeological sites over the last 8,500 years. They then assessed the patterns of hybridization (or interbreeding) after domestic cats were introduced to Europe over 2,000 years ago, and came into contact with native European wildcats.

The results of the studies demonstrate that, since their introduction, domestic cats and European wildcats generally avoided mating with each other. About 50 years ago in Scotland, however, that all changed and rates of interbreeding between wildcats and domestic cats rose rapidly. This may have happened as a result of dwindling wildcat populations and a lack of opportunity to mate with other wildcats.

Success of Wolbachia-infected mosquitoes in fighting dengue may be underestimated

Alex Perkins, associate professor of biological science
Photo Credit: Courtesy of University of Notre Dame

The fight against dengue fever has a new weapon: a mosquito infected with the bacteria Wolbachia, which prevents the spread of the virus. These mosquitoes have now been deployed in several trials demonstrating their potential in preventing disease transmission.

Now, researchers at the University of Notre Dame have conducted an analysis of the World Mosquito Program’s randomized control trial of Wolbachia-infected mosquitoes in Indonesia, looking at how excluding transmission dynamics impacted the original interpretation of the trial’s results.

“Randomized controlled trials are the gold standard for evaluating the efficacy of any medical or public health intervention. That is very difficult for vector interventions against dengue because incidence of the disease can be somewhat unpredictable and sporadic, requiring very large-scale trials,” said Alex Perkins, associate professor of biological sciences at Notre Dame and senior author on the study.

Improving the efficacy of cancer immunotherapy with modified CAR-T cells

Water color art illustrates the publication by Velasco et al. The authors systematically engineered novel Chimeric Antigen Receptors (CARs), each containing one of the signaling chains of the natural T cell receptor: epsilon, gamma, delta and zeta (from left to right, from top to bottom) to create innovative CAR T cells. The work demonstrated that each signaling chain imprints the functioning of the CAR T cells (represented by the different colors) impacting thus their anti-tumor activity.
Illustration Credit: Sara Wossning Minguet

CAR-T cell therapy is a last hope for many patients with blood, bone marrow or lymph gland cancer when other treatments such as chemotherapy are unsuccessful. A limiting factor of this otherwise very effective and safe therapy is that the cells used in the process quickly reach a state of exhaustion. Researchers at the University of Freiburg have now been able to prevent this exhaustion and thus significantly improve the effect of the therapy in a preclinical animal model. The new results have been published in the journal Nature Immunology.

Using the body’s own defenses against cancer

CAR-T cells are one of the personalized cancer therapies and have been used in specialized centers in Europe since 2018. In this complex treatment, immune cells, or more precisely T cells, are taken from the blood of cancer patients, genetically engineered in the laboratory with a chimeric antigen receptor (CAR) and then re-administered. The receptor helps the T cells to identify and kill cancer cells. As a result, the therapy utilizes the body’s own cells to permanently eradicate the cancer.

Parkinson's: New hope when treatment options seem exhausted

Prof. Paul Lingor
Photo Credit: Courtesy of Technical University of Munich

As Parkinson's progresses, more invasive therapies are used that require brain surgery, for example. When these no longer deliver the desired results, physicians often conclude that treatment options are exhausted. A study led by researchers at the Technical University of Munich (TUM) now shows that such patients can still benefit from a change in treatment. So far, however, this option has only been used very rarely.

A team led by Prof. Paul Lingor has examined data from 22 German Parkinson's centers. The result: although there are several options for therapies in the late stages of the disease, rarely is more than one used - although those affected often benefit from them.

Parkinson's disease is the world’s second-most common neurodegenerative disease after Alzheimer's. So far it has proved incurable. Only the symptoms can be treated. In the early stages, tablets can generally provide relief from complaints. As the disease progresses, this is often no longer enough.

Phytoplankton uptake of methylmercury is controlled by thiols

In the sea, phytoplankton are the first step when methylmercury is absorbed into the food web. The image was taken under a microscope and shows a spring bloom of phytoplankton in the Bothnian Sea.
 Image Credit: Marlene Johansson

Methylmercury is one of the chemicals that poses the greatest threat to global public health. People ingest methylmercury by eating fish, but how does the mercury end up in the fish? A new study shows that the concentrations of so-called thiols in the water control how available methylmercury is to living organisms.

For methylmercury to enter the food web, it must be absorbed from the water by organisms and the uptake takes place primarily by phytoplankton. This results in a dramatic enrichment, where the levels of methylmercury can increase by a factor of 10,000 to 100,000. However, there is a great deal of variation between different aquatic environments, and it has so far been unclear what controls the process and why the variation is so large.

Higher risk of 17 cancers after high BMI in late teens

Aron Onerup, Institute of Clinical Sciences, and Maria Åberg, Institue of Medicine, Sahlgrenska Academy at the University of Gothenburg.
Photo Credit: Anna Onerup, Johan Wingborg

Men who are overweight or obese at age 18 have a higher risk of 17 different cancers later in life. This has been shown in a study at the University of Gothenburg. The research also describes how the youth obesity epidemic is expected to affect the cancer situation over the next 30 years.

In August, a study on higher cancer risk in men who had lower aerobic fitness recorded at the time of compulsory conscription for military service at the age of 18 was presented. The results were independent of any overweight or obesity at conscription.

In two new studies published in the journals Obesity and Cancer Medicine, the same research team is now focusing on body mass index (BMI), while the results are independent of the participants' aerobic fitness level. And it turns out that higher BMI at age 18 can be linked to even more cancers later in life than poor fitness at the same age.

High BMI at conscription was associated with a higher risk of 17 cancers: lung, head and neck, brain, thyroid, esophageal, stomach, pancreatic, liver, colon, rectal, kidney, and bladder cancer, as well as malignant melanoma, leukemia, myeloma, and lymphoma (both Hodgkin's and non-Hodgkin's).

Mystery Resolved: Black Hole Feeding and Feedback at the Center of an Active Galaxy

Fig. 1
An illustration depicting the distribution of interstellar medium in the active galactic nucleus based on the results of this observation.
Illustration Credit: ©ALMA (ESO/NAOJ/NRAO), T. Izumi et al.

An international research team led by Takuma Izumi, an assistant professor at the National Astronomical Observatory of Japan, has observed in high resolution (approximately 1 light year) the active galactic nucleus of the Circinus Galaxy - one of the closest major galaxies to the Milky Way. The observation was made possible by the Atacama Large Millimeter/Submillimeter Array (ALMA) astronomical observatory in Chile.

This breakthrough marks the world's first quantitative measurement at this scale of gas flows and their structures of a nearby supermassive black hole in all phase gases, including plasma, atomic, and molecular. Such high resolution allowed the team to team to capture the accretion flow heading towards the supermassive black hole, revealing that this accretion flow is generated by a physical mechanism known as 'gravitational instability.' Furthermore, the team also found that a significant portion of this accretion flow does not contribute to the growth of the black hole. Instead, most of the gas is expelled from the vicinity of the black hole as atomic or molecular outflows, and returns to the gas disk to participate again into an accretion flow towards the black hole, much like how water gets recycled in a water fountain. These findings represent a crucial advancement towards a greater understanding of the growth mechanisms of supermassive black holes.

Nanosatellite to Test Novel AI Technologies

Image Credit: Julius-Maximilians-Universität Würzburg

A new Würzburg space mission is on the home straight: The SONATE-2 nanosatellite will test novel artificial intelligence hardware and software technologies in orbit.

After more than two years of development, the nanosatellite SONATE-2 is about to be launched. The lift-off into orbit by a rocket is expected in March 2024. The satellite was designed and built by a team led by aerospace engineer Professor Hakan Kayal from Julius-Maximilians-Universität (JMU) Würzburg in Bavaria, Germany.

JMU has been developing small satellite missions for around 20 years. SONATE-2 now marks another high point.

The satellite will test novel artificial intelligence (AI) hardware and software technologies in near-Earth space. The goal is to use it to automatically detect anomalies on planets or asteroids in the future. The Federal Ministry of Economic Affairs is funding the project with 2.6 million euros.

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