. Scientific Frontline: September 2023

Friday, September 29, 2023

Ancient plant wax reveals how global warming affects methane in Arctic lakes

A 2014 field photo from Wax Lips Lake on northwest Greenland with the Greenland Ice Sheet in the background and three of the study authors (Jamie McFarlin, Everett Lasher, Yarrow Axford).
Photo Credit: Alex P. Taylor

By studying fossils from ancient aquatic plants, Northwestern University and University of Wyoming (UW) researchers are gaining a better understanding of how methane produced in Arctic lakes might affect — and be affected by — climate change.

In a new study, the researchers examined the waxy coatings of leaves preserved as organic molecules within sediment from the early-to-middle Holocene, a period of intense warming that occurred due to slow changes in Earth’s orbit 11,700 to 4,200 years ago. These wax biomarkers — which were once a part of common aquatic brown mosses — were preserved in sediment buried beneath four lakes in Greenland.

Monitoring changes in methane levels

By studying these biomarkers, the researchers discovered that past warming during the middle Holocene caused lakes across a wide range of Greenland’s climates to generate methane. Because methane is a more potent greenhouse gas than carbon dioxide, any changes in methane production with warming are important to understand.

New study shows signs of early creation of modern human identities

SapienCE researchers have publiched a new study which provides vital information about how and when we may have started developing modern human identities. Image showing excavation at Blombos Cave, South Africa.
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Resized Image using AI by SFLORG
Photo Credit: UiB, SapienCE

The study, which is newly published in the Journal of Human Evolution, confirms previous scant evidence, and supports a multistep evolutionary scenario for the culturalization of the human body.

Eye-catching shells made into ornaments

The new study is conducted by Francesco d'Errico, Karen Loise van Niekerk, Lila Geis and Christopher Stuart Henshilwood. The significant findings provide vital information about how and when we may have started developing modern human identities.

“The discovery of eye-catching unmodified shells with natural holes from 100 to 73 ka confirms previous scant evidence that marine shells were collected, taken to the site and, in some cases, perhaps worn as personal ornaments before a stage in which shells belonging to selected species were systematically, and intentionally perforated with suitable techniques to create composite beadworks”, van Niekerk says.

Similar shells have been found in North Africa, other sites in South Africa and the Mediterranean Levant, which means that the argument is supported by evidence from other sites, not just Blombos Cave.

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.

A lethal parasite’s secret weapon: infecting non-immune cells

Photomicrograph of spleen tissue showing the presence of numerous Leishmania donovani parasites in the amastigote form they take after infecting a host.
Image Credit: Centers for Disease Control and Prevention

The organisms that cause visceral leishmaniasis, a potentially deadly version of the parasitic disease that most often affects the skin to cause disfiguring disease, appear to have a secret weapon, new research suggests: They can infect non-immune cells and persist in those uncommon environments. 

Researchers found the Leishmania donovani parasites in blood-related stem cells in the bone marrow of chronically infected mice – precursor cells that can regenerate all types of cells in the blood-forming system. The finding may help explain why some people who develop visceral leishmaniasis, which is fatal if left untreated, often also have blood disorders such as anemia. 

Identifying these cells and other unexpected locations in which these parasites live improve scientists’ understanding of the disease and may lead to new treatment options, said senior study author Abhay Satoskar, professor of pathology in The Ohio State University College of Medicine. 

A new bioinfomatics pipeline solves a 50-year-old blood group puzzle

Photo Credit: Belova59

Currently, a lot is known about which genes are responsible for our individual blood groups, however not much is understood about how and why the levels of the blood group molecules differ between one person to another. This can be important for blood transfusion safety. Now a research group at Lund University in Sweden has developed a toolbox that finds the answer – and in doing so, has solved a 50-year-old mystery.

The study was published recently in Nature Communications.

For the past 30 years, the research group in Lund has studied the genetic basis of our many blood groups and their research has laid the foundation for six new blood group systems. On the surface of the red blood cell are found proteins and carbohydrates that are very similar between people.

However, small differences in these molecules have been shown to be due to genetic variants that encode what we know as blood group antigens. What has not been understood until now is why people with the same blood group can have different amounts of a certain blood group antigen on their red blood cells.

Study shows that Basophil Activation Test (BAT) is key for predicting allergic reactions

Photo Credit: Jakub Kapusnak

Researchers have found that BAT was the best biomarker to predict severity and threshold of allergic reactions to eggs

New research, published in the European Journal of Allergy and Clinical Immunology, has found that Basophil Activation Test (BAT) can be used to better detect allergies and predict the severity of allergic reactions than traditional predictions made via clinical criteria.

The MRC-funded Basophil Activation Test to Diagnose Food Allergy (BAT2) Study, led by Professor Alexandra Santos of King’s College London, aimed to identify if BAT testing could be used to predict the risk of severe allergic reactions and/or low threshold of reactivity.

For the study one hundred and fifty children, recruited from specialized tertiary Pediatric Allergy clinics in London, underwent double-blind placebo-controlled food challenge to determine possible allergies to baked egg. Patients who passed this underwent a similar process but this time with loosely cooked egg, with the severity of allergic reactions classified following Practall guidelines.

Intense Lasers Shine new Light on the Electron Dynamics of Liquids

An intense laser pulse (in red) hits a flow of water molecules, inducing an ultrafast dynamics of the electrons in the liquid.
Illustration Credit: ©J. Harms, MPSD

The behavior of electrons in liquids plays a big role in many chemical processes that are important for living things and the world in general. For example, slow electrons in liquid have the capacity to cause disruptions in the DNA strand.

But electron movements are extremely hard to capture because they take place within attoseconds: the realm of quintillionths of a second. Since advanced lasers now operate at these timescales, they can offer scientists glimpses of these ultrafast processes via a range of techniques.

An international team of researchers has now demonstrated that it is possible to probe electron dynamics in liquids using intense laser fields and to retrieve the electron's mean free path - the average distance an electron can travel before colliding with another particle.

"We found that the mechanism by which liquids emit a particular light spectrum, known as the high-harmonic spectrum, is markedly different from the ones in other phases of matter like gases and solids," said Zhong Yin from Tohoku University's International Center for Synchrotron Radiation Innovation Smart (SRIS) and co-first author of the paper. "Our findings open the door to a deeper understanding of ultrafast dynamics in liquids."

Good news for the world’s rarest marine dolphin?

Māui dolphins.
Photo Credit: University of Auckland/Department of Conservation

The tiny population – only about 54 Māui dolphins remain – lives off the west coast of the North Island.

Once seen from Cook Strait to north of Kaipara, the dolphins’ range is now considerably smaller, with most sightings between Muriwai and Raglan.

The creatures' median age dropped by about a year over the course of a decade, according to research from the University of Auckland – Waipapa Taumata Rau, Oregon State University and University of California Los Angeles.

It could be good news: a population with younger dolphins will produce more calves than an older population, ultimately increasing the population size, which is vital for the dolphins' future.

“The population may be getting younger because individuals born after 2008, the year a marine sanctuary was introduced off the west coast of the North Island, have better chances of survival, since they are less likely to be accidentally caught in fishing nets,” suggests Professor Rochelle Constantine.

However, it’s also possible that older dolphins aren’t living to expected maximum ages of about 20 years.

Soil bacteria prevail despite drought conditions

ClimGrass, the field experiment in Styria, in which drought is simulated in combination with future climate conditions.
Photo Credit: Markus Herndl, HBLFA Raumberg-Gumpenstein

Recent research uncovers the resilience of certain soil microorganisms in the face of increasing drought conditions. While many bacteria become inactive during dry spells, specific groups persist and even thrive. This study, conducted by the Centre for Microbiology and Environmental Systems Science (CeMESS) at the University of Vienna, offers ground-breaking insights into bacterial activity during drought periods, with implications for agriculture and our understanding of climate change impacts. The study has been published in the renowned scientific journal Nature Communications.

The images of the parched Po Valley in 2022 and this year's forest fires in Greece underscore the reality of extreme droughts – not just as news headlines but as immediate threats. The repercussions for humans and plant life are evident: crop failures, withered meadows, and water rationing. However, the impact of drought on soil microorganisms remains hidden from the naked eye.

Soil microorganisms play a pivotal role in ecosystems. They contribute to soil fertility, assist plants in nutrient absorption, and determine whether soils store or release CO2, thereby influencing climate change trajectories. Until now, measuring the activity of microorganisms in dry soils and identifying which species remain active was challenging. Thanks to a novel method developed by scientists at the University of Vienna, bacterial activity during drought periods can now be observed.

Giant molecular rotors operate in solid crystal

Artistic depiction of a giant rotor molecule rotating in the solid state.
Illustration Credit: Rempei Ando, et al. Angewandte Chemie International Edition.

Concave, umbrella-like metal complexes provide space to enable the largest molecular rotor operational in the solid-state.

Solid materials are generally known to be rigid and unmoving, but scientists are turning this idea on its head by exploring ways to incorporate moving parts into solids. This can enable the development of exotic new materials such as amphidynamic crystals—crystals which contain both rigid and mobile components—whose properties can be altered by controlling molecular rotation within the material. 

A major challenge to achieving motion in crystals—and in solids in general—is the tightly packed nature of their structure. This restricts dynamic motion to molecules of a limited size. However, a team led by Associate Professor Mingoo Jin from the Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University has set a size record for such dynamic motion, demonstrating the largest molecular rotor shown to be operational in the solid-state.

A molecular rotor consists of a central rotating molecule that is connected by axis molecules to stationary stator molecules, similar to the way that a wheel and axle are connected to a car frame. Such systems have been previously reported, but the crystalline material in this study features an operational rotor consisting of the molecule pentiptycene, which is nearly 40% larger in diameter than previous rotors in the solid-state, marking a significant advancement. 

Thursday, September 28, 2023

Biochemistry innovation to aid reef restoration, management

Close-up of coral shows individual polyps.
Photo Credit: Ty Roach

Using an innovative new approach to sampling corals, researchers at the University of Hawaiʻi at Mānoa are now able to create maps of coral biochemistry that reveal with unprecedented detail the distribution of compounds that are integral to the healthy functioning of reefs. The study was published in Communications Biology.

“This work is a major step in understanding the coral holobiont [the coral animal and all of its associated microorganisms], which is critical for reef restoration and management,” said lead author Ty Roach, who conducted this study as a postdoctoral researcher at the Hawaiʻi Institute of Marine Biology (HIMB) in the UH Mānoa School of Ocean and Earth Science and Technology.

Despite occupying a tiny fraction of the ocean, coral reefs are one of the most diverse and productive ecosystems on the planet and provide critical habitats for many species and protection for coastal communities.

Biochemicals, such as amino acids, compounds that affect development and growth, and others that have antibacterial or antioxidant properties, have a direct relation to how resilient coral will be in the face of stressors, such as warmer ocean temperatures and ocean acidification.

Why Are Killer Whales Harassing and Killing Porpoises Without Eating Them

A killer whale in the Salish Sea is observed harassing a porpoise, a behavior that has long perplexed scientists. A study from Wild Orca and UC Davis’ SeaDoc Society investigates what may be behind it.
 Photo Credit: Courtesy Wild Orca

For decades, fish-eating killer whales in the Pacific Northwest have been observed harassing and even killing porpoises without consuming them — a perplexing behavior that has long intrigued scientists.

A study published today in Marine Mammal Science, co-led by Deborah Giles of Wild Orca and Sarah Teman of the SeaDoc Society, a program of the UC Davis School of Veterinary Medicine, looked at more than 60 years of recorded interactions between Southern Resident killer whales and porpoises in the Salish Sea to better understand why they exhibit this behavior.

Southern Resident killer whales are an endangered population, numbering only 75 individuals. Their survival is intimately tied to the fortunes of chinook salmon — also an endangered species. Without enough chinook salmon, these whales are in danger of extinction.

“I am frequently asked, why don’t the Southern Residents just eat seals or porpoises instead?” said Giles. “It's because fish-eating killer whales have a completely different ecology and culture from orcas that eat marine mammals — even though the two populations live in the same waters. So we must conclude that their interactions with porpoises serve a different purpose, but this purpose has only been speculation until now.”

Researchers uncover critical clues about the origin of heart arrhythmias

Immunofluorescent staining demonstrating fibroblasts expressing the Channelrhodopsin protein in heart scar tissue. The ChR2-expressing fibroblast (green, arrow) is in close proximity to cardiomyocytes (red) within scar.
Image Credit: Courtesy of UCLA Health

In a research article published today in the journal Science, UCLA researchers have found that fibroblasts – scar-forming cells that reside in the scar tissue of an injured heart -- directly play a role in promoting a disturbance of the heart rhythm, otherwise known as an arrhythmia. This finding holds promise for novel approaches to life threatening rhythm problems of the heart. 

Every year in the U.S., sudden cardiac death kills upwards of 350,000 people who have had no previous symptoms of heart disease, and in the majority of cases, the underlying cause is an arrhythmia. While there is a strong association between the amount of scar tissue in the heart and the likelihood of an arrhythmia to occur, whether fibroblasts in scar tissue directly communicated with cardiac muscle cells to promote arrhythmias was not known.

In cardiac scar tissue, cardiac muscle cells are surrounded by cardiac fibroblasts and often come in close contact with cardiac fibroblasts. "For decades, scientists have wondered whether the cardiac fibroblasts are electrically passive and just form scar tissue or whether by coming in close contact with myocytes, they directly increased the excitability of cardiac muscle cells and promoted life threatening arrhythmias in vivo," said Dr. Arjun Deb, senior author, professor of medicine and director of the UCLA Cardiovascular Theme, at the David Geffen School of Medicine. 

Ultrasound may rid groundwater of toxic ‘forever chemicals’

PFAS is notoriously difficult to clean from the environment, but ultrasound may offer a more effective solution compared to past efforts.
Photo Credit: Edward Jenner

New research suggests that ultrasound may have potential in treating a group of harmful chemicals known as PFAS to eliminate them from contaminated groundwater.

Invented nearly a century ago, per- and poly-fluoroalkyl substances, also known as “forever chemicals,” were once widely used to create products such as cookware, waterproof clothing and personal care items. Today, scientists understand that exposure to PFAS can cause a number of human health issues such as birth defects and cancer. But because the bonds inside these chemicals don’t break down easily, they’re notoriously difficult to remove from the environment.

Such difficulties have led researchers at The Ohio State University to study how ultrasonic degradation, a process that uses sound to degrade substances by cleaving apart the molecules that make them up, might work against different types and concentrations of these chemicals.

By conducting experiments on lab-made mixtures containing three differently sized compounds of fluorotelomer sulfonates – PFAS compounds typically found in firefighting foams – their results showed that over a period of three hours, the smaller compounds degraded much faster than the larger ones. This is in contrast to many other PFAS treatment methods in which smaller PFAS are actually more challenging to treat.

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.”

Solar cell material can assist self-driving cars in the dark

Rui Zhang, postdoc fellow at IFM is one of the principle authors to the article published in Nature Photonics.
Photo Credit: Olov Planthaber

Material used in organic solar cells can also be used as light sensors in electronics. This is shown by researchers at Linköping University who have developed a type of sensor able to detect circularly polarized red light. Their study, published in Nature Photonics, paves the way for more reliable self-driving vehicles and other uses where night vision is important.

Some beetles with shiny wings, firefly larvae and colorful mantis shrimps reflect a particular kind of light known as circularly polarized light. This is due to microscopic structures in their shell that reflect the electromagnetic light waves in a particular way.

Circularly polarized light also has many technical uses, such as satellite communication, bioimaging and other sensing technologies. This is because circularly polarizing light carries a vast amount of information, due to the fact that the electromagnetic field around the light beam spirals either to the right or to the left.

Purdue researchers develop a new type of intelligent architected materials for industry applications

Products made with intelligent architected materials developed at Purdue University have the ability to change from one stable configuration to another stable configuration and back again. The technology is being tested in new aircraft runway mats, nonpneumatic tires and other applications.
Image Credit: Provided by the researchers. Courtesy of Purdue University

Purdue University civil engineering researchers have developed patent-pending intelligent architected materials that can dissipate energy caused by bending, compression, torque and tensile stresses, avoiding permanent plastic deformation or damage, and may also exhibit shape memory properties that allow them to have actuation capacity.

Avoiding damage makes the material reusable and improves human safety and structure durability in products across several industrial sectors.

Pablo Zavattieri, the Jerry M. and Lynda T. Engelhardt Professor in Civil Engineering, leads the research team that has developed this new class of intelligent architected materials.

“These materials are designed for fully recoverable, energy-dissipating structures, akin to what is referred to as architected shape memory materials, or phase transforming cellular materials, known as PXCM,” Zavattieri said. “They can also exhibit intelligent responses to external forces, changes in temperature and other external stimuli.”

Intelligent architected materials such as these have a wide range of potential applications due to their unique properties.

Hunting anything that flies

Pillar from Göbekli Tepe depicting a vulture with its wings spread. 
Photo Credit: © Nadja Pöllath / SNSB-SPM

Birds were an important source of food for hunter-gatherer communities in Upper Mesopotamia at the beginning of the Neolithic period. Besides mammals, ranging from aurochs to hares, or fish, foragers also pursued an impressively large spectrum of bird species in Southeast Anatolia 11,000 years ago. They were hunted mainly, but not exclusively, in autumn and winter – at the time of year, when many bird species form larger flocks and migratory birds cross the area. The species lists are therefore very extensive: At the famous Early Neolithic settlement and the world's oldest temple complex of Göbekli Tepe, for example, c. 18 km northeast of present-day Şanlıurfa (SE Anatolia, Turkey), the researchers identified the remains of at least 84 bird species. Dr. Nadja Pöllath, curator at the Bavarian State Collection for Palaeoanatomy (Staatssammlung für Paläoanatomie München SNSB-SPM) and Prof. Joris Peters, chair of the Institute for Palaeoanatomy, Domestication Research and History of Veterinary Medicine at LMU München and director of the state collection, identified the Neolithic bird bones with the aid of the reference skeletons of the state collection.

The researchers were surprised by the large number of small passerine birds identified at Göbekli Tepe, comprising mainly starlings and buntings. In principle, the Early Neolithic inhabitants of Göbekli Tepe hunted birds in all habitats – mainly in the open grassland and wooded steppe in their direct surroundings, but also in the wetlands and gallery forest somewhat further away.

Listening to atoms moving at the nanoscale

Professor Jan Seidel and his research lab have been using specialised techniques to listen to atoms moving.
Photo Credit: UNSW FLEET Centre.

Understanding how the phenomenon of ‘crackling noise’ occurs at the microscopic scale could have implications for new research in materials science and medicine.

Scientists from UNSW Sydney and the University of Cambridge have used novel methods to listen to the sounds of atoms moving under pressure – a phenomenon known as ‘crackling noise’.

These atomic movements occur in avalanches – they are similar to snow avalanches, but made of atoms – and follow very well-defined statistical rules.

Crackling noise can be observed every day, from crumpling paper and candy wrapping, to the crackling of your cereal, as well as in natural occurrences, such as earthquakes.

In a study recently published in Nature Communications, Professor Jan Seidel and his lab, from the School of Material Science and Engineering, were able to record the crackling noise of just a few hundred atoms, in experiments that lasted over eight hours.

Parkinson’s: are our neurons more vulnerable at night?

More dopaminergic neurons in the adult Drosophila brain survive in control flies (left) than in flies mutant for the circadian cycle (right).
Image Credit: © Lou Duret

Disturbances in sleep patterns and the internal biological clock are frequently associated with Parkinson’s disease. However, the link between biological rhythm and neuronal degeneration remains unclear. A team from the University of Geneva (UNIGE) investigated the destruction of neurons at different times of the day, using the fruit fly as a study model. The scientists discovered that the type of cellular stress involved in Parkinson’s disease was more deleterious to neurons when it occurred at night. This work can be read in the journal Nature Communications.

Parkinson’s disease is a progressive neurodegenerative disorder characterized by the destruction of certain neurons in the brain: dopamine neurons. The main symptoms of this disease are tremors, slowness of movement and muscular stiffness. Epidemiological studies show that other disorders may be associated, such as disturbances of sleep and of the circadian cycle.

This cycle, defined by the alternate periods of wakefulness and sleep, lasts around 24 hours and constitutes the human body’s internal clock that regulates almost all its biological functions. In particular, the circadian clock controls the secretion of the ‘‘sleep hormone’’(melatonin) at the end of the day, variations in body temperature (lower in the early morning and higher during the day), and metabolism in periods of fasting (during sleep) or energy intake (during daytime meals).

Topological Insulator Catalysts for High-Yield Room-Temperature Synthesis of Organoureas

The unique quantum properties of bismuth selenide make it a promising catalyst for the synthesis of organic ureas, as demonstrated by scientists at Tokyo Tech. Thanks to its topological surface states, the proposed catalyst exhibits remarkably high catalytic activity and durability when used for the synthesis of various urea derivatives, which are widely utilized as nitrogen fertilizers.

Synthetic fertilizers, one the most important developments in modern agriculture, have enabled many countries to secure a stable food supply. Among them, organic ureas (or organoureas) have become prominent sources of nitrogen for crops. Since these compounds do not dissolve immediately in water, but instead are slowly decomposed by soil microorganisms, they provide a stable and controlled supply of nitrogen, which is crucial for plant growth and function.

However, traditional methods to synthesize organoureas are environmentally harmful due to their use of toxic substances, such as phosgene. Although alternative synthesis strategies have been demonstrated, these either rely on expensive and scarce noble metals or employ catalysts that cannot be reused easily.

Low-grade intestinal inflammation a long time after radiotherapy

Photo Credit: Jo McNamara

Patients who have undergone pelvic radiotherapy may live with low-grade chronic inflammation of the lower intestine 20 years after the treatment. This has been shown in a study by researchers at the University of Gothenburg.

Radiotherapy is often necessary to cure or slow down cancer. Even though today’s radiotherapies feature a high level of precision, healthy tissue in and around the radiation field is still affected. This study highlights a previously unknown side effect of radiotherapy to the lower abdomen.

The mucous membrane of the large intestine is normally protected against contact with bacteria in feces by a thin barrier of mucus. In the current study, researchers at the University of Gothenburg have shown that radiotherapy to the pelvic area affects this thin layer of mucus, allowing bacteria to come into contact with cells on the surface of the intestine. This could be a reason for the low-grade inflammation that the researchers also found in intestines that had been exposed to radiotherapy several years previously.  

“Anti-tangle” molecule could aid search for new dementia treatments, say scientists

Scientists at Bath have found a way of blocking the protein tangles that are associated with dementia diseases
Photo Credit: NCI

Scientists have identified a molecule that can prevent tangling of a brain protein that is linked to diseases such as Parkinson’s. The findings may provide insights into new ways of treating or diagnosing the early stages of dementia.

Alpha-synuclein, a protein found in brain cells, is commonly associated with neurodegenerative diseases such as Parkinson's, a debilitating neurological disorder affecting millions worldwide.

Like all proteins, it is made up of a long strand of molecules called amino acids. When it’s made, this strand folds in on itself to form a complex but precise 3D shape, made up of sub-structures and loops.

In healthy individuals, alpha-synuclein interacts with cell membranes where it plays a role in how brain cells (neurons) communicate with each other, but as a person ages, the 3D shape of the protein can malformed, or “misfolded”, causing it to start sticking together to form toxic clumps in the brain.

Over time these clumps continue to stack, forming fibers that can interfere with the protein’s normal role, eventually killing brain cells, contributing to the development of Parkinson's and related dementia diseases.

Plants on Ash Dumps Experience Nutrient Deficiency

Scientists studied two ash dumps in the Middle Urals.
Photo Credit: From the personal archive of Anna Betekhtina

Many nutrients, especially nitrogen, are not available to plants on ash dumps, biologists from the Ural Federal University and the Institute of Plant and Animal Ecology of the Ural Branch of the Russian Academy of Sciences (IPAE UB RAS) have found out. Despite the fact that nitrogen accumulates in the soil of ash dumps as a result of overgrowth, its availability to plants is very low. This situation is unique, because usually the nitrogen content in the soil is directly related to nitrogen content in plants. The description of chemical analysis of plants and soils of ash dumps scientists published in the journal "Ecology". 

"Nitrogen is one of the most important elements of plant nutrition, and its availability determines the productivity of plant communities. At various natural sites, a single pattern has been shown: when the nitrogen content in the soil increases, its amount in plants also increases. Such dynamics is described in many works of Russian and foreign scientists. However, our results turned out to be quite different. The results obtained on other natural objects cannot be transferred to technogenic landscapes, such as ash dumps", explains Anna Betekhtina, senior researcher of the Laboratory of Restorative Ecology at UrFU.

Two-decade monitoring of M87 unveils a precessing jet connecting to a spinning black hole

Schematic representation of the tilted accretion disk model. The black hole spin axis is assumed to align vertically. The jet direction stands almost perpendicular to the disk plane. The misalignment between the black hole spin axis and disk rotation axis triggers the precession of disk and jet.
Illustration Credit: Yuzhu Cui et al. (2023), Intouchable Lab@Openverse and Zhejiang Lab.

In a tale of cosmic patience spanning more than two decades, it has been discovered that the nearby radio galaxy M87, located 55 million light-years from the Earth and harboring a black hole 6.5 billion times more massive than the Sun, exhibits an oscillating jet. This investigation found the jet swinging up and down with an amplitude of about 10 degrees.

The international collaboration team consisting of researchers from 45 institutions around the world, including Dr. Satoko Sawada-Satoh of Osaka Metropolitan University’s Graduate School of Science, analyzed data observed from 2000 to 2022. They unveiled a recurring 11-year cycle in the precessing motion of the jet base, as predicted by Einstein’s general relativity. This work successfully linked the dynamics of the jet with the central supermassive black hole, offering evidence for the existence of M87’s black hole spin.

Wednesday, September 27, 2023

Noninvasive, ultrasound-based brain biopsy is feasible

Graduate student Lu Xu wears a device designed by engineers, at Washington University in St. Louis, that targets ultrasound waves to precise spots in the brain. Such targeting is the first step in a sonobiopsy, a noninvasive technique invented by Washington University researchers that uses ultrasound and microbubbles to release biomolecules from brain tumors. The biomolecules then can be collected via a blood draw, analyzed and used to inform treatment decisions. Xu is part of a research team that demonstrated that sonobiopsy is safe and feasible for use in people.
Photo Credit: Courtesy of Hong Chen

The blood-brain barrier, the body’s way of shielding sensitive brain tissue from viruses, toxins and other harmful substances in the blood, can pose a problem for physicians caring for patients with suspected brain diseases such as cancer. Molecular and genetic information would be invaluable for confirming a diagnosis and guiding treatment decisions, but such molecules are normally confined to the brain by the barrier. Neurosurgeons routinely perform surgical brain biopsies to obtain this data on brain tumors, but such procedures carry risks and are not feasible for all tumors or for many other kinds of brain diseases.

Researchers at Washington University in St. Louis have developed an anatomically precise technique called sonobiopsy that uses ultrasound and microbubbles to disrupt the barrier temporarily and allow RNA, DNA and proteins from the brain to spill out into the blood, where they can be detected and analyzed. The researchers developed and previously tested the technique in animals. In a new study, available online in the journal NPJ Precision Oncology, they showed that the technique is feasible and safe for use in people, and could open the door to noninvasive biopsies for suspected brain tumors and other brain diseases.

Important additional driver of insect decline identified

The grape wood borer (Chlorophorus varius) is one of over 33,000 insect species in Germany. The development of the insect biomass depends significantly on weather conditions, as a study published in "Nature" in 2023 shows.
Photo Credit: Didier Descouens
(CC BY-SA 3.0)

Combinations of unfavorable weather conditions over several years can cause a decline in insect biomass. This is shown by a study published in "Nature" with TUD being involved.

Insects react sensitively when temperature and precipitation deviate from the long-term average. In an unusually dry and warm winter, their survival probabilities are reduced; in a wet and cold spring, hatching success is impaired. A cool, wet summer hampers bumblebees and other flying insects from reproducing and foraging.

If several such weather anomalies occur in combination and over several years, this can lead to a decline in insect biomass on a large scale and in the long term. This is shown in a new report in the journal Nature.

According to the report, weather conditions and accumulations of unfavorable weather anomalies in the course of climate change can be important drivers of global insect decline. Only insect populations with a large number of individuals, as found in sufficiently large and high-quality habitats, appear to be able to survive under such adverse conditions.

Saturated fat may interfere with creating memories in aged brain

The study in cell cultures found the omega-3 fatty acid DHA, found in fish and a common supplement, may help protect the brain from an unhealthy diet’s effects by curbing fat-induced inflammation at the cellular source.
Photo Credit: Leohoho

New research hints at a few ways fatty foods affect cells in the brain, a finding that could help explain the link between a high-fat diet and impaired memory – especially as we age.

The Ohio State University study in cell cultures found the omega-3 fatty acid DHA may help protect the brain from an unhealthy diet’s effects by curbing fat-induced inflammation at the cellular source. 

Separate experiments using brain tissue from aging mice showed a high-fat diet may lead specific brain cells to overdo cell-signaling management in a way that interferes with the creation of new memories. 

The same lab found in an earlier study in aging rats that a diet of highly processed ingredients led to a strong inflammatory response in the brain that was accompanied by behavioral signs of memory loss – and that DHA supplementation prevented those problems. 

“The cool thing about this paper is that for the first time, we’re really starting to tease these things apart by cell type,” said senior author Ruth Barrientos, an investigator in Ohio State’s Institute for Behavioral Medicine Research and associate professor of psychiatry and behavioral health and neuroscience in the College of Medicine. 

Tree rings reveal a new kind of earthquake threat to the Pacific Northwest

Price Lake, in the eastern Olympic Mountains, formed when the Saddle Mountain fault impounded a stream and flooded the forest. Lead author Bryan Black and his team of divers collected the samples using an underwater hydraulic chainsaw.
Photo Credit: Bryan Black

In February, a 7.8-magnitude earthquake shook the Turkey-Syria border, followed by one nearly as large nine hours later. Shallow faults less than 18 miles beneath the surface buckled and ruptured, causing violent focused quakes that leveled thousands of buildings and killed tens of thousands.

Similar shallow faults ruptured about 1,000 years ago in the Puget Lowlands in western Washington, according to new University of Arizona-led research. Tree rings helped pinpoint that the seismic event occurred in late A.D. 923 or early 924. Their findings mean that a repeat event has the potential to again shake the region that is now home to over 4 million people, including Seattle, Tacoma and Olympia. The results were published in the journal Science Advances.

The ancient quake was either the result of all the shallow faults in the region rupturing together to produce an estimated 7.8-magnitude earthquake or – like in Turkey and Syria – twin quakes that occurred back-to-back with estimated magnitudes of 7.5 and 7.3, researchers found. Shallow faults typically result in more violent and focused shaking than earthquakes generated from other geological configurations.

How the Heart Starts Beating

Researchers were surprised to discover that heart cells in developing zebrafish abruptly start beating all at once, and quickly become regular. Here, heart cells are labeled with green fluorescent protein, which becomes brighter when calcium levels spike during each heartbeat.
Image Credit: Bill Jia

Becoming a full-fledged organism out of a handful of cells, complete with functioning tissues and organs, is a messy yet highly synchronized process that requires cells to organize themselves in a precise manner and begin working together.

This process is especially dramatic in the heart, where static cells must start beating in perfect unison.

Now, a cross-school collaboration led by researchers at Harvard Medical School and Harvard University has provided a glimpse into exactly how cells in the heart start beating.

In a study conducted in zebrafish, the team discovered that heart cells start beating suddenly and all at once as calcium levels and electrical signals increase. Moreover, each heart cell has the ability to beat on its own, without a pacemaker, and the heartbeat can start in different places, the researchers discovered. The findings are published Sep. 27 in Nature.

Extreme Weight Loss: Star Sheds Unexpected Amounts of Mass Just Before Going Supernova

Artist's conception of pre-explosion mass loss by the progenitor star of SN 2023ixf. In the year prior to going supernova the red supergiant star now known as SN 2023ixf shed an unexpected amount of mass equivalent to the mass of the Sun. This artist's conception illustrates what the final stages of mass loss might have looked like before the star exploded. 
Illustration Credit: Melissa Weiss/CfA

A newly discovered nearby supernova whose star ejected up to a full solar mass of material in the year prior to its explosion is challenging the standard theory of stellar evolution. The new observations are giving astronomers insight into what happens in the final year prior to a star’s death and explosion.

SN 2023ixf is a new Type II supernova discovered in May 2023 by amateur astronomer Kōichi Itagaki of Yamagata, Japan shortly after its progenitor, or origin star, exploded. Located about 20 million light-years away in the Pinwheel Galaxy, SN 2023ixf's proximity to Earth, the supernova's extreme brightness, and its young age make it a treasure trove of observable data for scientists studying the death of massive stars in supernova explosions.

Type II or core-collapse supernovae occur when red supergiant stars at least eight times, and up to about 25 times the mass of the Sun, collapse under their own weight and explode. While SN 2023ixf fits the Type II description, follow-up multi-wavelength observations led by astronomers at the Center for Astrophysics | Harvard & Smithsonian (CfA), and using a wide range of CfA's telescopes, have revealed new and unexpected behavior.

Tiny CRISPR tool could help shred viruses

Model of a minimal CRISPR-Cas13bt3 molecule generated with a cryo-electron microscope. The RNA to be recognized and cleaved is colored in light blue, while the scissor is formed by the magenta and cyan colored domains. The two loops for controlling the CRISPR-Cas13bt3 are shown in green and red.
 Illustration Credit: Courtesy of the Yang Gao lab/Rice University

Small and precise: These are the ideal characteristics for CRISPR systems, the Nobel-prize winning technology used to edit nucleic acids like RNA and DNA.

Rice University scientists have described in detail the three-dimensional structure of one of the smallest known CRISPR-Cas13 systems used to shred or modify RNA and employed their findings to further engineer the tool to improve its precision. According to a study published in Nature Communications, the molecule works differently than other proteins in the same family.

“There are different types of CRISPR systems, and the one our research was focused on for this study is called CRISPR-Cas13bt3,” said Yang Gao, an assistant professor of biosciences and Cancer Prevention and Research Institute of Texas Scholar who helped lead the study. “The unique thing about it is that it is very small. Usually, these types of molecules contain roughly 1200 amino acids, while this one only has about 700, so that’s already an advantage.”

Atlantic walrus more vulnerable than ever to Artic warming

Photo Credit: Rod Long

Past cycles of climate change, along with human exploitation, have led to only small and isolated stocks of Atlantic walrus remaining. The current population is at high risk of the same issues affecting them severely, according to a new study led by Lund University in Sweden.

Today, the last remaining stocks of Atlantic walrus are more at danger than ever, due to a combination of Arctic warming and a long history of devastating human exploitation. Rising global temperatures are significantly impacting Arctic marine ecosystems and their inhabitants. However, little is known about exactly how this combination of stress factors will impact Arctic species.

Now, researchers have examined how walrus coped with past cycles of climate change. Using breakthroughs in ancient genomics, the team was able to extract, sequence and interpret ancient genetic information contained in teeth and bone that survive well in the Arctic’s frozen archaeological sites. These DNA results were integrated with modern genetic samples, enabling them to reconstruct how the genetic diversity of Atlantic walrus had changed under earlier cycles of global warming.

Understanding bacterial motors may lead to more efficient nanomachine motors

The FliG protein in the "bacterial motor"
Illustration Credit: Atsushi Hijikata, Yohei Miyanoiri, Osaka University

A research group led by Professor Emeritus Michio Homma (he, him) and Professor Seiji Kojima (he, him) of the Graduate School of Science at Nagoya University, in collaboration with Osaka University and Nagahama Institute of Bio-Science and Technology, have made new insights into how locomotion occurs in bacteria. The group identified the FliG molecule in the flagellar layer, the ‘motor’ of bacteria, and revealed its role in the organism. These findings suggest ways in which future engineers could build nanomachines with full control over their movements. They published the study in iScience

As nanomachines become smaller, researchers are taking inspiration from microscopic organisms for ways to make them move and operate. In particular, the flagellar motor can rotate clockwise and counterclockwise at a speed of 20,000 rpm. If scaled up, it would be comparable to a Formula One engine with an energy conversion efficiency of almost 100% and the capacity to change its rotation direction instantly at high speeds. Should engineers be able to develop a device like a flagellar motor, it would radically increase the maneuverability and efficiency of nanomachines. 

Curtin study suggests rare echidna noises could be the ‘language of love’

Echidnas, sometimes known as spiny anteaters, are quill-covered monotremes (egg-laying mammals) belonging to the family Tachyglossidae
Photo Credit: Emmanuel Higgins

Curtin University researchers have captured rare recordings of echidnas cooing, grunting and making a range of other sounds, but only during the breeding season.

Lead author Dr Christine Cooper, from Curtin’s School of Molecular and Life Sciences, said there had been ongoing scientific debate around the ability of echidnas to vocalize as a way of communicating or if the sounds they make are simply sniffing noises related to breathing.

“We observed wild short-beaked echidnas at Dryandra National Park, near Narrogin, Western Australia, making cooing and grunting sounds, in addition to the wheezing and exhalation noises that the animals are known to make,” Dr Cooper said.

“Our team managed to capture some of these sounds with hand-held microphones as well as a camera and microphone left unattended at the entrance to a cave popular with echidnas.

Could RNA folding play a role in the origin of life?

New research in membaneless compartments that model protocells reveals that naturally occurring chemical modifications to RNA molecules help them fold better into functional structures. Image of the structures of tRNA molecules from protocells determined by high-throughput sequencing using tRNA structure-seq are overlaid on and image of the membraneless compartments made through liquid-liquid phase separation.
(CC BY-NC-ND 4.0)
Image Credit: Bevilacqua and Keating Labs / Penn State.

New research in model protocells reveals naturally occurring chemical modifications to RNA molecules help them properly fold into functional structures

To investigate potential early steps taken by the first life to develop on Earth, researchers have been studying a model of pre-life protocells comprising membraneless compartments. Now, a team of Penn State scientists have found that RNA molecules within these compartments fold better when they have naturally occurring chemical modifications. These modifications that allow for better folding in RNAs may offer a hint into how the molecules evolved from arbitrary chemical compounds to the dynamic, organized building blocks of life. The new study, published by a team of Penn State scientists in the journal Science Advances, used high-throughput genetic sequencing to determine the structure of the RNAs, which also has implications for the design of delivery methods for RNA-based therapeutics that rely on properly folded RNAs to function.

Double Trouble: Infamous “Eagle Killer” Bacterium Produces Not One, But Two Toxins

Colony of A. hydrillicola
Photo Credit: Lenka Štenclová

The cyanobacterium Aetokthonos hydrillicola produces not just one, but two highly potent toxins. In the latest issue of the journal Proceedings of the National Academy of Sciences (PNAS), an international team led by Martin Luther University Halle-Wittenberg (MLU) and Freie Universität Berlin describes the second toxin, which had remained elusive until now. Even in low concentrations, it can destroy cells and is similar to substances currently used in cancer treatment. Two years ago, the same team established that the first toxin from the cyanobacterium is the cause of a mysterious disease among bald eagles in the USA.

Aetokthonos hydrillicola is particularly challenging for researchers. It is notoriously difficult to cultivate and produces one of its toxins only under specific conditions. The fact that it produces two toxins with very different chemical makeups is also unusual. Cyanobacteria normally produce only one toxin - and A. hydrillicola was established as the source of aetokthonotoxin in 2021. This discovery was made by Professor Susan Wilde from the University of Georgia (USA) and Professor Timo Niedermeyer, who worked at MLU until July 2023 and has now joined the researchers at Freie Universität Berlin. This toxin solved a riddle that had kept scientists busy for decades: it triggers the disease vacuolar myelinopathy (VM) among bald eagles in the United States. VM causes holes to form in the brain and, as a result, the birds lose control of their bodies. Science ran the breakthrough as a cover story at the time, and the international team picked up several awards for its work.

Tuesday, September 26, 2023

Study sheds new light on strange lava worlds

Lava worlds are likely still in the early stages of their evolution, as some theories suggest Earth too was once entirely molten.
Image Credit: NASA’s Goddard Space Flight Center/Chris Smith (KBRwyle)

Lava worlds, massive exoplanets home to sparkling skies and roiling volcanic seas called magma oceans, are distinctly unlike the planets in our solar system.  

To date, nearly 50% of all rocky exoplanets yet discovered have been found capable of maintaining magma on their surfaces, likely because these planets are so close to their host stars they orbit in fewer than 10 days. Being so close causes the planet to be bombarded by harsh weather and forces surface temperatures to the extreme, making it all but completely inhospitable to life as we know it today. 

Now, in a new study, scientists have shown that these sweeping molten oceans have a large influence on the observed properties of hot rocky Super-Earths, such as their size and evolutionary path.  

Their research, published recently in The Astrophysical Journal, found that due to lava’s extremely compressible nature, oceans of magma can cause lava-rich planets without atmospheres to be modestly denser than similarly sized solid planets as well as impact the structure of their mantles, the thick inner layer that surrounds a planet’s core.  

From Seafloor to Space: New Bacterial Proteins Shine Light on Climate and Astrobiology

Methane clathrate (white, ice-like material) under a rock from the seafloor of the northern Gulf of Mexico. Deposits such as these demonstrate that methane and other gases cross the seafloor and enter the ocean.
Photo Credit: NOAA

Gigatons of greenhouse gas are trapped under the seafloor, and that’s a good thing. Around the coasts of the continents, where slopes sink down into the sea, tiny cages of ice trap methane gas, preventing it from escaping and bubbling up into the atmosphere.

While rarely in the news, these ice cage formations, known as methane clathrates, have garnered attention because of their potential to affect climate change. During offshore drilling, methane ice can get stuck in pipes, causing them to freeze and burst. The 2010 Deepwater Horizon oil spill is thought to have been caused by a buildup of methane clathrates.

But until now, the biological process behind how methane gas remains stable under the sea has been almost completely unknown. In a breakthrough study, a cross-disciplinary team of Georgia Tech researchers discovered a previously unknown class of bacterial proteins that play a crucial role in the formation and stability of methane clathrates.

Researcher to help send swarm of marine robots on climate change quest beneath ocean ice

Retreating ice has exposed the rocky shoreline of Cape Rasmussen on the Antarctic Peninsula. Xi Yu, a West Virginia University engineer, is leading robotics research that could help a nationwide consortium of researchers learn more about glacial melt and changing levels of ocean ice.
Phot Credit: Derek Ford/University of Hawaii, Manoa

Research from West Virginia University mechanical and aerospace engineer Xi Yu could help scientists reach ocean waters hidden away beneath ice shelves. The inaccessible waters under ocean ice contain information critical to understanding the impact of climate change, and Yu said she believes multiple marine robots, carried and coordinated by an intelligent mothership, can reach those depths and communicate what they learn.

An assistant professor at the Benjamin M. Statler College of Engineering and Mineral Resources and a member of WVU Robotics, Yu has received National Science Foundation support for a three-year project developing technologies to control swarms of “passenger robots,” intended for release by their autonomous mothership into an icy subaquatic world.

She is part of a coast-to-coast network of oceanographers and engineers who have come together to collaborate on the increasingly urgent problem of how to access oceanic ice cavities. The community of partners working together toward the proof-of-concept mothership-and-passenger system originated at Oregon State University and has expanded outward to include computer engineers, roboticists, oceanographers and glaciologists from Brigham Young, Temple, Purdue and the Woods Hole Oceanographic Institution, in addition to WVU.

Deciphering the secrets of the brain

Adrian Wanner is delighted with the exceptional international recognition from the US National Institute of Health (NIH).
Photo Credit: Scanderbeg Sauer Photography

PSI researchers are to receive funding from the US National Institutes of Health (NIH) as part of its “BRAIN Initiative”. Their aim is to produce a comprehensive map of a mouse’s brain.

Unlocking the secrets of the brain, especially its architecture and wiring, is one of the big challenges in modern life sciences. That is why the National Institutes of Health (NIH) in the USA, one of the world’s largest research agencies, has included this in its program. As part of the NIH BRAIN Initiative, a Swiss researcher has now been awarded a major grant of up to 2.6 million US dollars. The neurobiologist Adrian Wanner, a group leader at the Paul Scherrer Institute PSI, is the project’s principal investigator. Andreas Schaefer from the Francis Crick Institute in London is also closely involved.

The NIH’s decision to invest such a large sum in a project at a Swiss institute demonstrates the exceptional competitiveness of Swiss researchers and confirms PSI’s position as a center for world-class research. “For a young research group leader to receive such a large grant, especially from another country, is by no means commonplace; it testifies to his great scientific talent and the confidence that the international community has in Switzerland as a research location,” says Gebhard Schertler, Head of the Department of Biology and Chemistry, who is delighted with the good news from the United States. Schaefer adds, “This funding will further strengthen the existing collaboration between our groups and institutes.”

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