. Scientific Frontline: March 2023

Friday, March 31, 2023

Fast light pulse triggers the charge transfer into the water

The study was only made possible by the new laser laboratories in the ZEMOS research building, in which all external interference signals are minimized.
Photo Credit: © RUB, Marquard

With new technology, researchers were able to observe live what happens in the first picosecond when a proton detaches from a dye after light.

In certain molecules, the so-called photoc acids, a proton can be released locally by excitation with light. The solution suddenly changes the pH - a kind of fast switch that is important for many chemical and biological processes. So far, however, it is still unclear what actually happened at the moment of proton release. This is exactly what researchers in the Ruhr Explores Solvation Cluster of Excellence could do RESOLV the Ruhr University Bochum is now experimentally observing using new technology. They saw a tiny quake that only lasted three to five picoseconds before the proton came loose. They report on this in the journal Chemical Sciences.

Scientists Get Closer to Curing Alzheimer's and Parkinson's Diseases

In Russia, the incidence of dementia, Parkinson's disease and Alzheimer's disease will reach the epidemiological threshold of 5%
Image Credit: Gerd Altmann

Prospective compounds for the treatment of neurodegenerative diseases have been synthesized by Russian scientists. The compounds are of great interest for medicinal chemistry, especially for the development of treatments for Alzheimer's and Parkinson's diseases.

According to Timofey Moseev, a member of the group and an employee of the UrFU Chemical Pharmaceutical Center, the researchers managed to test the toxicity of the compounds in vitro on the kidney cells of a healthy human embryo. The researchers used the strategy of nucleophilic hydrogen substitution (a substitution reaction in which the substrate is attacked by a nucleophile, a reagent that carries a pair of unshared electrons). The process does not require metal catalysis, which is particularly important in the production of biologically active compounds, where any metal impurity can significantly distort toxicity and activity data.

To assess the ability of the synthesized molecules to bind to biotargets (proteins that play an important role in a particular disease), the researchers conducted experiments using docking - a molecular modeling technique. Docking allows predicting with a certain probability how a molecule interacts with targeted proteins.

Thursday, March 30, 2023

Predatory dinosaurs such as T. rex sported lizard-like lips

A juvenile Edmontosaurus disappears into the enormous, lipped mouth of Tyrannosaurus.
Illustration Credit Dr Mark Witton

A new study suggests that predatory dinosaurs, such as Tyrannosaurus rex, did not have permanently exposed teeth as depicted in films such as Jurassic Park, but instead had scaly, lizard-like lips covering and sealing their mouths.

Researchers and artists have debated whether theropod dinosaurs, the group of two-legged dinosaurs that includes carnivores and top predators like T. rex and Velociraptor, as well as birds, had lipless mouths where perpetually visible upper teeth hung over their lower jaws, similar to the mouth of a crocodile.

However, an international team of researchers challenge some of the best-known depictions, and say these dinosaurs had lips similar to those of lizards and their relative, the tuatara - a rare reptile found only in New Zealand, which are the last survivors of an order of reptiles that thrived in the age of the dinosaurs.

In the most detailed study of this issue yet, the researchers examined the tooth structure, wear patterns and jaw morphology of lipped and lipless reptile groups and found that theropod mouth anatomy and functionality resembles that of lizards more than crocodiles. This implies lizard-like oral tissues, including scaly lips covering their teeth.

Watch nanoparticles grow into crystals

Liquid-phase TEM video of layer-by-layer growth of a crystal with smooth surface from gold concave nanocubes. Surface particles on the growing crystal are tracked (center positions overlaid with yellow dots).

For the first time ever, researchers have watched the mesmerizing process of nanoparticles self-assembling into solid materials. In the stunning new videos, particles rain down, tumble along stairsteps and slide around before finally snapping into place to form a crystal’s signature stacked layers.

Led by Northwestern University and the University of Illinois, Urbana-Champaign, the research team says these new insights could be used to design new materials, including thin films for electronic applications.

The research was published today (March 30) in the journal Nature Nanotechnology

Described by the researchers as an “experimental tour de force,” the study used a newly optimized form of liquid-phase transmission electron microscopy (TEM) to gain unprecedented insights into the self-assembly process. Before this work, researchers used microscopy to watch micron-sized colloids — which are 10 to 100 times larger than nanoparticles — self-assemble into crystals. They also have used X-ray crystallography or electron microscopy to visualize single layers of atoms in a crystalline lattice. But they were unable to watch atoms individually move into place.

“We know that atoms use a similar scheme to assemble into crystals, but we have never seen the actual growth process,” said Northwestern’s Erik Luijten, who led the theoretical and computational work to explain the observations. “Now we see it coming together right in front of our eyes. By viewing nanoparticles, we are watching particles that are larger than atoms, but smaller than colloids. So, we have completed the whole spectrum of length scales. We are filling in the missing length.”

Was plate tectonics occurring when life first formed on Earth?

Plate tectonics melts and mixes rocks to create magmas with specific chemical makeups. Rochester geologists are using that chemical evidence to unlock information about plate tectonic activity on Earth more than 4 billion years ago.
Photo Credit: Tetiana Grypachevska

Zircon crystals and magmas reveal new information about plate tectonic activity on Earth billions of years ago.

Earth is a dynamic and constantly changing planet. From the formation of mountains and oceans to the eruption of volcanoes, the surface of our planet is in a constant state of flux. At the heart of these changes lies the powerful force of plate tectonics—the movements of Earth’s crustal plates. This fundamental process has shaped the current topography of our planet and continues to play a role in its future.

But what was plate tectonic activity like during early Earth? And was the process even occurring during the time when life is thought to have formed?

“The dynamic tectonic nature of the modern Earth is one of the reasons why life exists today,” says Wriju Chowdhury, a postdoctoral research associate in the lab of Dustin Trail, an associate professor of earth and environmental sciences at the University of Rochester. “Exploring the geodynamics and the lithological diversity of the early Earth could lead to revelations of how life first began on our planet.”

AI predicts enzyme function better than leading tools

An Illinois research team created an AI tool to predict an enzyme’s function from its sequence using the campus network and resource group servers. Pictured, from left: Tianhao You, Haiyang (Ocean) Cui, Huimin Zhao and Guangde Jiang.   
Photo Credit: Fred Zwicky

A new artificial intelligence tool can predict the functions of enzymes based on their amino acid sequences, even when the enzymes are unstudied or poorly understood. The researchers said the AI tool, dubbed CLEAN, outperforms the leading state-of-the-art tools in accuracy, reliability and sensitivity. Better understanding of enzymes and their functions would be a boon for research in genomics, chemistry, industrial materials, medicine, pharmaceuticals and more.

“Just like ChatGPT uses data from written language to create predictive text, we are leveraging the language of proteins to predict their activity,” said study leader Huimin Zhao, a University of Illinois Urbana-Champaign professor of chemical and biomolecular engineering. “Almost every researcher, when working with a new protein sequence, wants to know right away what the protein does. In addition, when making chemicals for any application – biology, medicine, industry – this tool will help researchers quickly identify the proper enzymes needed for the synthesis of chemicals and materials.”

The researchers will publish their findings in the journal Science and make CLEAN accessible online March 31.

Allies or enemies of cancer: the dual fate of neutrophils

Neutrophils infiltrating tumors are heterogeneous and different neutrophil types can have opposing effects on cancer progression. The image shows artistic rendering of a lung tumor nodule (in blue) infiltrated by various neutrophil types (shown in green, orange and red) including some (in red) that are expanded by immunotherapy and are required for tumor elimination.
Illustration Credit: © Mate Kiss, Evangelia Bolli and Mikael Pittet

An international team including scientists from the UNIGE and Harvard has discovered a new type of immune cell whose action is essential for the success of immunotherapies.

Why do cancer immunotherapies work so extraordinarily well in a minority of patients, but fail in so many others? By analyzing the role of neutrophils, immune cells whose presence usually signals treatment failure, scientists from the University of Geneva (UNIGE), from Harvard Medical School, and from Ludwig Cancer Center have discovered that there is not just one type of neutrophils, but several. Depending on certain markers on their surface, these cells can either promote the growth of tumors, or fight them and ensure the success of a treatment. By boosting the appropriate factors, neutrophils could become great agents of anti-tumor immunity and reinforce the effects of current immunotherapies. These results can be read in Cell.

Ultrasmall swirling magnetic vortices detected in iron-containing material

Simulation capturing the different swirling textures of skyrmions and merons observed in ferromagnet thin film.
Image Credit: University of Edinburgh/based on microscopy images collected by Argonne on samples prepared at MagLab

Microelectronics forms the foundation of much modern technology today, including smartphones, laptops and even supercomputers. It is based on the ability to allow and stop the flow of electrons through a material. Spin electronics, or spintronics, is a spinoff. It is based on the spin of electrons, and the fact that the electron spin along with the electric charge creates a magnetic field.

“This property could be exploited for building blocks in future computer memory storage, brain-like and other novel computing systems, and high-efficiency microelectronics,” said Charudatta Phatak, group leader in the Materials Science division at the U.S. Department of Energy’s (DOE) Argonne National Laboratory.

A team including researchers at Argonne and the National High Magnetic Field Laboratory (MagLab) discovered surprising properties in a magnetic material of iron, germanium and tellurium. This material is in the form of a thin sheet that is only a few to 10 atoms in thickness. It is called a 2D ferromagnet.

The team discovered that two kinds of magnetic fields can coexist in this ultrathin material. Scientists call them merons and skyrmions. They are like miniature swirling storm systems dotting the flat landscape of the ferromagnet. But they differ in their size and swirling behavior.

A key mechanism that controls human heart development discovered

A human cardiac organoid (Cardioid), one of the models the researchers used to reconstruct human cardiac development in 3D. Cardiac mesoderm stage human Cardioid visualizing Phalloidin (grey) and β-catenin (Magenta).
Image Credit: Deniz Bartsch

Writing in ‘Science Advances’ researchers of the University of Cologne describe a key mechanism that controls the decision-making process that allows human embryonic stem cells to make the heart. These discoveries enable better insights into how the human heart forms in an embryo and what can go wrong during heart formation, causing cardiac disease or, in the worst case, embryo termination.

In humans, a specialized mRNA translation circuit predetermines the competence for heart formation at an early stage of embryonic development, a research team at the Center for Molecular Medicine Cologne (CMMC) and the University of Cologne’s Cluster of Excellence in Aging Research CECAD led by Junior Professor Dr Leo Kurian has discovered. While it is well known that cardiac development is prioritized at the early stages of embryogenesis, the regulatory program that controls the prioritization of the development of the heart remained unclear until now. Kurian and his team investigated how the prioritization of heart development is regulated at the molecular level. They found that the protein RBPMS (RNA-binding protein with multiple splicing) is responsible for the decision to make the heart by programming mRNA translation to approve future cardiac fate choice. The study is published under the title ‘mRNA translational specialization by RBPMS presets the competence for cardiac commitment’ in Science Advances.

“Exquisite” sabertooth skull offers clues about Ice Age predator

Dave Easterla, left, Distinguished University Professor Emeritus of Biology at Northwest Missouri State University and Matthew Hill, associate professor of anthropology at Iowa State, with a fossilized complete skull from a sabertooth cat from southwest Iowa.
Photo Credit: Christopher Gannon/Iowa State University.

The recent discovery of a sabertooth cat skull in southwest Iowa is the first evidence the prehistoric predator once inhabited the state.

The chance of finding any fossilized remains from a sabertooth cat is slim, said Matthew Hill, an associate professor of archaeology at Iowa State and expert on animal bones. The remarkably well-preserved skull found in Page County is even rarer, and its discovery offers clues about the iconic Ice Age species before its extinction roughly 12-13,000 years ago.

“The skull is a really big deal,” said Hill. “Finds of this animal are widely scattered and usually represented by an isolated tooth or bone. This skull from the East Nishnabotna River is in near perfect condition. It’s exquisite.”

Hill analyzed the specimen in collaboration with David Easterla, Distinguished University Professor Emeritus of Biology at Northwest Missouri State University. Their findings are newly published in Quaternary Science Reviews.

Machine learning models rank predictive risks for Alzheimer’s disease

Xiaoyi Raymond Gao, PhD Associate Professor
Photo Credit: Courtesy of Ohio State University

Once adults reach age 65, the threshold age for the onset of Alzheimer’s disease, the extent of their genetic risk may outweigh age as a predictor of whether they will develop the fatal brain disorder, a new study suggests. 

The study, published recently in the journal Scientific Reports, is the first to construct machine learning models with genetic risk scores, non-genetic information and electronic health record data from nearly half a million individuals to rank risk factors in order of how strong their association is with eventual development of Alzheimer’s disease.

Researchers used the models to rank predictive risk factors for two populations from the UK Biobank: White individuals aged 40 and older, and a subset of those adults who were 65 or older. 

Results showed that age – which constitutes one-third of total risk by age 85, according to the Alzheimer’s Association – was the biggest risk factor for Alzheimer’s in the entire population, but for the older adults, genetic risk as determined by a polygenic risk score was more predictive. 

“We all know Alzheimer’s disease is a later-onset disease, so we know age is an important risk factor. But when we consider risk only for people age 65 or older, then genetic information captured by a polygenic risk score ranks higher than age,” said lead study author Xiaoyi Raymond Gao, associate professor of ophthalmology and visual sciences and of biomedical informatics in The Ohio State University College of Medicine. “That means it’s really important to consider genetic information when we work on Alzheimer’s disease.” 

Lab-made antibodies offer potential cure for yellow fever

Captured through a microscope, this enlarged image illustrates how yellow fever virus (purple coloring) is below detectable levels in the blood of research animals given a monoclonal antibody after being exposed to the virus (bottom squares). By comparison, yellow fever virus is clearly visible in the blood of research animals that didn’t receive a monoclonal antibody (top squares). This research suggests lab-made antibodies may be able to cure people who get sick with yellow fever, a disease for which there is no approved treatment.
Image Credit: Oregon Health & Science University

New research from Oregon Health & Science University and collaborators indicates lab-made antibodies may be able to cure people infected with yellow fever, a virus for which there is no treatment.

The natural immune response to invading pathogens normally involves making protective proteins called antibodies. A study published in Science Translational Medicine suggests that a single monoclonal antibody infusion can strengthen the body’s fight against yellow fever.

In the study, the yellow fever virus was undetectable in all animals that received monoclonal antibody infusions after being exposed to the virus.

“Two monoclonal antibodies that we evaluated completely removed all signs of infection from research animals,” said the study’s corresponding author, Ben Burwitz, Ph.D., associate professor at OHSU’s Vaccine and Gene Therapy Institute and affiliate associate professor at OHSU’s Oregon National Primate Research Center.

Vegan protein supports muscle building as effectively as animal protein

Photo Credit: Daniela

Fungi-derived mycoprotein is just as effective at supporting muscle building during resistance training as animal protein, according to the findings of a new study from the University of Exeter.

The study, published in the Journal of Nutrition, is the first to explore if a vegan diet rich in mycoprotein – the naturally high-fiber fungi that is best known as Quorn – can support muscle growth during resistance training to the same extent as an omnivorous diet. It comes as a growing number of adults are eating less meat1, with latest figures showing that there are approximately 7.2m adults who now follow a meat free diet2.

The randomized trial was split into two phases: in the first phase, 16 healthy young adults completed a three-day diet where their protein was derived from either omnivorous or exclusively vegan (predominantly Quorn’s mycoprotein) sources, whilst detailed measures of metabolism were taken. In phase two, 22 healthy young adults completed a 10-week high volume progressive resistance training program while consuming a high protein omnivorous diet or a vegan diet rich in mycoprotein.

The results demonstrated comparable increases in muscle mass and strength in response to both diets, with no significant differences between the two. The group on the high protein omnivorous diet gained 2.6 kg of whole-body lean mass, while the group on the vegan diet gained 3.1 kg. Both groups also increased the size of their thigh muscles by the same amount (8.3%) over the course of the trial.

Juvenile black rockfish affected by marine heat wave but not always for the worse, research shows

A juvenile black rockfish
Photo Credit: Will Fennie

Larvae produced by black rockfish, a linchpin of the West Coast commercial fishing industry for the past eight decades, fared better during two recent years of unusually high ocean temperatures than had been feared, new research by Oregon State University shows.

“The study is important for gauging the conditions and making management plans that will affect the species’ survival as the ocean experiences increasing variability because of climate change,” said Will Fennie, the study’s lead author.

Findings were published in Nature’s Scientific Reports.

Rockfish, a diverse genus with many species, are a group of ecologically as well as economically important fishes found from Baja California to British Columbia.

They are known for lifespans that can reach triple digits, an ability to produce prodigious numbers of offspring and variable survival during their early life stages, during which they are highly sensitive to environmental conditions.

Coconuts and lemons enable a thermal wood for indoor heating and cooling

Peter Olsén and Céline Montanari, researchers in the Department of Biocomposites at KTH Royal Institute of Technology in Stockholm, say the new wood composite uses components of lemon and coconuts to both heat and cool homes.
Photo Credit: David Callahan

A building material that combines coconuts, lemons and modified wood could one day be enough to heat and cool your home. The three renewable sources provide the key components of a wood composite thermal battery, which was developed by researchers at KTH Royal Institute of Technology in Stockholm.

Researchers reported the development in the scientific journal Small. Peter Olsén, researcher in the Department of Biocomposites at KTH, says the material is capable of storing both heat and cold. If used in housing construction, the researchers say that 100 kilos of the material can save about 2.5 kWh per day in heating or cooling—given an ambient temperature of 24C.

KTH researcher Céline Montanari says that besides sunlight, any heat source can charge the battery. “The key is that the temperature fluctuates around the transition temperature, 24C, which can of course be tailored depending on the application and location,” she says.

Wednesday, March 29, 2023

Deep ocean currents around Antarctica headed for collapse

Direct measurements taken from the deep ocean have established that warming is already underway.
Photo Credit: Pixabay

Antarctic circulation could slow by more than 40 per cent over the next three decades, with significant implications for oceans and the climate.

The deep ocean circulation that forms around Antarctica could be headed for collapse, say scientists.

Such a decline would stagnate the bottom of the oceans and affect climate and marine ecosystems for centuries to come.

The results are detailed in a new study coordinated by Scientia Professor Matthew England, Deputy Director of the ARC Centre for Excellence in Antarctic Science (ACEAS) at UNSW Sydney. The work, published today in Nature, includes lead author Dr Qian Li – formerly from UNSW and now at the Massachusetts Institute of Technology (MIT) – as well as co-authors from the Australian National University (ANU) and CSIRO.

Cold water that sinks near Antarctica drives the deepest flow of the overturning circulation – a network of currents that spans the world’s oceans. The overturning carries heat, carbon, oxygen and nutrients around the globe. This influences climate, sea level and the productivity of marine ecosystems. 

Drug overdose fatalities among US older adults has quadrupled over 20 years

Photo Credit: Christina Victoria Craft

Overdose mortality among people age 65 and older quadrupled over 20 years, suggesting the need for greater mental health and substance use disorder policies addressed at curbing the trend, a new research paper finds.

The deaths stemmed from both suicides and accidental overdoses, with nearly three-fourths of the unintended fatalities involving illicit drugs such as synthetic opioids like fentanyl, heroin, cocaine, and methamphetamines.  Prescription opioids, antidepressants, benzodiazepines, antiepileptics and sedatives were used in 67% of intentional overdoses.

“The dramatic rise in overdose fatalities among adults over 65 years of age in the past two decades underscores how important it is for clinicians and policymakers to think of overdose as a problem across the lifespan,” said co-author Chelsea Shover, assistant professor of medicine in the division of general internal medicine and health services research at the David Geffen School of Medicine at UCLA. “Updating Medicare to cover evidence-based treatment for substance use disorders is crucial, as is providing harm reduction supplies such as naloxone to older adults.”

Mimicking biological enzymes may be key to hydrogen fuel production

Nickel-iron hydrogenase, described by researchers as “one of nature’s most complicated and beautiful enzymes,” may be crucial in the world’s push toward a renewable energy economy. 
Illustration Credit: Courtesy Mirica group

An ancient biological enzyme known as nickel-iron hydrogenase may play a key role in producing hydrogen for a renewables-based energy economy. Careful study of the enzyme has led chemists from the University of Illinois Urbana-Champaign to design a synthetic molecule that mimics the hydrogen gas-producing chemical reaction performed by the enzyme.

The researchers reported their findings in the journal Nature Communications

Currently, industrial hydrogen is usually produced by separating hydrogen gas molecules from oxygen atoms in water using a process called electrolysis. To boost this chemical reaction in the industrial setting, platinum metal is used as a catalyst in the cathodes that direct the reaction. However, many studies have shown that the expense and rarity of platinum make it unattractive as the world pushes toward more environmentally sound energy sources.

Rainbow Trout Subspecies Newly Named

The McCloud River Redband Trout is known as “cali sulat” in the Winnemem Wintu language, with “cali” meaning good or beautiful and “sulat” the term for trout.
Photo Credit: Steve MacMillan

The McCloud River redband trout, or O. mykiss calisulat, is newly identified as its own distinct subspecies of rainbow trout in a study from the University of California, Davis. It is the first newly identified subspecies of Pacific trout since 2008 and the youngest rainbow trout subspecies by more than 100 years.

The study, published in the journal Zootaxa, notes that fish biologists have suspected the McCloud River redband trout was its own subspecies since at least the 1970s, but only newer genetics techniques — including genomewide DNA sequencing — allowed the UC Davis-led team to tease the puzzle apart and confirm it as a subspecies.

Northern California’s McCloud River originates from spring-fed streams near Mount Shasta before passing over a series of waterfalls, the McCloud Falls. The waterfalls are impassable to upstream movement of fishes and divide the Upper McCloud River from the Lower McCloud River.

The McCloud River redband trout is the only known native fish found in the Upper McCloud Basin.

“It’s persisted so long in isolation,” said lead author Matthew “Mac” Campbell, a research affiliate with the Department of Animal Science’s Genomic Variation Laboratory. “They’ve survived in glacial refugia during the Pleistocene era and have been above those waterfalls for at least 10,000 years.”

Cell mapping and ‘mini placentas’ give new insights into human pregnancy

Cells of the placenta 
Image Credit: Kenny Roberts, Wellcome Sanger Institute

Researchers from the University of Cambridge, the Wellcome Sanger Institute, the Friedrich Miescher Institute for Biomedical Research (FMI), Switzerland, EMBL’s European Bioinformatics Institute (EMBL-EBI), and collaborators, have created an in-depth picture of how the placenta develops and communicates with the uterus.

The study, published today in the journal Nature, is part of the Human Cell Atlas initiative to map every cell type in the human body. It informs and enables the development of experimental models of the human placenta.

"For the first time, we have been able to draw the full picture of how the placenta develops and describe in detail the cells involved in each of the crucial steps. This new level of insight can help us improve laboratory models to continue investigating pregnancy disorders, which cause illness and death worldwide,” said Anna Arutyunyan, co-first author at the University of Cambridge and Wellcome Sanger Institute.

The placenta is a temporary organ built by the fetus that facilitates vital functions such as fetal nutrition, oxygen and gas exchange, and protects against infections. The formation and embedding of the placenta into the uterus, known as placentation, is crucial for a successful pregnancy.

Three newly discovered sea worms that glow in the dark

 Polycirrus onibi, a newly discovered marine worm that glows in the dark was named after a creature from Japanese folklore.
Photo Credit: Naoto Jimi / Nagoya University

A research group from Nagoya University in central Japan has discovered three new species of bioluminescent polycirrus worms from different parts of Japan. Usually found in shallow water, polycirrus are small worms, known for their bioluminescence. The researchers named one of their discoveries after a ghostly yokai, a creature in Japanese folklore; another after a lantern yokai; and the other after an influential Japanese marine biologist. They published their findings in the journal Royal Society Open Science

Scientists have studied only a small fraction of the more than 7,000 species of luminescent organisms in the world. Research remains limited to certain species because of the existence of specimens that are difficult to classify into species. Without correct identification of the species, comparisons of different results are of limited use.  

Naoto Jimi (he/him) and Special Assistant Professor Manabu Bessho-Uehara (he/him) at Nagoya University’s Graduate School of Science, led a research group with members from AIST, Olympus Corporation, and Japan Underwater Films Corporation, that organized Polycirrus according to their diversity. They discovered three new species, all of which emit blue-violet light.   

Ancient DNA reveals entwined African and Asian ancestry along the Swahili coast of eastern Africa

Rice researchers Mary Prendergast and Jeffrey Fleisher.
Photo Credit: Brandon Martin.

A new genetic study of medieval people who lived along the Indian Ocean coast of eastern Africa — an area often called the “Swahili coast” for its language and culture — revealed that they had both African and Persian ancestry.

The results suggest that maritime trade connections long recognized by archaeologists based on imported goods and architectural influences fostered relationships between Asian merchants and African traders and their families.

“Entwined African and Asian genetic roots of medieval peoples of the Swahili coast” was published today in Nature. It examines genetic ancestry and cultural influences in eastern Africa by using DNA from the skeletal remains of 80 individuals who were buried in six medieval and early modern coastal towns in Kenya and Tanzania dating to the years 1250-1800 and an inland town in Kenya dating to after 1650.

Analysis of the genetic data enabled scientists to estimate that people of African and Persian ancestry began to have children together around the year 1000, centuries before the burials themselves.

How the gut creates a cozy home for beneficial microbiome species

Image Credit: Courtesy of Carnegie Institution for Science

The digestive tract of fruit flies remodels itself to accommodate beneficial microbiome species and maintain long-term stability of the gut environment, according to new research led by Carnegie’s William Ludington and Allan Spradling. Their findings are published in Nature Communications.

The gut microbiome is an ecosystem of hundreds to thousands of microbial species living within the human body. These populations affect our health, fertility, and longevity. But there is still so much to learn about how these microbial species interact with our bodies and with each other.

“Every day, we encounter, and even ingest, a diverse array of bacterial species,” explained Ludington, who has been probing microbiome acquisition and composition for several years at Carnegie. “Despite this, the gut microbiome remains relatively stable over time—a phenomenon that is maintained across many species ranging from mammals to insects.”

He, Spradling, and their collaborators wanted to determine how our guts can maintain such remarkably consistent microbiome compositions. Because the human microbiome is so complex, they studied fruit flies, which are only colonized by a handful of microbial species.

Birth of a very distant cluster of galaxies from the early Universe

This image shows the protocluster around the Spiderweb galaxy (formally known as MRC 1138-262), seen at a time when the Universe was only 3 billion years old. Most of the mass in the protocluster does not reside in the galaxies that can be seen in the centre of the image, but in the gas known as the intracluster medium (ICM). The hot gas in the ICM is shown as an overlaid blue cloud.   The hot gas was detected with the Atacama Large Millimeter/submillimeter Array (ALMA), of which ESO is a partner. As light from the cosmic microwave background –– the relic radiation from the Big Bang –– travels through the ICM, it gains energy when it interacts with the electrons in the hot gas. This is known as the Sunyaev-Zeldovich effect. By studying this effect, astronomers can infer how much hot gas resides in the ICM, and show that the Spiderweb protocluster is in the process of becoming a massive cluster held together by its own gravity. 
Full Size Image
Image Credit: ESO/Di Mascolo et al.; HST: H. Ford

Using the Atacama Large Millimeter/submillimeter Array (ALMA), of which ESO is a partner, astronomers have discovered a large reservoir of hot gas in the still-forming galaxy cluster around the Spiderweb galaxy — the most distant detection of such hot gas yet. Galaxy clusters are some of the largest objects known in the Universe and this result, published today in Nature, further reveals just how early these structures begin to form.

Galaxy clusters, as the name suggests, host a large number of galaxies — sometimes even thousands. They also contain a vast “intracluster medium” (ICM) of gas that permeates the space between the galaxies in the cluster. This gas in fact considerably outweighs the galaxies themselves. Much of the physics of galaxy clusters is well understood; however, observations of the earliest phases of formation of the ICM remain scarce.

Previously, the ICM had only been studied in fully-formed nearby galaxy clusters. Detecting the ICM in distant protoclusters — that is, still-forming galaxy clusters – would allow astronomers to catch these clusters in the early stages of formation. A team led by Luca Di Mascolo, first author of the study and researcher at the University of Trieste, Italy, were keen to detect the ICM in a protocluster from the early stages of the Universe. 

Retinoic Acid Could Be Key to Preventing Gut Infections

Brian Sheridan conducts research on CD8 T cells to investigate immune responses with the hope of laying groundwork for new therapies and vaccines. 
Photo Credit: John Griffin, Stony Brook University

A team of scientists from the Renaissance School of Medicine (RSOM) at Stony Brook University have identified a distinct role of retinoic acid, a metabolite of vitamin A, during the immune response of the gut. This finding, detailed in a paper published in the Journal of Experimental Medicine, and highlighted in a broader piece in the journal, could help lead to ways to control the retinoic acid response and therefore could be used as a therapy or for vaccine development against infection or even to treat GI tumors.

Led by Brian Sheridan, associate professor in the Department of Microbiology and Immunology and the Center for Infectious Diseases, the study involves basic research that centers on unraveling the factors that control the generation of cytotoxic memory CD8 T cells, which are an important arm of the body’s anti-pathogen immune response as they kill pathogen-infected cells and produce anti-pathogen cytokines. In fact, memory CD8 T cells provide long-lived and frontline protection at barrier tissues, highlighting their importance in vaccine design.

To date, scientists have known that retinoic acid in the gut-draining lymph nodes promotes effector CD8 T cell migration to the intestines, enhancing the immune response. Additionally, vitamin A deficiency is associated with increased infections and poor vaccine efficiency.

Smells influence metabolism and ageing in mice

Photo Credit: Nick Fewings

Exposure to female odors and pheromones causes weight loss and extend the life spans of mice, which may have implications for humans, University of Otago researchers have found.

Lead researcher Dr Michael Garratt, of the Department of Anatomy, says while it was already known that sensory cues in humans and animals influence the release of sex hormones, this study shows that these cues could have more wide-spread physiological effects on metabolism and ageing.

“Our studies show that female odors slow the sexual development of female mice, but consequently extends their lifespan. And we also show that the smell of females can increase male mouse energy expenditure, which subsequently influences their body weight and body fat levels,” he says.

Newborn mice were exposed to odors from adult females until they were 60 days old. Those females exposed to the odors reached sexual maturity later and lived an average 8 per cent longer than those not exposed.

There was no effect of male odors on female mouse lifespan, or changes in lifespan in males in response to odors from either sex.

ORNL-led team designs molecule to disrupt SARS-CoV-2 infection

Oak Ridge National Laboratory led a team of scientists to design a molecule that disrupts the infection mechanism of the SARS-CoV-2 coronavirus and could be used to develop new treatments for COVID-19 and future virus outbreaks.
Video Credit: Michelle Lehman/ORNL, U.S. Dept. of Energy

A team of scientists led by the Department of Energy’s Oak Ridge National Laboratory designed a molecule that disrupts the infection mechanism of the SARS-CoV-2 coronavirus and could be used to develop new treatments for COVID-19 and other viral diseases.

The molecule targets a lesser-studied enzyme in COVID-19 research, PLpro, that helps the coronavirus multiply and hampers the host body’s immune response. The molecule, called a covalent inhibitor, is effective as an antiviral treatment because it forms a strong chemical bond with its intended protein target.

“We’re attacking the virus from a different front, which is a good strategy in infectious disease research,” said Jerry Parks, who led the project and leads the Molecular Biophysics group at ORNL.

The research, detailed in Nature Communications, turned a previously identified noncovalent inhibitor of PLpro into a covalent one with higher potency, Parks said. Using mammalian cells, the team showed that the inhibitor molecule limits replication of the original SARS-CoV-2 virus strain as well as the Delta and Omicron variants.

Extinction of steam locomotives derails assumptions about biological evolution

The Union Pacific Big Boy Steam Engine (one of the largest steam engines ever built and still functioning) visited Lawrence on Sept. 2, 2021.
Photo Credit: Bruce Lieberman

When the Kinks’ Ray Davies penned the tune “Last of the Steam-Powered Trains,” the vanishing locomotives stood as nostalgic symbols of a simpler English life. But for a paleontologist at the University of Kansas, the replacement of steam-powered trains with diesel and electric engines, as well as cars and trucks, might be a model of how some species in the fossil record died out.

Bruce Lieberman, professor of ecology & evolutionary biology and senior curator of invertebrate paleontology at the KU Biodiversity Institute & Natural History Museum, sought to use steam-engine history to test the merits of “competitive exclusion,” a long-held idea in paleontology that species can drive other species to extinction through competition.

Working with former KU postdoctoral researcher Luke Strotz, now of Northwest University in Xi’an, China, Lieberman found the fossil record largely lacks the detailed data verifying competitive exclusion found in the history of steam engines: “It's really hard to actually see any evidence that competition does play a big role in evolution,” Lieberman said.

Their findings have just been published in the paper “The end of the line: competitive exclusion and the extinction of historical entities2” in the peer-reviewed journal Royal Society Open Science.

Tur­bu­lence: Decades-old the­ory gets a major remake

Ivana Stiperski and the students from the Field Course in Alpine Meteorology setting up the instruments at the “Hochhäuser” i-Box station in the Inn Valley.
Photo Credit: Tobias Posch

Turbulence plays an essential role in weather and climate, and correctly representing its effects in numerical models is crucial for accurate weather forecasts and climate projections. However, the theory describing the effect of turbulence has not changed since its conception in 1950s, despite the fact that it is not representative for the majority of the Earth’s land surface, especially over mountains and polar regions. The Innsbruck meteorologist Ivana Stiperski has now extended the turbulence theory to complex atmospheric conditions. The researcher thus paves the way for the first generalized turbulence theory over complex terrain.

Turbulence is the most important exchange mechanism between the Earth's surface and the overlying atmosphere. However, this mechanism remains one of the last great puzzles of classical physics and mathematics. Ivana Stiperski, head of the research group "Atmospheric Turbulence" at the Department of Atmospheric and Cryospheric Sciences at the University of Innsbruck, has dedicated her work to the study of turbulence over mountains, and since 2020 her team is working on the topic within the framework of an ERC Consolidator Grant. "Turbulence affects phenomena as diverse as climate, storm systems, air pollution and glacier melt. Accurate weather forecasts and climate predictions therefore require a precise description of turbulence, and over the complex terrain of mountainous regions this is particularly difficult as very little is known about how complex terrain modifies turbulence, and no major advance has happened over the past 70 years", Stiperski explains. Until now, the understanding of atmospheric turbulence and how it is included in weather and climate models has been based on the so-called similarity theory, more specifically the "Monin-Obukhov similarity theory " first postulated in 1954. This decades-old theory of turbulence, however, assumes that the Earth’s surface is flat and horizontally homogeneous (i.e., has uniform characteristics in the horizontal, such as for example infinite grasslands or corn fields), and therefore it is not representative for the majority of the Earth’s land surface. This incorrect representation of turbulence adds uncertainty to weather prediction and climate projections.

Wild animals stop the spread of socially transmitted misinformation

For wild animals, false alarms are the most widespread form of misinformation.
Photo Credit: Kaylee Rose Fahimipour

Despite the benefits of learning about the world through social ties, social connections also provide a conduit for misinformation that impedes effective decision-making.

For wild animals, false alarms are the most widespread form of misinformation. For example, when an individual animal in a group makes the decision to produce an alarm signal or initiate an escape maneuver in the absence of a real threat. This initial action produces sensory stimuli that can be perceived by others in the group as an indication of danger, resulting in a cascade of erroneous escape responses that can spread contagiously.

Behavioral and neurophysiological studies suggest that relatively simple behavioral strategies control decision-making in many of these settings. Yet, it is unknown whether these strategies somehow account for the possibility of exposure to misinformation.

How whale shark rhodopsin evolved to see, in the deep blue sea!

Whale shark
Photo Credit: Mitsumasa Koyanagi, OMU

A new study reveals that the photoreceptor rhodopsin of whale sharks (Rhincodon typus), pictured here, evolved to improve sight for the low-light low-temperature deep-sea environment in a unique way.

A research group including Professors Mitsumasa Koyanagi and Akihisa Terakita of the Osaka Metropolitan University Graduate School of Science has investigated both the genetic information and structure of the photoreceptor rhodopsin, responsible for detecting dim light, of whale sharks to investigate how they can see in the dim light at extreme depths. The research group compared the whale sharks to zebra sharks, which are considered their closest relative, and brown-banded bamboo sharks, which are in the same group: the order orectolobiformes—commonly known as carpet sharks.

“This research used genetic information and molecular biological techniques to achieve stunning results—without harming whale sharks’ or their biology. Our research approach is to use these techniques to provide clues that reveal the mysteries of how these organisms live,” explained Professor Koyanagi. “The beautiful part is that it even works for species where information is limited, such as large or wild animals that are difficult to observe or follow in their natural habitat.”

Coronavirus causes chaos in infected cells’ RNA

Illustration Credit: Fusion Medical Animation

Coronavirus disease (COVID-19) hijacks parts of infected cells' vital RNA machinery, thereby blocking important functions in the cells. These damaging changes in the RNA can likely be reversed, potentially leading to new drugs against COVID-19, University of Gothenburg researchers show.

Genetic material in the body's cells consists of DNA, which serves as long-term storage of genetic information. RNA carries this encoded information to the cells for transcription and translation. These processes enable them to make proteins, which perform most intracellular tasks. The cells' RNA is modifiable to allow correct transfer of the DNA information to the proteins. In recent years, scientific understanding of the complexity and importance of these RNA modifications has grown.

Drastic impact

It has been shown that RNA modifications take place in various viruses, but exactly how the viruses affect the RNA modification processes when they infect cells is unknown. This study reports that SARS-CoV-2 infection disrupts the RNA modifications, and the extent of these RNA modification changes surprised the researchers.

One of the modifications affected by SARS-CoV-2, known as m6A (a multifaceted regulator of gene expression), is highly important for RNA’s basic functions, including transportation of data to the protein-making parts of the cell, and transcription and translation into amino acids there.

“We were surprised at the extent and drastic scale of m6A RNA modification loss in SARS-CoV-2 infection. We also found that the coronavirus variants have differing effects on m6A levels,” says Tanmoy Mondal, researcher at Sahlgrenska Academy, University of Gothenburg, who led the project.

Tuesday, March 28, 2023

Preserving the stars: light pollution and what you can do about it

Astrophysicist Ms Kirsten Banks explains what we can do to reverse the impact of "light glow".
Photo Credit: UNSW Sydney.

An astrophysicist from UNSW Sydney explains why it’s so important that we can all look up and see the stars. 

Astronomer Carl Sagan famously said that there were more stars in the universe than grains of sand on earth.  

It has been estimated that there are over 100 billion stars in the Milky Way galaxy. While there is a limit to how many stars we can see from earth with the naked eye, that number is dramatically reducing due to light pollution. 

“We should be able to see around 2500 stars with the naked eye on any night, and we can see about 125 of them at best in Sydney,” says astrophysicist, proud Wiradjuri woman and UNSW PhD candidate Ms. Kirsten Banks.

In fact, in a recent study published in Science, data collected by citizen scientists around the world found light pollution is increasing at a rate that is equivalent to the brightness of the sky doubling every eight years.  

This latest research continues to expose the extent to which we’re losing the darkness of our night sky. Not being able to look up and see the stars will have significant cultural impacts, but there are steps we can all be taking to reduce the effect of light pollution.

Turtle and crocodile species with unique characteristics are more likely to go extinct

A Mugger Crocodile (Crocodylus palustris). In Pakistan, this species is still illegally hunted for its skin.
Image Credit: Bishnu Sarangi

New research led by the University of Oxford has revealed that the most endangered turtle and crocodile species are those that are most unique. Their loss could have widespread impacts on the ecosystems they live in since they carry out critical processes important for many other species. The results have been published in Nature Communications.

"When it comes to the conservation of turtles and crocodiles, we are dealing with a critical scenario. Furthermore, our actions are affecting unevenly more so those species that are characterized by unique life strategies. Once they are gone, these life strategies will be gone too, with no other species being able to provide a back-up." 
Professor Rob Salguero-Gómez, Department of Biology, University of Oxford

Turtles and crocodiles are two of the world's most endangered animal groups, with approximately half of the species globally threatened (International Union for Conservation of Nature, IUCN). Greater understanding of which species are most threatened and why is urgently needed to inform conservation efforts to save them.

In a new study led by researchers at the Department of Biology, University of Oxford, an international team examined the greatest risks to wild populations of turtles and crocodiles worldwide. The results demonstrate that the most endangered turtles and crocodile species are those that have evolved unique life strategies. These species typically carry out highly specific roles within their ecosystems that are unlikely to be taken up by other species if they disappear.

Separated at last

In the new method, laser pulses of different power (green) are combined in such a way that single excitation (blue), double excitation (red) and triple excitation (yellow) can be distinguished, for example, in biological light-harvesting complexes.
Illustration Credit: Julian Lüttig / Universität Würzburg

Scientists at the Universities of Würzburg and Ottawa have solved the decades-old problem of distinguishing between single and multiple light excitations. They present their new method in the journal Nature.

The construction of the first laser in 1960 ushered in commercial applications with light that have become an integral part of our everyday lives. At the same time, this development opened up the scientific field of laser spectroscopy – a technique that is central to the analysis of materials and the study of fundamental physical phenomena.

Despite all the successes, however, research teams have struggled since the 1970s with the problem that a laser shining on a sample can excite it not just once, but several times per experiment. In this case, the measurement results of the single excitation and the multiple excitations overlap and usually cannot be separated, making it difficult to understand the material.

Climate change threatens lemurs on Madagascar

A female grey mouse lemur (Microcebus murinus) carrying an infant.
Photo Credit: Manfred Eberle

They are small, have a high reproductive output and live in the forests of Madagascar. During the 5-month rainy season, offspring are born and a fat pad is created to survive the cool dry season when food is scarce. But what happens when the rainy season becomes drier and the dry season warmer? Can mouse lemurs adapt to climate change thanks to their high reproductive output? Researchers from the German Primate Center – Leibniz Institute for Primate Research, together with colleagues from the University of Zurich, have analyzed long-term data from Madagascar and found that climate change is destabilizing mouse lemur populations and increasing their risk of extinction. The fact that climate change is leading to greater fluctuations in population density and thus increases extinction risk in a fast-paced, ecological generalist is an alarming warning signal for potential biodiversity losses in the tropics.

Effects of climate change have mostly been studied in large, long-lived species with low reproductive output. Small mammals with high reproductive rates can usually adapt well to changing environmental conditions, so they have been studied little in the context of climate change. Claudia Fichtel and Peter Kappeler from the German Primate Center – Leibniz Institute for Primate Research (DPZ) have been researching lemurs on Madagascar for many years and have thus built up a unique data set to fill this knowledge gap.

Adipose tissue as a culprit: How obesity leads to diabetes

A high-fat diet leads to obesity and the development of diabetes.
Photo Credit: Muffin Creatives

A research team at the University of Basel has discovered that a high-fat diet alters the function of adipose tissue, thus impairing its ability to regulate blood sugar. This explains why a high-fat diet poses a significant health risk, particularly for diabetes.

Diabetes is a medical condition in which the body is unable to keep blood sugar in a healthy range. Normally, the pancreas produces sufficient insulin to regulate the blood sugar level and maintain homeostasis. However, in diabetics, the body has lost this ability, leading to hyperglycemia.

Blood sugar levels that are persistently too high can cause long-term damage to blood vessels and lead to severe complications such as blindness or kidney failure. It has been known for some time that obese patients are particularly at risk of developing type 2 diabetes and that adipose tissue plays a critical role in the onset of the disease. In their recent study, researchers led by Professor Michael N. Hall at the Biozentrum, University of Basel, revealed how a high-fat diet triggers diabetes.

Electricity from Air

Graphic illustration of titanium-air battery properties, in the style of the periodic table of elements
Illustration Credit: Courtesy of Technion – Israel Institute of Technology

Scientists at Forschungszentrum Jülich have developed and successfully lab-tested a novel titanium-air battery in cooperation with researchers at the Technion – Israel Institute of Technology in Haifa. This is the first time that experimental results of such a battery have been published, in which titanium is used as an active material. The metal is of interest as an electricity storage material because each atom can donate up to four electrons for charge transfer, while at the same time being relatively light and extremely resistant.

Scientific Results

Titanium is known as a passive, stable material. The researchers succeeded in utilizing its electrochemical potential for the storage of electrical energy by applying an ionic liquid called EMIm(HF)2.3F. Ionic liquids consist of salts with an atypical, very low melting point, which are used in a variety of applications due to their special electrical and material properties.

Early study shows cones in retinal degeneration, thought to be dormant, may retain visual function

“While the sensitivity of the cones was about 100-1000 fold less than normal, we were surprised to find that that the drop-off in sensitivity for the ganglion cells that project to the brain was much less,” said senior author Alapakkam Sampath.
Photo Credit: Miranda Scalabrino

New UCLA research in mice suggests that “dormant” cone photoreceptors in the degenerating retina are not dormant at all, but continue to function, producing responses to light and driving retinal activity for vision.  

The cells in the retina that produce the visual experience are rods and cones. Rods are active in dim light and cones in daylight. Mutations in rods that cause them to die trigger most inherited retinal degeneration. Cones can remain alive after nearly all the rods die, but they retract key parts of the cells and appear “dormant.”  

But while past literature suggested that dormant cells were not functional, and earlier attempts to record from them revealed no light-driven activity, the new study indicates for the first time that the cells are still viable. Furthermore, downstream signals recorded from the retina show that visual processing is not as compromised as may be expected. The authors say their findings demonstrate that therapeutic interventions to protect these cells, or enhance their sensitivity, have the capability to preserve nearly normal daytime vision. 

New Study Reveals Potential Link Between Two of Astronomy’s Most Mysterious Phenomena

Artist's conception of fast radio burst reaching Earth.
Illustration Credit: Jingchuan Yu, Beijing Planetarium

International team of scientists reports a possible correlation between gravitational waves from neutron star mergers and fast radio bursts; results could improve understanding of how some deep-space bursts occur.

The secrets of deep space may be starting to reveal themselves, as rapid advances in technology and stronger research collaborations are making it possible for astronomers to piece together cosmological clues like never before.

  In the March 27 issue of the journal Nature Astronomy, an international team of scientists shows for the first time a possible relationship between neutron star mergers and fast radio bursts (FRBs) – two of the most mysterious cosmological phenomena studied over the past two decades.

  The team, which includes researchers from UNLV, University of Western Australia (UWA), and Curtin University, reports on the observation of a deep space neutron star merger followed just 2 ½ hours later by an observed FRB. If confirmed, the correlation between the two events could unlock part of the mystery of how FRBs are generated.

  Fast radio bursts (FRBs) are millisecond-long pulses of electromagnetic radio waves that occur in deep space and produce the energy equivalent to the sun’s annual output. Most FRBs occur as one-off events, while others present as repeating bursts. Though their origins are still a bit of a mystery, the fraction of FRBs emitted as repeated bursts are likely produced by highly magnetized neutron stars known as magnetars.

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