Revealed: Some microbiome species regulate their entire bacterial ecosystem

Image Credit: Scientific Frontline 

A team of mathematicians and biologists led by Carnegie’s Will Ludington and Technische Universität Berlin’s Michael Joswig developed a new approach to reveal key genes and species that regulate biological networks. Their work, published this week in Proceedings of the National Academy of Sciences, identifies genes in cells and species in ecosystems that sit at the top of a regulatory hierarchy and drive evolutionary and ecological trajectories.

Charles Darwin concluded On the Origin of Species with the famous “tangled bank” analogy to explain how organisms in an ecosystem affect one another’s fitness. “It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth,” Darwin wrote. “And to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us.” 

To map these interactions in ecosystems, ecologists use network analysis to study the connections. Keystone species, such as wolves, have a disproportionately large impact on their communities and the other organisms within them.

New Strategy Improves Perovskites' Oxygen Reduction Performance in Hydrogen Fuel Cells

Evidence of calcium leaching during ORR, leading to the high surface area of the LCMO64.
Illustration Credit: ©Hao Li et al.

A research group has reported on a new method to enhance the electrochemical surface area (ECSA) in a calcium-doped perovskite, La0.6Ca0.4MnO3 (LCMO64), thereby overcoming a common bottleneck in the application of perovskite oxides as electrocatalysts in hydrogen fuel cells.

Perovskite oxides exhibit interesting and diverse properties, making them valuable in various technological applications. Their high intrinsic activities also position them as a promising alternative to noble metal catalysts for efficiently catalyzing the oxygen reduction reaction (ORR). However, their application is still hampered by their poor electrical conductivity and low specific surface area.

Acid Sensor and Calcium Store Discovered in Plants

When exposed to blue light, the light-gated H+ channel KCR2 kicks into action, causing a rapid increase in cytosolic H+ concentration. This heightened H+ level is then detected by a H+-sensitive Ca2+ channel (HSCA), prompting the subsequent opening of its gate for Ca2+ release from the endoplasmic reticulum. This chain of events ultimately triggers the opening of SLAC anion channels, leading to stomatal closure.
Image Credit: Huang/Hedrich (JMU)

Using optogenetics, Würzburg researchers have detected a new acid sensor in plant cells that is addressing a cell-internal calcium store, as they report in the journal Science.

When plants are infected by pathogens, suffer from a lack of water or have to react to other external stimuli, the first thing they do is increase the proton and calcium concentration in the affected cells. The protons and calcium ions then act like messenger substances that trigger further reactions in the cell.

The interactions between protons and calcium ions in this process were previously largely unknown. An article in the journal Science by a team led by biophysicist Professor Rainer Hedrich from Julius-Maximilians-Universität (JMU) Würzburg in Bavaria, Germany, has now shed new light on this subject.

Using a sophisticated optogenetic approach, the researchers have discovered a previously unknown endogenous acid sensor in plant cells. And they have discovered in the guard cells of leaves that there is a calcium store that plays an important role in processing proton signals in cellular responses.

Deadly chicken disease: ancient DNA reveals evolution of virulence

With the increase in poultry farming, Marek's disease virus evolved
Photo Credit: Heidi-Ann Fourkiller

Using genetic analyses, an international team led by LMU paleogeneticist Laurent Frantz has revealed the evolutionary history of the pathogen of a fatal disease in chickens.

A notifiable animal disease in Germany, Marek’s disease is caused by the globally distributed Marek’s disease virus (MDV). Over the past century, the virus, which causes tumors in chickens and has a high mortality rate, has become increasingly aggressive. Combating the disease costs the poultry industry over a billion dollars every year. With the help of ancient DNA, an international team of scientists led by LMU paleogenomicist Professor Laurent Frantz and Professor Greger Larson and Professor Adrian Smith from the University of Oxford has now decoded the evolution of MDV and shed light on what is behind the growing virulence.

The international team from the fields of paleogenetics, archeology, and biology isolated viral genomes from chicken bones up to 1,000 years old from 140 archeological sites in Europe and the Near East. “Our data shows that the virus was already widely distributed at least 1,000 years before the first description of the disease in 1907,” says Frantz. When the disease was first described, it was said to produce only mild symptoms in older chickens. With the dramatic increase in poultry farming in the 1950s and 1960s, the virus evolved and has become increasingly virulent despite the development of several vaccines.

How the Immune System Fights to Keep Herpes at Bay

These microscope images show how interferon in the nucleus raises levels of the protective protein IFI16 (stained green) from low background levels (left) to the higher levels needed to resist herpes infection (right).
Image Credit: HMS MicRoN core imaging facility/Nicolas Romero Rata

Herpes simplex virus (HSV) is extremely common, affecting nearly two-thirds of the world’s population, according to the World Health Organization.

Once inside the body, HSV establishes a latent infection that periodically awakens, causing painful blisters on the skin, typically around the nose and mouth. While a mere nuisance for most people, HSV can also lead to dangerous eye infections and brain inflammation in some people and cause life-threatening infections in newborns.

Researchers have long known that the virus and the host immune system are in a perpetual competition, but why does this battle reach a stasis in most people while causing serious infections in others?

More important, precisely how does the battle unfold at the level of cells and molecules? This question has continued to bedevil scientists and hamper the quest for treatments that prevent or cure infections.

A recent study by researchers at Harvard Medical School, conducted using lab-engineered cells and published in PNAS, unveils the precise maneuvers used by host and pathogen in the fight for dominance of the cell.

Long-sought binary star population found! Discovery could answer questions about hydrogen-poor supernova origins

An artist’s conception of the hydrogen being stripped from one half of a binary system, leaving a very hot, helium rich exposed core that will eventually explode as a hydrogen-poor core collapse supernova.
 Illustration Credit: Navid Marvi, courtesy of the Carnegie Institution for Science.

A team of astronomers has found a long- “missing” population of stars that could answer long-standing questions about the origins of a mysterious type of supernova. Their discovery, published in Science, could help researchers understand how hydrogen-poor core-collapse supernovae and neutron star collisions occur—major stellar events that are the source of many of the elements on the periodic table.

The project’s leaders, the University of Toronto’s Maria Drout and the Institute of Science and Technology Austria’s Ylva Götberg, met as junior researchers, and both went on to complete postdoctoral positions at the Carnegie Observatories—where the majority of this work was done—and have since moved onto assistant professor positions at their respective institutions.

Supernovae are violent stellar explosions that spew material into their cosmic surroundings, seeding the next generation of stars. But astronomers are still working to elucidate how they originate and what their various stellar progenitors look like—which differ between types of supernovae.

Drout and Götberg were particularly interested in one type of supernovae that stands out from their celestial peers for being hydrogen poor.

Custom software speeds up, stabilizes high-profile ocean model

The illustration depicts ocean surface currents simulated by MPAS-Ocean.
Illustration Credit: Los Alamos National Laboratory, E3SM, U.S. Dept. of Energy

On the beach, ocean waves provide soothing white noise. But in scientific laboratories, they play a key role in weather forecasting and climate research. Along with the atmosphere, the ocean is typically one of the largest and most computationally demanding components of Earth system models like the Department of Energy’s Energy Exascale Earth System Model, or E3SM.

Most modern ocean models focus on two categories of waves: a barotropic system, which has a fast wave propagation speed, and a baroclinic system, which has a slow wave propagation speed. To help address the challenge of simulating these two modes simultaneously, a team from DOE’s Oak Ridge, Los Alamos and Sandia National Laboratories has developed a new solver algorithm that reduces the total run time of the Model for Prediction Across Scales-Ocean, or MPAS-Ocean, E3SM’s ocean circulation model, by 45%. 

The researchers tested their software on the Summit supercomputer at ORNL’s Oak Ridge Leadership Computing Facility, a DOE Office of Science user facility, and the Compy supercomputer at Pacific Northwest National Laboratory. They ran their primary simulations on the Cori and Perlmutter supercomputers at Lawrence Berkeley National Laboratory’s National Energy Research Scientific Computing Center, and their results were published in the International Journal of High Performance Computing Applications.

Lightning, camera, gamma ray!

Lightning captured with the highspeed camera at 40,000 frames per second.
Photo Credit: Rasha Abbasi

In September 2021, an unprecedented thunderstorm blew across Utah’s West Desert. Lightning from this storm produced at least six gamma ray flashes that beamed downward to Earth’s surface and activated detectors at the University of Utah-led Telescope Array. The storm was noteworthy on its own—the array usually clocks one or two of the lightning-triggered gamma rays per year—but recent upgrades led to a new observation by the Telescope Array scientists and their lightning collaborators.

For the first time ever, they captured video footage of lightning-triggered downward terrestrial gamma-ray flashes (TGFs). A special camera running at 40,000 frames per second gave an unprecedented look at how gamma rays burst downwards to the Earth’s surface from cloud-to-ground lightning strikes. They found that not only were multiple gamma rays produced at later lightning stages than previously thought, but the rays were also associated with a pulse of optical light that had never been recorded.

“This is an important step in lightning research that could lead us to the physics producing these downward gamma rays,” said lead author Dr. Rasha Abbasi, now an assistant professor of physics at Loyola University Chicago. Abbasi began the research on TGFs as a postdoctoral scholar at the University of Utah.

New study eyes nutrition-rich chia seed for potential to improve human health

Chia seeds.
Photo Credit: Pankaj Jaiswal.

Oregon State University scientists have sequenced the chia genome and in doing so provided a blueprint for future research that capitalizes on the nutritional and human health benefits of the plant.

In the just-published paper, the researchers identified chia genes associated with improving nutrition and sought after properties for pharmaceuticals that could be used to treat everything from cancer to high blood pressure. The seeds of the chia plant have received widespread attention in recent years because of the nutritional punch they pack.

Others have sequenced the chia genome, but this paper provides a more detailed look at the molecular level and the potential of genetic data mining with a keen focus on human health applications.

“This research opens up possibilities for scientists to study chia seed through the lens of improving human health while at the same time continuing to further our knowledge of all the nutritional benefits of chia,” said Pankaj Jaiswal, a professor in the Department of Botany and Plant Pathology in the College or Agricultural Sciences at Oregon State.

Camera traps uncover mysterious lesula monkey’s ‘business’

Camera traps equipped with infrared sensors automatically and non-invasively captured videos of Africa’s lesula monkey in the central Congo Basin in the Democratic Republic of the Congo without any disturbance to their social groups.

Video Credit: Florida Atlantic University

Strategically placed camera traps have uncovered the mysterious behavior of an elusive species of African monkey – Cercopithecus lomamiensis, commonly known as the “lesula.”

In much the same way that Ring home security cameras capture both mundane and extraordinary events, strategically placed camera traps have uncovered the mysterious behavior of an elusive species of African monkey – Cercopithecus lomamiensis, commonly known as the “lesula.” With its large human-like eyes, golden mane and pink face, this cryptic species was discovered in 2012 in the central Congo Basin in the Democratic Republic of the Congo.

Because of the lesula’s mysterious behavior, traditional observational methods in the field are challenging. To date, no behavioral study has been done to evaluate this species’ degree of terrestriality.

To address a lack of comprehensive ecological knowledge on this lineage, Florida Atlantic University researchers were the first to design and employ an intensive camera trap study to document the lesula’s terrestrial movement, daytime activity pattern, birth seasonality, group size and social organization.

Camera traps, equipped with infrared sensors to automatically and non-invasively capture videos, provided the researchers with the best approach to estimate group counts from non-habituated lesula individuals without any disturbance to their social groups.

Tropical ice cores offer deeper insights into Earth’s temperature record

Ice cores recovered from tropical locations act as unique records of Earth's complex climate history.
Huascarán, Huaraz, Perú
Photo Credit: Jean Simón

A new study suggests ice recovered from high tropical mountains can reveal key insights about Earth’s past climate changes.  

Led by scientists at The Ohio State University, the study showed that oxygen-stable isotope records stored in tropical mountain glacier ice cores can be used to provide scientists with a distinct paleoclimate history of the planet’s middle and upper troposphere. By combining ice core proxy records, paleoclimate simulations and modern satellite measurements and comparing the results to those from previous climate models, they found that the temperature in this region of the atmosphere cooled by 7.35 degrees Celsius during the Earth’s glacial period, which for many researchers illuminates new theories about climate dynamics throughout the ages.  

“Typically, you need hundreds of pieces of data to construct a record of global mean temperature,” said Zhengyu Liu, lead author of the study and a professor of geography at The Ohio State University. “It turns out, in that region in the tropics and at that height, you can use just one, and it’s very consistent with many other independent constructions available, which rely primarily on sea surface temperature proxies.” 

Researchers Find Way to Weld Metal Foam Without Melting Its Bubbles

Composite metal foam (CMF) components
Image Credit: Courtesy of North Carolina State University

Researchers at North Carolina State University have now identified a welding technique that can be used to join composite metal foam (CMF) components together without impairing the properties that make CMF desirable. CMFs hold promise for a wide array of applications because the pockets of air they contain make them light, strong and effective at insulating against high temperatures.

CMFs are foams that consist of hollow, metallic spheres – made of materials such as stainless steel or titanium – embedded in a metallic matrix made of steel, titanium, aluminum or other metallic alloys. The resulting material is both lightweight and remarkably strong, with potential applications ranging from aircraft wings to vehicle armor and body armor.

In addition, CMF is better at insulating against high heat than conventional metals and alloys, such as steel. The combination of weight, strength and thermal insulation means that CMF also holds promise for use in storing and transporting nuclear material, hazardous materials, explosives and other heat-sensitive materials.

However, in order to realize many of these applications, manufacturers would need to weld multiple CMF components together. And that has posed a problem.

Quantum batteries break causality

Charging quantum batteries in indefinite causal order.
In the classical world, if you tried to charge a battery using two chargers, you would have to do so in sequence, limiting the available options to just two possible orders. However, leveraging the novel quantum effect called ICO opens the possibility to charge quantum batteries in a distinctively unconventional way. Here, multiple chargers arranged in different orders can exist simultaneously, forming a quantum superposition.
Illustration Credit: ©2023 Chen et al.
CC BY-ND 4.0 DEED

Batteries that exploit quantum phenomena to gain, distribute and store power promise to surpass the abilities and usefulness of conventional chemical batteries in certain low-power applications. For the first time, researchers including those from the University of Tokyo take advantage of an unintuitive quantum process that disregards the conventional notion of causality to improve the performance of so-called quantum batteries, bringing this future technology a little closer to reality.

When you hear the word “quantum,” the physics governing the subatomic world, developments in quantum computers tend to steal the headlines, but there are other upcoming quantum technologies worth paying attention to. One such item is the quantum battery which, though initially puzzling in name, holds unexplored potential for sustainable energy solutions and possible integration into future electric vehicles. Nevertheless, these new devices are poised to find use in various portable and low-power applications, especially when opportunities to recharge are scarce.

Bats declined as Britain felled trees for colonial shipbuilding

A western barbastelle.
Photo Credit: Antton Alberdi

Bat numbers declined as Britain’s trees were felled for shipbuilding in the early colonial period, new research shows.

The study, by the University of Exeter and the Bat Conservation Trust (BCT), found Britain’s Western barbastelle bat populations have dropped by 99% over several hundred years.

Animals’ DNA can be analyzed to discover a “signature” of the past, including periods when populations declined, leading to more inbreeding and less genetic diversity.

Scientists used this method to discover the historic decline of Western barbastelles in Britain – and also analyzed modern landscapes to see what helps and harms bats.

They found more genetic diversity among bats in areas rich in broadleaf woodland and diverse habitats.

Artificial light reduced connectivity between populations, probably because bats avoid areas with bright lighting, while rivers and woodlands increased connectivity.

“These bats usually roost in mature oak and beech trees, and move around every few nights – so they benefit from areas with substantial woodland cover,” said Dr Orly Razgour, from the University of Exeter.

Enabling early detection of cancer

With his group’s new method and the use of artificial intelligence, G.V. Shivashankar hopes to improve tumor diagnosis.
Photo Credit: Paul Scherrer Institute/Markus Fischer

Blood cells reveal tumors in the body. Researchers at the Paul Scherrer Institute achieve an advance with the development of a test for early diagnosis of cancer.

The ability to detect a developing tumor at a very early stage and to closely monitor the success or failure of cancer therapy is crucial for a patient’s survival. A breakthrough on both counts has now been achieved by researchers at the Paul Scherrer Institute PSI. Researchers led by G.V. Shivashankar, head of PSI‘s Laboratory for Nanoscale Biology and professor of Mechano-Genomics at ETH Zurich, were able to prove that changes in the organization of the cell nucleus of some blood cells can provide a reliable indication of a tumor in the body. With their technique – using artificial intelligence – the scientists were able to distinguish between healthy and sick people with an accuracy of around 85 percent. Besides that, they managed to correctly determine the type of tumor disease – melanoma, glioma, or head and neck tumor. “This is the first time anyone, worldwide, has achieved this,” Shivashankar says happily. The researchers have published their results in the journal npj Precision Oncology.