Genetic Diversity of Wild North American Grapes Mapped

Dario Cantù, a professor in the Department of Viticulture and Enology, in the grape orchard outside the Robert Mondavi Institute for Wine and Food Science.
Photo Credit: Jael Mackendorf/UC Davis

Wild North American grapes are now less of a mystery after an international team of researchers led by the University of California, Davis, decoded and catalogued the genetic diversity of nine species of this valuable wine crop.

The research, published in the journal Genome Biology, uncovers critical traits that could accelerate grape breeding efforts, particularly in tackling challenges like climate change, saline environments and drought.

“This research marks a significant step in understanding the genetics of grapevines,” said Dario Cantù, the senior author on the journal article and a professor in the Department of Viticulture and Enology. “It lays the groundwork for future advancements in grape breeding by identifying key genes responsible for important traits.”

The research team developed and used state-of-the-art technology to construct a comprehensive pangenome, which is a complete genetic blueprint, of wild grape species.

This so-called super-pangenome of nine species allowed the team to map genetic diversity, identify similarities or differences among them, and pinpoint specific traits that breeders may want to incorporate. First author Noé Cochetel, a postdoctoral researcher in Cantù’s lab, did the analyses and played a pivotal role in the project.

Scientists reveal superconductor with on-off switches

(A) The material used in this study consists of stacked layers of ferromagnetic atoms and superconducting atoms. (B) Applying a small magnetic field induces superconductivity, while (C) low temperatures boost that superconductivity.
Illustration Credit: Courtesy Shua Sanchez, University of Washington

As industrial computing needs grow, the size and energy consumption of the hardware needed to keep up with those needs grows as well. A possible solution to this dilemma could be found in superconducting materials, which can reduce that energy consumption exponentially. Imagine cooling a giant data center full of constantly running servers down to nearly absolute zero, enabling large-scale computation with incredible energy efficiency.

Physicists at the University of Washington and the U.S. Department of Energy’s (DOE) Argonne National Laboratory have made a discovery that could help enable this more efficient future. Researchers have found a superconducting material that is uniquely sensitive to outside stimuli, enabling the superconducting properties to be enhanced or suppressed at will. This enables new opportunities for energy-efficient switchable superconducting circuits. The paper was published in Science Advances.

Superconductivity is a quantum mechanical phase of matter in which an electrical current can flow through a material with zero resistance. This leads to perfect electronic transport efficiency. Superconductors are used in the most powerful electromagnets for advanced technologies such as magnetic resonance imaging, particle accelerators, fusion reactors and even levitating trains. Superconductors have also found uses in quantum computing.

A temporary tug-of-war: a minimal system unlocks cellular transport secrets

A visual representation of the findings. The net number of cargo-bound kinesin or dynein motor proteins engaging with the microtubule track decides whether it is moved in positive or negative direction. When both, kinesins and dyneins engage with the microtubule, the transport is often interrupted. Occasionally, the cargo is being pulled by motor proteins in opposite directions before one finally wins.
Illustration Credit: Diez Lab

Cells are busy conglomerates. Different molecules and organelles have to be delivered to different locations at a specific time.  How exactly they are reaching their destinations is a long-standing question in biology. Researchers from the Diez group at the B CUBE – Center for Molecular Bioengineering of TUD Dresden University of Technology and the Santen group at the Center for Biophysics at the Saarland University have now built a minimal version of a cell transport system outside a cell. Using the minimal system, the team discovered the principles of how cells control the direction of transport. The new study was published in the journal Nature Communications.

Cells are like busy factories. They need to transport molecules and organelles (cargo) reliably to different destinations within the cell. Defects in cellular transport have been associated with many diseases including Alzheimer’s, Parkinson’s, and Huntington’s. The transport relies on a system of cellular train tracks known as microtubules. Two types of motor proteins, kinesin and dynein, can move in opposite directions along the microtubules to carry the cargo to its destination. At any given time, the cargo is attached to multiple copies of kinesin and dynein. Yet, it moves in only one direction. It is unclear what determines the moving direction.

When the Cellular Waste Collector Doesn’t Show Up

Verian Bader and Konstanze Winklhofer (right) are on the trail of the development of neurodegenerative diseases.
Photo Credit: © RUB, Marquard

Researchers have identified a mechanism that promotes the breakdown of harmful protein deposits. If it malfunctions, it can lead to Parkinson’s disease.

NEMO, a protein that is primarily associated with signaling processes in the immune system, prevents the deposition of protein aggregates that occur in Parkinson’s disease. For this purpose, it binds to certain protein chains that serve as markers for cellular waste removal, thus promoting the degradation of the harmful aggregates. A research team headed by Professor Konstanze Winklhofer from Ruhr University Bochum, Germany, has shed light on how this mechanism works. The team published their findings in the journal Nature Communications on December 19, 2023. In follow-up studies, the team is investigating ways to harness the findings for therapeutic strategies.

Looking for targeted therapeutic approaches

Neurodegenerative diseases, such as Parkinson’s or Alzheimer’s disease, are associated with the deposition of protein aggregates in the brain. These aggregates accumulate when the cellular waste removal system is defective or overloaded. In Parkinson’s disease, aggregates consisting primarily of the protein ⍺-synuclein are found in certain regions of the brain. “The fact that such aggregates occur, which are referred to as Lewy bodies, is a key feature of Parkinson’s disease,” explains Konstanze Winklhofer.

The misfolding and aggregation of ⍺-synuclein is of crucial importance for processes that lead to the loss of function and death of neuronal cells and contribute to the progression of the disease. Researchers from various disciplines around the world are therefore aiming to decipher these processes at a cellular and molecular level, in order to develop targeted therapeutic approaches.

Coral atoll islands may outpace sea-level rise

Atoll Coastline
Photo Credit: xiSerge

Ecological restoration may save coral atoll islands from the rising seas of climate change, according to an international team of scientists, conservationists, and an indigenous leader.

While global carbon emission reduction is imperative, local measures could be the key to the islands outpacing sea levels, they argue in the journal Trends in Ecology & Evolution.

“Far from being doomed, in their natural state most coral atoll islands could adapt to sea level rise,” says Dr Sebastian Steibl from Waipapa Taumata Rau, University of Auckland, lead author of the study. “This paper is a global call to identify and quantify the best measures for restoring atoll island growth.”

The world’s 320 tropical coral atolls are made up of thousands of islands and are a treasure trove of biodiversity, homes to millions of turtles and seabirds. These islands are naturally growing up to 1 cm a year by accreting sediment – enough to outpace most predictions of sea level rise.

Ecologically restoring this natural process holds the key to climate change resilience for the islands, says the team of scientists, who are already trialing restoration methods on atolls such as Tetiaroa and Palmyra in the eastern Pacific Ocean and Aldabra in the western Indian Ocean.

Can we decode the language of our primate cousins?

The UNIGE team wanted to find out whether the frontal and orbitofrontal regions of our brain activate in the same way when faced with human and simian vocalizations.
Image Credit: © Leonardo Ceravolo

Are we able to differentiate between the vocal emissions of certain primates? A team from the University of Geneva (UNIGE) asked volunteers to categorize the vocalizations of three species of great apes (Hominidae) and humans. During each exposure to these "onomatopoeia", brain activity was measured. Unlike previous studies, the scientists reveal that phylogenetic proximity - or kinship - is not the only factor influencing our ability to identify these sounds. Acoustic proximity - the type of frequencies emitted - is also a determining factor. These results show how the human brain has evolved to process the vocal emissions of some of our closest cousins more efficiently. Find out more in the journal Cerebral Cortex Communications.

Our ability to process verbal language is not based solely on semantics, i.e. the meaning and combination of linguistic units. Other parameters come into play, such as prosody, which includes pauses, accentuation and intonation. Affective bursts - "Aaaah!" or ‘‘Oh!’’ for example - are also part of this, and we share these with our primate cousins. They contribute to the meaning and understanding of our vocal communications.

When such a vocal message is emitted, these sounds are processed by the frontal and orbitofrontal regions of our brain. The function of these two areas is, among other things, to integrate sensory and contextual information leading to a decision. Are they activated in the same way when we are exposed to the emotional vocalizations of our close cousins, the chimpanzees, macaques and bonobos? Are we able to differentiate between them?

Researchers invent "Methane Cleaner": could become a permanent fixture in cattle and pig barns

A look inside the MEPS reactor (Methane Eradication Photochemical System), where chlorine atoms are formed by UV light and react with methane gas.
Photo Credit: Morten Krogsbøll.

In a spectacular new study, researchers from the University of Copenhagen have used light and chlorine to eradicate low-concentration methane from air. The result gets us closer to being able to remove greenhouse gases from livestock housing, biogas production plants and wastewater treatment plants to benefit the climate. The research has just been published in the journal Environmental Research Letters. 

The Intergovernmental Panel on Climate Change (IPCC) has determined that reducing methane gas emissions will immediately reduce the rise in global temperatures. The gas is up to 85 times more potent of a greenhouse gas than CO2, and more than half of it is emitted by human sources, with cattle and fossil fuel production accounting for the largest share.

A unique new method developed by a research team at the University of Copenhagen’s Department of Chemistry and spin-out company Ambient Carbon has succeeded in removing methane from the air.

"A large part of our methane emissions comes from millions of low-concentration point sources like cattle and pig barns. In practice, methane from these sources has been impossible to concentrate into higher levels or remove. But our new result proves that it is possible using the reaction chamber that we’ve have built," says Matthew Stanley Johnson, the UCPH atmospheric chemistry professor who led the study.

Earlier, Johnson presented the research results at COP 28 in Dubai via an online connection and in Washington D.C. at the National Academy of Sciences, which advises the US government on science and technology.

Some coral species might be more resilient to climate change than previously thought

OSU coral researcher Alex Vompe off the north shore of Mo'orea
Photo Credit: Mackenzie Kawahara

Some coral species can be resilient to marine heat waves by “remembering” how they lived through previous ones, research by Oregon State University scientists suggests.

The study also contains evidence that the ecological memory response is likely linked to the microbial communities that dwell among the corals.

The findings, published today in Global Change Biology, are important because coral reefs, crucial to the functioning of planet Earth, are in decline from a range of human pressures including climate change, said the study’s lead author, Alex Vompe.

“It is vital to understand how quickly reefs can adapt to ever more frequent, repeated disturbances such as marine heat waves,” said Vompe, a doctoral student who works in the lab of microbiology professor Rebecca Vega Thurber. “The microbiomes living within their coral hosts might be a key component of rapid adaptation.”

Heat waves are likely to increase in frequency and severity because of climate change, he added. Slowing down the rate of coral cover and species loss is a major conservation goal, and predicting and engineering heat tolerance are two important tools.

Giant bacterium powers itself with unique processes

Micrograph of a group of Epulopiscium viviparus bacteria.
Image Credit: Esther Angert

Not all bacteria are created equal.

Most are single-celled and tiny, a few ten-thousandths of a centimeter long. But bacteria of the Epulopiscium family are large enough to be seen with the naked eye and 1 million times the volume of their better-known cousins, E. coli.

In a study published Dec. 18 in Proceedings of the National Academy of Sciences, researchers from Cornell and Lawrence Berkeley National Laboratory have for the first time described the full genome of one species of the family of giants, which they’ve named Epulopiscium viviparus.

“This incredible giant bacterium is unique and interesting in so many ways: its enormous size, its mode of reproduction, the methods by which it meets its metabolic needs and more,” said Esther Angert, professor of microbiology in the College of Agriculture and Life Sciences, and corresponding author of the study. “Revealing the genomic potential of this organism just kind of blew our minds.”

The first member of the Epulopiscium family was discovered in 1985. All members of the species live symbiotically within the intestinal tracts of certain surgeonfish in tropical marine coral reef environments, such as the Great Barrier Reef and in the Red Sea.

Recent volcanism on Mars reveals a planet more active than previously thought

This image taken by the European Space Agency's Mars Express orbiter shows an oblique view focusing on one of the vast lava flows in Elysium Planitia.
Image Credit: ESA/DLR/FU Berlin

A vast, flat, "featureless" plain on Mars surprised researchers by revealing a much more tumultuous geologic past than expected, according to a study led by researchers at the University of Arizona. Enormous amounts of lava have erupted from numerous fissures as recently as one million years ago, blanketing an area almost as large as Alaska and interacting with water in and under the surface, resulting in large flood events that carved out deep channels.

Lacking plate tectonics – shifting chunks of crust that constantly reshape Earth's surface – Mars has long been thought to be a geologically "dead" planet where not much is happening. Recent discoveries have researchers questioning this notion, however. Just last year, a team of planetary scientists, also at UArizona, presented evidence for a giant mantle plume underneath the region Elysium Planitia, driving intense volcanic and seismic activity in a relatively recent past.

In the most recent study, a team led by Joana Voigt and Christopher Hamilton at UArizona's Lunar and Planetary Laboratory combined spacecraft images and measurements from ground-penetrating radar to reconstruct in three-dimensional detail every individual lava flow in Elysium Planitia. The extensive survey revealed and documented more than 40 volcanic events, with one of the largest flows infilling a valley named Athabasca Valles with almost 1,000 cubic miles of basalt.

Plant metabolism proves more complicated than previously understood

Ying Li, associate professor of horticulture and landscape architecture at Purdue University.
Photo Credit: Purdue Agricultural Communications /Tom Campbell

Plants have evolved fiendishly complicated metabolic networks. For years, scientists focused on how plants make secondary metabolites, the compounds that plants produce to enhance their defense and survival mechanisms.

“Only recently we started appreciating that the genes involved in making those specialized, secondary metabolites are being regulated,” said Ying Li, associate professor of horticulture and landscape architecture at Purdue University. “They are turned on when plants need to make secondary metabolites. And they are turned off when plants will no longer need to make them.”

Purdue’s Natalia Dudareva, Distinguished Professor of Biochemistry and Horticulture and Landscape Architecture, said, “Also, secondary metabolites are often toxic to cells when they accumulate to high levels, as we saw when we manipulated the resistance of the barriers that volatile secondary metabolites have to pass through to be released into the atmosphere. However, cells sense the accumulation of these toxic compounds and downregulate genes responsible for the formation of precursors for these volatiles.”

Genetic sequencing uncovers unexpected source of pathogens in floodwaters

A NASA image containing visible and infrared data revealing the presence of dissolved organic matter – including potential antibiotic-resistant pathogens – in the waterways along coastal North Carolina after Hurricane Florence.
Image Credit: Courtesy NASA

Researchers report in the journal Geohealth that local rivers and streams were the source of the Salmonella enterica contamination along coastal North Carolina after Hurricane Florence in 2018 – not the previously suspected high number of pig farms in the region. 

These findings have critical implications for controlling the spread of disease caused by antibiotic-resistant pathogens after flooding events, particularly in the coastal regions of developing countries that are being highly impacted by the increase in tropical storms. 

The study, led by civil and environmental engineering professor Helen Nguyen and graduate student Yuqing Mao, tracks the presence and origin of S. enterica from environmental samples from coastal North Carolina using genetic tracing. 

“Infections caused by antibiotic-resistant pathogens are responsible for approximately 2.8 million human illnesses and 36,000 deaths per year in the U.S. alone,” Nguyen said. “These infections spread easily across the globe and are a major burden on burgeoning health care systems, but they are preventable through mitigation.”

Study underlines impact of air pollution on people with asthma

PhD researcher Amy McCarron
Faculty of Natural Sciences
"By better understanding how air pollution impacts those most vulnerable in their day to day lives and how they practically manage this, we can work towards creating more effective communications and advice aimed at encouraging behavior change."
Photo Credit: Courtesy of University of Stirling

The study could offer an opportunity to improve the effectiveness of advice.

New research by the University of Stirling has offered a greater understanding of how people with asthma in Scotland are affected by air pollution.

The study could offer an opportunity to improve the effectiveness of advice aimed at helping individuals to reduce their personal exposure to air pollution.

Asthma is the world’s most widespread chronic respiratory condition and more than 368,000 people receive treatment for asthma in Scotland, 7% of the population.

Meanwhile, air pollution causes seven million premature deaths every year, with an estimated 2500–3500 of those in Scotland.

Exposure to air pollution is a known asthma trigger and University of Stirling researchers interviewed 36 people in Scotland who spoke in detail about the impact on their lives.

Dramatic rise in antibiotic use in first year of pandemic in primary care

Excessive use of antibiotics can give rise to bacterial resistance to these drugs, making bacterial infections increasingly hard to treat
Image Credit: Arek Socha

Antibiotics have no effect on viruses, and that includes the coronavirus. Yet in the first year of the pandemic, primary care physicians in Switzerland prescribed antibacterial medications twice as frequently as before, report researchers at the University of Basel. A risky practice, warns the research team.

It was a time of great uncertainty. When the first wave of the new coronavirus swept across Switzerland in winter and spring 2020, there were no diagnostic tests, no vaccines, and no effective medications. During this precarious phase, primary care physicians based in Switzerland seem to have increasingly resorted to treating patients with antibiotics, even though these medications have no effect on viruses. This was the conclusion reached by a research team led by Professor Heiner C. Bucher from the Department of Clinical Research at the University of Basel and University Hospital Basel.

As the team reports in the journal Clinical Microbiology and Infection, the use of antibiotics doubled from around eight to 16 prescriptions per 100 consultations. During the first wave of SARS-CoV-2 at the beginning of 2020, a massive rise in prescriptions of antibiotics became apparent. Prescriptions then remained at an above-average level throughout the year compared with previous years (2017-2019).

For this emergent class of materials, ‘solutions are the problem’

Alec Ajnsztajn (left) and Jeremy Daum
Photo Credit: Gustavo Raskosky/Rice University

Rice University materials scientists developed a fast, low-cost, scalable method to make covalent organic frameworks (COFs), a class of crystalline polymers whose tunable molecular structure, large surface area and porosity could be useful in energy applications, semiconductor devices, sensors, filtration systems and drug delivery.

“What makes these structures so special is that they are polymers but they arrange themselves in an ordered, repeating structure that makes it a crystal,” said Jeremy Daum, a Rice doctoral student and lead author of a study published in ACS Nano. “These structures look a bit like chicken wire ⎯ they’re hexagonal lattices that repeat themselves on a two-dimensional plane, and then they stack on top of themselves, and that’s how you get a layered 2D material.”

Alec Ajnsztajn, a Rice doctoral alumnus and the study’s other lead author, said the synthesis technique makes it possible to produce ordered 2D crystalline COFs in record time using vapor deposition.

“A lot of times when you make COFs through solution processing, there’s no alignment on the film,” Ajnsztajn said. “This synthesis technique allows us to control the sheet orientation, ensuring that pores are aligned, which is what you want if you’re creating a membrane.”