Thursday, January 13, 2022

Study Challenges Evolutionary Theory That DNA Mutations Are Random

Studying the genome of thale cress, a small flowering weed, led to a new understanding about DNA mutations.
Credit: Pádraic Flood

A simple roadside weed may hold the key to understanding and predicting DNA mutation, according to new research from University of California, Davis, and the Max Planck Institute for Developmental Biology in Germany.

The findings, published in the journal Nature, radically change our understanding of evolution and could one day help researchers breed better crops or even help humans fight cancer.

Mutations occur when DNA is damaged and left unrepaired, creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected.

“We always thought of mutation as basically random across the genome,” said Grey Monroe, an assistant professor in the UC Davis Department of Plant Sciences who is lead author on the paper. “It turns out that mutation is very non-random and it’s non-random in a way that benefits the plant. It’s a totally new way of thinking about mutation.”

Researchers spent three years sequencing the DNA of hundreds of Arabidopsis thaliana, or thale cress, a small, flowering weed considered the “lab rat among plants” because of its relatively small genome comprising around 120 million base pairs. Humans, by comparison, have roughly 3 billion base pairs.

“It’s a model organism for genetics,” Monroe said.

Researchers Discover Destructive Southern Pine Beetle in Northern Forests

Close up image of one of the southern pine beetles found in Maine and New Hampshire by researchers at the University of New Hampshire.
Photo Credit: Caroline Kanaskie / UNH Collections

Researchers at the University of New Hampshire have discovered the southern pine beetle, one of the most damaging tree-dwelling insects in the Southeast, in forests in Maine and New Hampshire. The southern pine beetle has never been seen this far north and has forestry experts concerned, specifically about the pitch pine barren trees found throughout New England.

“Warmer winter temperatures make it easier for beetles to survive further north,” said Jeff Garnas, associate professor of forest ecosystem health, whose research team made the discovery. “While not exactly surprising, this finding is a stark reminder of how species, including those of significant ecological and economic importance, are already responding to the changing climate.”

Microplastic pollution lingers in rivers for years before entering oceans

Study sampling site on the Severn River, downstream from Birmingham, England.

Microplastics can deposit and linger within riverbeds for as long as seven years before washing into the ocean, a new study has found.

Because rivers are in near-constant motion, researchers previously assumed lightweight microplastics quickly flowed through rivers, rarely interacting with riverbed sediments.

Now, researchers led by Northwestern University and the University of Birmingham in England, have found hyporheic exchange — a process in which surface water mixes with water in the riverbed — can trap lightweight microplastics that otherwise might be expected to float.

The study was published in the journal Science Advances. It marks the first assessment of microplastic accumulation and residence times within freshwater systems, from sources of plastic pollution throughout the entire water stream. The new model describes dynamical processes that influence particles, including hyporheic exchange, and focuses on hard-to-measure but abundant microplastics at 100 micrometers in size and smaller.

“Most of what we know about plastics pollution is from the oceans because it’s very visible there,” said Northwestern’s Aaron Packman, one of the study’s senior authors. “Now, we know that small plastic particles, fragments and fibers can be found nearly everywhere. However, we still don’t know what happens to the particles discharged from cities and wastewater. Most of the work thus far has been to document where plastic particles can be found and how much is reaching the ocean.

Study shows COVID-19 vaccines offer lasting protection

Photo by Brandon Bieltz/UNC-Chapel Hill
Vaccination offers long-lasting protection from the worst outcomes of COVID-19, according to a new study by the University of North Carolina at Chapel Hill.

The emergence of the delta and omicron variants has raised questions about whether breakthrough infections are caused by waning immunity or by the more transmissible variants.

Results of the study published in the New England Journal of Medicine suggest that declining immunity is responsible for breakthrough infections, but vaccines maintained protection from hospitalization and severe disease nine months after getting the first shot.

“The primary takeaway message from our study is that unvaccinated people should get vaccinated right away,” said lead study author Danyu Lin, Dennis Gillings Distinguished Professor of Biostatistics at the UNC Gillings School of Global Public Health. “The results of our study also underscore the importance of booster shots, especially for older adults.”

The study, which is a collaboration between the UNC-Chapel Hill and the North Carolina Department of Health and Human Services, examined data on COVID-19 vaccination history and health outcomes for 10.6 million North Carolina residents between December 2020 and September 2021.

The study results were used by the Centers for Disease Control and Prevention to support the use of booster shots.

‘Slushy’ magma ocean led to formation of the Moon’s crust

Magma ocean and first rocky crust on the Moon 
Credit: NASA/Goddard Space Flight Center
The scientists, from the University of Cambridge and the Ecole normale supérieure de Lyon, have proposed a new model of crystallization, where crystals remained suspended in liquid magma over hundreds of millions of years as the lunar ‘slush’ froze and solidified. The results are reported in the journal Geophysical Research Letters.

Over fifty years ago, Apollo 11 astronauts collected samples from the lunar Highlands. These large, pale regions of the Moon – visible to the naked eye – are made up of relatively light rocks called anorthosites. Anorthosites formed early in the history of the Moon, between 4.3 and 4.5 billion years ago.

Similar anorthosites, formed through the crystallization of magma, can be found in fossilized magma chambers on Earth. Producing the large volumes of anorthosite found on the Moon, however, would have required a huge global magma ocean.

"Cooling of the early magma ocean drove such vigorous convection that crystals remained suspended as a slurry, like the crystals in a slushy machine." 
Jerome Neufeld

Scientists believe that the Moon formed when two protoplanets, or embryonic worlds, collided. The larger of these two protoplanets became the Earth, and the smaller became the Moon. One of the outcomes of this collision was that the Moon was very hot – so hot that its entire mantle was molten magma, or a magma ocean.

Tuesday, January 11, 2022

Taking on decarbonization in the ag sector

Biofuels, such as those derived from the switchgrass being harvested in this field in Vonore, Tennessee, are just one of the technology-based solutions that ORNL summit participants identified recently as key to decarbonizing the agriculture sector.
Credit: Erin G. Webb, ORNL/U.S. Dept. of Energy.

Energy and sustainability experts from Oak Ridge National Laboratory, industry, universities and the federal government recently identified key focus areas to meet the challenge of successfully decarbonizing the agriculture sector, as well as scientific resources that the U.S. Department of Energy’s national laboratories can bring to the table.

The challenge is significant. Agriculture is responsible for emitting 10% of the nation’s greenhouse gases, some 629 million metric tons of carbon dioxide-equivalent emissions per year, according to the U.S. Environmental Protection Agency. Key sources for those emissions are agricultural soil and livestock waste management, crop cultivation and fuel combustion largely related to farm equipment.

The ORNL Virtual Summit on Decarbonizing the Agriculture Sector featured three topic areas in breakout sessions in which the challenges and potential technology- and practice-based solutions were discussed. These solutions included soil health, nitrogen production and fixation, and agricultural equipment and operations.

Sustainable Manufacturing

Illustration by Jeffrey C. Chase
Reducing the world’s reliance on petroleum and natural gas is a worthy goal, one that could help us achieve a smaller carbon footprint. It will, however, mean rethinking how we create many of the products in our everyday lives.

Chemical manufacturing, the practice of taking raw materials and turning them into products using chemical processes, is an $800 billion industry that supports over 6 million jobs in the United States each year. It contributes to the production of everything from food, buildings and clothing to items found in industries such as health care, electronics and transportation.

Traditional chemical manufacturing relies on non-renewable fossil energy sources for power and raw materials. A more sustainable option gaining steam is the use of electrolyzers, devices that instead use electricity to convert raw materials like carbon dioxide (CO2) into useful molecules for chemicals and products.

One hurdle that keeps promising CO2 electrolyzer technologies in academic laboratories rather than being scaled for industrial use — where they could make a dent in our carbon dioxide emission problem — is that the critical materials needed for the job, including membranes and catalysts, aren’t yet durable or efficient enough to operate over long periods of time.

University of Delaware engineers Feng Jiao, Yushan Yan and Koffi Pierre Yao and colleagues at Louisiana State University (LSU) are collaborating to overcome these challenges.

The work is funded through a $4 million grant from the National Science Foundation’s Established Program to Stimulate Competitive Research (NSF EPSCoR) program. A total $1.9 million of the funding was awarded directly to UD.

Common household cleaner can boost effort to harvest fusion energy on Earth

PPPL physicist Federico Nespoli at the Large Helical Device in Japan.
Photo courtesy of the Japanese National Institute of Fusion Science. Collage by Kiran Sudarsanan.

Scientists have found that adding a common household cleaning agent – the mineral boron contained in such cleaners as Borax – can vastly improve the ability of some fusion energy devices to contain the heat required to produce fusion reactions on Earth the way the sun and stars do.

Physicists at the U.S. Department of Energy’s (DOE) Princeton Plasma Physics Laboratory (PPPL) working with Japanese researchers, made the observation on the Large Helical Device (LHD) in Japan, a twisty magnetic facility that the Japanese call a “heliotron.” The results demonstrated for the first time a novel regime for confining heat in facilities known as stellarators, similar to the heliotron. The findings could advance the twisty design as a blueprint for future fusion power plants.

Higher confinement

Researchers produced the higher confinement regime by injecting tiny grains of boron powder into the LHD plasma that fuels fusion reactions. The injection through a PPPL-installed dropper sharply reduced turbulent swirls and eddies and raised the confined heat that produces the reactions.

“We could see this effect very clearly,” said PPPL physicist Federico Nespoli, lead author of a paper that detailed the process in the journal Nature Physics. “The more power we put into the plasma the bigger the increase in heat and confinement, which would be ideal in real reactor conditions.”

Researchers discover a new approach to breaking bacterial antibiotic resistance and rescue frontline drug treatments

Researchers may have uncovered a key to making existing frontline antibiotics work again, against the deadly bacteria that cause pneumonia.

The international team from the Peter Doherty Institute for Infection and Immunity (Doherty Institute – a joint venture between the University of Melbourne and the Royal Melbourne Hospital), the University of Queensland, Griffith University, the University of Adelaide, and St Jude Children’s Research Hospital (USA), found how to repurpose a molecule called PBT2 - originally developed as a potential treatment for disorders such as Alzheimer's, Parkinson’s and Huntington’s diseases – to break bacterial resistance to commonly used frontline antibiotics.

Led by University of Melbourne Professor Christopher McDevitt, a laboratory head at the Doherty Institute, this discovery may see the comeback of readily available and cheap antibiotics, such as penicillin and ampicillin, as effective weapons in the fight against the rapidly rising threat of antibiotic resistance.

In a paper published today in Cell Reports, Professor McDevitt and his collaborators described how they discovered a way to break bacterial drug resistance and then developed a therapeutic approach to rescue the use of the antibiotic ampicillin to treat drug-resistant bacterial pneumonia caused by Streptococcus pneumoniae in a mouse model of infection.

Last year the World Health Organization (WHO) described antibiotic resistance as one of the greatest threats to global health, food security, and development. Rising numbers of bacterial infections – such as pneumonia, tuberculosis, gonorrhoea, and salmonellosis – are becoming harder to treat as the antibiotics used against them are becoming less effective.

Researchers Find Concerns for Animals Tied to Same Habitats

Many animals display strong site fidelity, including these
(clockwise from top left): Adélie penguins, mule deer, great gray owls,
sockeye salmon and northern elephant seals.
Credits: Daniel Costa, Jonathan Armstrong and Amanda Hancock 
Some wildlife are stuck in their ways. Like humans, wild animals often return to the same places to eat, walk on the same paths to travel and use the same places to raise their young.

A team of researchers led by scientists from the University of Wyoming and the University of Washington has reviewed the scientific literature and found that, while this “consistent” behavior may be beneficial when environmental conditions don’t change very fast, those benefits may not be realized in the ever-changing world dominated by humans. The research was published today (Tuesday) in the scientific journal Frontiers in Ecology and the Environment.

Ecologists use the term “site fidelity” to describe the behavior of animals that are stuck in their ways. Site fidelity is the tendency to return to previously visited locations and is common across many species, from fish to birds to mammals and insects. Think salmon returning to their natal streams to spawn, or birds returning year after year to the same nest site -- site fidelity is all around us in nature.

As animals become familiar with a place, site fidelity can help them know where to find good food or hiding spots from predators, and can help them move efficiently to and from these resources. However, the authors uncovered an emerging theme in the scientific literature.

“Animals that have strong site fidelity are having a tough time adjusting to the novel landscapes that are showing up around them as a result of humans,” says Jerod Merkle, an assistant professor at the University of Wyoming and the co-lead author of the paper.

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