Neutrons take a deep dive into water networks surrounding DNA

Vanderbilt University researchers used neutrons at ORNL to reveal the hydrogen bonding patterns between water molecules (shown in blue) and DNA. The findings could help provide insights into how water influences DNA function.

Credit: ORNL/Jill Hemman

Water plays several important roles within the human body, even affecting the DNA in our cells. The entire surface of a DNA double helix is coated in layers of water molecules. This sheath of water attaches to the genetic material through hydrogen bonds, made by sharing hydrogen atoms between molecules. Through hydrogen bonds, water can influence how DNA takes shape and interacts with other molecules. In some cases, water can help proteins recognize DNA sequences.

Scientists can estimate where hydrogen bonds occur and how hydrogen atoms are shared, but it is difficult to gather experimental evidence. A research team led by Vanderbilt University has used a method that successfully captured the most detailed view to date of water’s hydrogen bonding patterns around DNA, opening new possibilities for studying how water impacts DNA function. Details on the methodology and the results, produced in part through neutron scattering at the Department of Energy’s (DOE’s) Oak Ridge National Laboratory (ORNL), are published in the journal Nucleic Acids Research.

“Water serves as a mediator between DNA and other molecules, even for very specific interactions. Before any molecule can bind to a segment of DNA, it must first go through this water shell,” said Martin Egli, a biochemistry professor at Vanderbilt University and corresponding author of the study. “To advance our understanding of DNA processes, it’s important to know exactly what the surrounding water does and how it arranges itself around molecules.”

Converting Methane to Methanol -- With and Without Water

This scanning tunneling electron microscope image shows the structure of a copper-zinc oxide catalyst that converts methane to methanol with and without water. Triangular zinc-oxide "islands" rest on a copper-oxide thin film (flat background) over a copper substrate (not seen). The "step" edges between copper-oxide and zinc-oxide (A, where blue is zinc, red is oxygen) are the main active sites for producing methanol when no water is present. The semi-flat areas have a relatively perfect crystal structure (B) and are inert during the reaction. The very rough areas are likely associated with defects—in this case with fewer zinc atoms and an oxygen-rich crystal structure (C)—and are the most active sites for methanol production when water is present.
Credit: Brookhaven National Laboratory

Chemists have been searching for efficient catalysts to convert methane—a major component of abundant natural gas—into methanol, an easily transported liquid fuel and building block for making other valuable chemicals. Adding water to the reaction can address certain challenges, but it also complicates the process. Now a team at the U.S. Department of Energy’s Brookhaven National Laboratory has identified a new approach using a common industrial catalyst that can complete the conversion effectively both with and without water. The findings, published in the Journal of the American Chemical Society, suggest strategies for improving catalysts for the water-free conversion.

“Water is like a trick that people have been using for a long time to get this reaction going—and it definitely helps. It improves the selectivity and it aids the ability to extract the methanol,” said José Rodriguez, a leader of Brookhaven Lab’s Catalysis Group, who has an adjunct appointment at Stony Brook University (SBU) in the departments of Chemistry and Materials Science and Chemical Engineering.

As shown in a recent related study by this group, adding water keeps the reaction from running away to transform the desired product, methanol, into carbon monoxide (CO) and carbon dioxide (CO2). But adding water also adds complexity and cost. Plus, at the temperatures and in the amounts required for this reaction, the water exists as large quantities of steam, which would have to be controlled in an industrial setting.

So, the Brookhaven team set out to explore if they could run the reaction without water by changing the catalyst—the substance that brings the reactants together and helps guide them along a particular reaction pathway.

Time crystals in the limelight

An artist’s impression of a discrete time crystal composed of nine qubits represented by the nuclear spins of nine carbon-13 atoms in diamond. The chain of connected spins is locked in a phase where they periodically invert their states.
(Image by Joe Randall and Tim Taminiau, courtesy of QuTech)

UC Berkeley physicist Norman Yao first described five years ago how to make a time crystal — a new form of matter whose patterns repeat in time instead of space. Unlike crystals of emerald or ruby, however, those time crystals existed for only a fraction of a second.

But the time has arrived for time crystals. Since Yao’s original proposal, new insights have led to the discovery that time crystals come in many different forms, each stabilized by its own distinct mechanism.

Using new quantum computing architectures, several labs have come close to creating a many-body localized version of a time crystal, which uses disorder to keep periodically-driven quantum qubits in a continual state of subharmonic jiggling — the qubits oscillate, but only every other period of the drive.

In a paper published in the journal Science, Yao and colleagues at QuTech — a collaboration between Delft University of Technology and TNO, an independent research group in the Netherlands — reported the creation of a many-body localized discrete time crystal that lasted for about eight seconds, corresponding to 800 oscillation periods. They used a quantum computer based upon a diamond, where the qubits — quantum bits, the analog of binary bits in digital computers — are the nuclear spins of carbon-13 atoms embedded inside the diamond.

Healable carbon fiber composite offers path to long-lasting, sustainable materials

Because of their high strength and light weight, carbon-fiber-based composite materials are gradually replacing metals for advancing all kinds of products and applications, from airplanes to wind turbines to golf clubs. But there’s a trade-off. Once damaged or compromised, the most commonly-used carbon fiber materials are nearly impossible to repair or recycle.

In a paper published Nov. 2 in the journal Carbon, a team of researchers describes a new type of carbon fiber reinforced material that is as strong and light as traditionally used materials but can be repeatedly healed with heat, reversing any fatigue damage. This also provides a way to break it down and recycle it when it reaches the end of its life.

"Developing fatigue-resistant composites is a major need in the manufacturing community," said co-lead author Aniruddh Vashisth, University of Washington assistant professor of mechanical engineering. "In this paper, we demonstrate a material where either traditional heat sources or radio frequency heating can be used to reverse and postpone its aging process indefinitely."

The material is part of a recently developed group known as carbon fiber reinforced vitrimers, named after the Latin word for glass, that show a mix of solid and fluid properties. The materials typically used today, whether in sporting goods or aerospace, are carbon fiber reinforced polymers.

Black holes of ‘all shapes and sizes’ in new gravitational-wave catalog

An international team of researchers, including Northwestern University astrophysicists, has released the largest-ever catalog of gravitational-wave events.

Of the 35 new events observed between November 2019 and March 2020, 33 were likely mergers between black holes of various shapes and sizes. The other two events were likely black holes merging with neutron stars — a much rarer event. Of these rare black hole and neutron star mergers, one event appears to show a massive black hole (about 33 times the mass of our sun) merging with a very low-mass neutron star (about 1.17 times the mass of our sun). This is one of the lowest-mass neutron stars ever detected.

Since the first gravitational-wave detection in 2015, astrophysicists have detected a total of 90 events. By calculating the masses of the merging objects, astrophysicists can better understand how stars live and die and what makes them collapse into black holes versus neutron stars upon death.

Christopher Berry

“Only now are we starting to appreciate the wonderful diversity of black holes and neutron stars,” said Christopher Berry, a key member of the Laser Interferometer Gravitational-Wave Observatory (LIGO) Scientific Collaboration (LSC). “Our latest results prove that they come in many sizes and combinations. We have solved some long-standing mysteries but uncovered some new puzzles too. Using these observations, we are closer to unlocking the mysteries of how stars — the building blocks of our universe — evolve.”

The research is now available online, with two accompanying papers forthcoming. The team includes researchers from the LSC, the Virgo Collaboration and the Kamioka Gravitational Wave Detector (KAGRA) project.

An expert in gravitational-wave parameter estimation, Berry is a lecturer at the University of Glasgow

Shared origins of irritable bowel syndrome and mental health disorders

3D still showing Irritable bowel syndrome 
Credit: Scientific Animations

IBS is a common condition world-wide, affecting around 1 in 10 people and causing a wide range of symptoms including abdominal pain, bloating and bowel dysfunction that can significantly affect people’s lives. Diagnosis is usually made after considering other possible conditions (such as Crohn’s disease or bowel cancer), with clinical tests coming back ‘normal’. The condition often runs in families and is also more common among people who are prone to anxiety. The causes of IBS are not well understood, but an international team of researchers has now identified several genes that provide clues into the origins of IBS.

The research team, including more than 40 institutions and coordinated by scientists in UK and Spain, looked at genetic data from 40,548 people who suffer with IBS from the UK Biobank and 12,852 from the Bellygenes initiative (a world-wide study aiming to identify genes linked to IBS) and compared them to 433,201 people without IBS (controls), focusing on individuals of European ancestry. The findings were repeated with de-identified data from the genomics company 23andMe Inc., provided by customers who have consented to research, by comparing 205,252 people with IBS to 1,384,055 controls.

The results showed that overall, heritability of IBS (how much your genes influence the likelihood of developing a particular condition) is quite low, indicating the importance of environmental factors such as diet, stress and patterns of behavior that may also be shared in the family environment.

Researchers uncover gene that doubles risk of death from COVID-19

Scientists at Oxford University have identified the gene responsible for doubling the risk of respiratory failure from COVID-19. Sixty percent of people with South Asian ancestry carry the high-risk genetic signal, partly explaining the excess deaths seen in some UK communities, and the impact of COVID-19 in the Indian subcontinent.

Previous work has already identified a stretch of DNA on chromosome 3 which doubled the risk of adults under 65 of dying from COVID. However, scientists did not know how this genetic signal worked to increase the risk, nor the exact genetic change that was responsible.

In a study published in Nature Genetics, a team lead by Professors James Davies and Jim Hughes at the University of Oxford’s MRC Weatherall Institute of Molecular Medicine used cutting edge technology to work out which gene was causing the effect, and how it was doing so.

Study co-lead Jim Hughes, Professor of Gene Regulation, said: ‘The reason this has proved so difficult to work out, is that the previously identified genetic signal affects the “dark matter” of the genome. We found that the increased risk is not because of a difference in gene coding for a protein, but because of a difference in the DNA that makes a switch to turn a gene on. It’s much harder to detect the gene which is affected by this kind of indirect switch effect.’

A child of darkness

The skull of the child presented in the current study was recovered during further work in the cramped spaces of the cave in 2017. The child’s skull was found alone, and no remains of its body have been recovered.

Meet Leti, a Homo naledi child discovered in the Rising Star Cave System that yielded Africa’s richest site for fossil hominins.

An international team of researchers, led by Professor Lee Berger from Wits University, has revealed the first partial skull of a Homo naledi child that was found in the remote depths of the Rising Star Cave in the Cradle of Humankind World Heritage Site near Johannesburg, South Africa.

Describing the skull and its context in two separate papers in the Open Access journal, PaleoAnthropology, the team of 21 researchers from Wits University and thirteen other universities announced the discovery of parts of the skull and teeth of the child that died almost 250,000 years ago when it was approximately four to six years old.

The first paper, of which Professor Juliet Brophy of Wits and Louisiana State Universities is lead author, describes the skull, while the second paper, of which Dr Marina Elliott, a National Geographic Explorer, is lead author, describe the context of the area and circumstances in which the skull was discovered.

Non-invasive breathing support for COVID-19 patients isn’t linked to heightened infection risk

The use of non-invasive breathing support, commonly known as CPAP or HFNO, to treat moderate to severe COVID-19 infection, isn’t linked to a heightened infection risk, as currently thought, suggest two new studies which included work led by University of Bristol researchers. The findings and a linked editorial are published today in Thorax.

Both assisted breathing methods produced little measurable air or surface viral contamination, and not more than simple oxygen therapy, while coughing produced far more aerosol than either method, the studies show.

The findings prompt the researchers to call for a thorough reassessment of the infection control measures deployed for these respiratory support methods, both of which have been categorized as ‘aerosol generating procedures’ that expose healthcare staff and other patients to a heightened infection risk.

Continuous positive airways pressure or CPAP for short, delivers a steady level of pressurized air and oxygen through a hose and mask to assist breathing; high-flow nasal oxygen or HFNO for short, pumps oxygen at a high flow rate through two small tubes in the nose.

Unlike mechanical ventilation, which requires intubation and sedation, CPAP and HFNO aren’t invasive. But they are thought to generate viral particles capable of contaminating the air and surfaces nearby, necessitating additional infection control precautions.

New research highlights the economic cost of climate change inaction

Different countries face different risks and opportunities as the world switches from fossil fuels to renewable energy, researchers say.

Green policies have traditionally been seen as costly to countries who implement them, while other nations can do nothing and “free-ride” – leading to global inaction on the climate crisis.

However, the research team – led by The Open University and the universities of Exeter, Cambridge, and Cambridge Econometrics – say this is a “poor description” of today’s reality. Instead, they say the transition is already happening and, for many countries, embracing it is the best strategy to reduce costs.

As the world economy transforms, free-riding may now be the risky approach – not only environmentally but also economically.

According to the new study, the risks and opportunities vary dramatically between countries, depending on their degree of competitiveness in fossil fuel markets. Countries fall into one of three categories – each with different incentives driven by the green transition.

Large fossil fuel importers like the EU and China will gain multiple benefits from decarbonizing.

Meanwhile, “large competitive fossil fuel exporters” like Saudi Arabia may avoid economic decline by flooding global markets with cut-price fossil fuels.