How Does a River Breathe?

Scientists at Pacific Northwest National Laboratory have been studying processes that affect how rivers and streams breathe, particularly in the Columbia River Basin, to help prepare for future changes related to water quality and climate change. 
Photo Credit: Andrea Starr | Pacific Northwest National Laboratory

Take a deep breath.

Pay attention to how air moves from your nose to your throat before filling your lungs with oxygen.

As you exhale your breath, a mix of oxygen and carbon dioxide leaves your nose and mouth.

Did you know that streams and rivers “breathe” in a similar way?

The United States is home to more than 250,000 of these flowing bodies of water that connect to coastal zones and oceans. They vary in size, from small streams to large rivers, but all take in oxygen and give off carbon dioxide and other greenhouse gases like methane. 

Over recent years, a team of scientists led by Pacific Northwest National Laboratory (PNNL) has been immersed in crucial research around the processes and interactions that contribute to greenhouse gas dynamics. Their work focuses on whole networks of streams and rivers, as well as the land surrounding these systems.       

Their work also includes factors that can disturb how streams and rivers breathe. Some of these disturbances happen beyond streams, like wildfires, but still impact how streams breathe by changing how material enters streams. Understanding these impacts is key to addressing challenges related to water quality, global carbon cycling, and climate change.

Possible ‘Trojan Horse’ found for treating stubborn bacterial infections

Transmission electron microscope (TEM) image of the bacterial cell with an extracellular vesicle attached.
Image Credit: Courtesy of Washington State University

Bacteria can be tricked into sending death signals to stop the growth of their slimy, protective homes that lead to deadly infections, a new study demonstrates.

The discovery by Washington State University researchers could someday be harnessed as an alternative to antibiotics for treating difficult infections. Reporting in the journal Biofilm, the researchers used the messengers, which they named death extracellular vesicles (D-EVs), to reduce growth of the bacterial communities by up to 99.99% in laboratory experiments.

“Adding the death extracellular vesicles to the bacterial environment, we are kind of cheating the bacteria cells,” said Mawra Gamal Saad, first author on the paper and a graduate student in WSU’s Gene and Linda Voiland School of Chemical Engineering and Bioengineering. “The cells don’t know which type of EVs they are, but they take them up because they are used to taking them from their environment, and with that, the physiological signals inside the cells change from growth to death.”

A Larger Area of Arctic Seafloor is Exposed to Sunlight

Photo Credit: © Ignacio Garrido

Most of the sunlight reaching the Arctic Ocean is reflected by sea ice, shielding ocean ecosystems from light. As Arctic sea ice continues to melt, larger areas of the ocean and seafloor become exposed to sunlight, potentially allowing more photosynthesis to occur and making the Arctic Ocean more productive. However, this does not seem to be occurring uniformly across the Arctic Ocean.

Over the past 25 years, the amount of summer Arctic sea ice has diminished by more than 1 million square kilometers. As a result, vast areas of the Arctic Ocean are now, on average, ice free in summer. Scientists are closely monitoring how this impacts sunlight availability and marine ecosystems in the far north.

Many questions arise when such large areas become ice-free and can receive sunlight. A prevailing paradigm suggests that the Arctic Ocean is rapidly becoming more productive as sunlight becomes more abundant in the marine environment. However, it is unclear how ecosystems will evolve in response to increasing sunlight availability and how different parts of the marine ecosystem will be affected, says Karl Attard, a marine scientist and Associate Professor at the Department of Biology.

Attard has led an international research team investigating sunlight availability and photosynthetic production on the understudied Arctic seafloor. Their study has been published in the scientific journal Proceedings of the National Academy of Sciences (PNAS).

Groundbreaking survey reveals secrets of planet birth around dozens of stars

This research brings together observations of more than 80 young stars that might have planets forming around them in spectacular discs. This small selection from the survey shows 10 discs from the three regions of our galaxy observed in the papers. V351 Ori and V1012 Ori are located in the most distant of the three regions, the gas-rich cloud of Orion, some 1600 light-years from Earth. DG Tau, T Tau, HP Tau, MWC758 and GM Aur are located in the Taurus region, while HD 97048, WW Cha and SZ Cha can be found in Chamaeleon I, all of which are about 600 light-years from Earth.  The images shown here were captured using the Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE) instrument mounted on ESO’s Very Large Telescope (VLT). SPHERE’s state-of-the-art extreme adaptive optics system corrects for the turbulent effects of Earth’s atmosphere, yielding crisp images of the discs around stars. The stars themselves have been covered with a coronagraph — a circular mask that blocks their intense glare, revealing the faint discs around them.  The discs have been scaled to appear roughly the same size in this composition. 
Full Size Zoomable Image
Image Credit: ESO/C. Ginski, A. Garufi, P.-G. Valegård et al.

In a series of studies, a team of astronomers has shed new light on the fascinating and complex process of planet formation. The stunning images, captured using the European Southern Observatory's Very Large Telescope (ESO’s VLT) in Chile, represent one of the largest ever surveys of planet-forming discs. The research brings together observations of more than 80 young stars that might have planets forming around them, providing astronomers with a wealth of data and unique insights into how planets arise in different regions of our galaxy.

“This is really a shift in our field of study,” says Christian Ginski, a lecturer at the University of Galway, Ireland, and lead author of one of three new papers published today in Astronomy & Astrophysics. “We’ve gone from the intense study of individual star systems to this huge overview of entire star-forming regions.”

How artificial intelligence learns from complex networks

Multi-layered, so-called deep neural networks are highly complex constructs that are inspired by the structure of the human brain. However, one shortcoming remains: the inner workings and decisions of these models often defy explanation.
Image Credit: Brian Penny / AI Generated

Deep neural networks have achieved remarkable results across science and technology, but it remains largely unclear what makes them work so well. A new study sheds light on the inner workings of deep learning models that learn from relational datasets, such as those found in biological and social networks.

Graph Neural Networks (GNNs) are artificial neural networks designed to represent entities—such as individuals, molecules, or cities—and the interactions between them. These networks have practical applications in various domains; for example, they predict traffic flows in Google Maps and accelerate the discovery of new antibiotics within computational drug discovery pipelines.

GNNs are notably utilized by AlphaFold, an acclaimed AI system that addresses the complex issue of protein folding in biology. Despite these achievements, the foundational principles driving their success are poorly understood.

A recent study sheds light on how these AI algorithms extract knowledge from complex networks and identifies ways to enhance their performance in various applications.

Scientists Have Created Organic Films to Charge Cardiac Pacemakers

The resulting films have high biocompatibility.
Photo Credit: Andrei Ushakov

UrFU scientists, together with colleagues from the University of Aveiro (Portugal), have succeeded in obtaining biocompatible crystalline films. They have high piezoelectric properties - they generate an electric current under mechanical or thermal stress. This property will be useful in the design of elements for invasive medical devices, such as pacemakers. Detailed information about the films obtained and the new method of their synthesis has been published by the scientists in ACS Biomaterials Science & Engineering. 

"We have succeeded in obtaining films from diphenylalanine that have high piezoelectric properties comparable to their inorganic counterparts. Under mechanical or thermal stress, these films generate electricity. The use of such films will be particularly useful for making invasive cardiac pacemakers - devices that reside inside the human body. When the heart moves or beats, these films generate electricity, which is stored in the pacemaker's batteries. Energy storage devices based on such materials could solve the problem of replacing depleted batteries and reduce the number of surgical procedures," explains Denis Alikin, Head of the Laboratory of Functional Nanomaterials and Nanodevices at the UrFU Research Institute of Physics and Applied Mathematics.

New dressing robot can ‘mimic’ the actions of care-workers

The world's first bimanual dressing robot system mimics how caregivers assist humans in dressing.
Photo Credit: Courtesy of University of York

Scientists have developed a new robot that can ‘mimic’ the two-handed movements of care-workers as they dress an individual.

Until now, assistive dressing robots, designed to help an elderly person or a person with a disability get dressed, have been created in the laboratory as a one-armed machine, but research has shown that this can be uncomfortable for the person in care or impractical. 

To tackle this problem, Dr Jihong Zhu, a robotics researcher at the University of York’s Institute for Safe Autonomy, proposed a two-armed assistive dressing scheme, which has not been attempted in previous research, but inspired by caregivers who have demonstrated that specific actions are required to reduce discomfort and distress to the individual in their care.

It is thought that this technology could be significant in the social care system to allow care-workers to spend less time on practical tasks and more time on the health and mental well-being of individuals. 

DNA Aptamer Drug Sensors Can Instantly Detect Cocaine, Heroin and Fentanyl – Even When Combined with Other Drugs

Photo Credit: Nastya Dulhiier

Researchers from North Carolina State University have developed a new generation of high-performance DNA aptamers and highly accurate drug sensors for cocaine and other opioids. The sensors are drug specific and can detect trace amounts of fentanyl, heroin, and cocaine – even when these drugs are mixed with other drugs or with cutting agents and adulterants such as caffeine, sugar, or procaine. The sensors could have far-reaching benefits for health care workers and law enforcement agencies.

“This work can provide needed updates to currently used tests, both in health care and law enforcement settings,” says Yi Xiao, associate professor of chemistry at NC State and corresponding author of two studies describing the work.

“For example, drug field testing currently used by law enforcement still relies on chemical tests developed a century ago that are poorly specific, which means they react to compounds that may not be the drug they’re looking for,” Xiao says.

“And the existing aptamer test for cocaine isn’t sensitive and specific enough to detect clinically relevant amounts of the drug in biological samples, like blood. The sensors we developed can detect cocaine in blood at nanomolar, rather than micromolar, levels, which represents a 1,000-fold improvement in sensitivity.”

Producing Hydrogen from Rocks Gains Steam as Scientists Advance New Methods

Researchers are studying chemical catalysts that can produce hydrogen gas from iron-rich rocks.
Photo Credit: Toti Larson / UT Austin.

In a project that could be a game changer for the energy transition, researchers at The University of Texas at Austin are exploring a suite of natural catalysts to help produce hydrogen gas from iron-rich rocks without emitting carbon dioxide.

If the scientists are successful, the project could jump-start a brand-new type of hydrogen industry: geologic hydrogen.

“We’re producing hydrogen from rocks,” said Toti Larson, a research associate professor at the UT Jackson School of Geosciences Bureau of Economic Geology and the lead researcher on the project. “It’s a type of non-fossil fuel production of hydrogen from iron-rich rocks that has never been attempted at an industrial scale.”

The research team recently received a $1.7 million grant from the Department of Energy and is collaborating with scientists at the University of Wyoming’s School of Energy Resources to explore the feasibility of this process on different rock types across the United States.

An evolutionary mystery 125 million years in the making

A bushel of tomatoes at the CSHL Uplands Farm.
Photo Credit: Courtesy of Cold Spring Harbor Laboratory

Plant genomics has come a long way since Cold Spring Harbor Laboratory (CSHL) helped sequence the first plant genome. But engineering the perfect crop is still, in many ways, a game of chance. Making the same DNA mutation in two different plants doesn’t always give us the crop traits we want. The question is why not? CSHL plant biologists just dug up a reason.

CSHL Professor and HHMI Investigator Zachary Lippman and his team discovered that tomato and Arabidopsis thaliana plants can use very different regulatory systems to control the same exact gene. Incredibly, they linked this behavior to extreme genetic makeovers that occurred over 125 million years of evolution.