. Scientific Frontline

Wednesday, January 4, 2023

Researchers detect fluoride in water with new simple color change test

Photo Credit: Henryk Niestrój

Test is first to use artificial cell sensors to detect environmental contaminant

A team of synthetic biologists at Northwestern is developing a sensor platform that will be able to detect a range of environmental and biological targets in real-world samples.

Environmental contaminants like fluoride, lead and pesticides exist all around and even within us. While researchers have simple ways to measure concentrations of such contaminants inside lab environments, levels are much more difficult to test in the field. That’s because they require costly specialized equipment.

Recent efforts in synthetic biology have leveraged cellular biosensors to both detect and report environmental contaminants in a cost-effective and field-deployable manner. Even as progress is being made, scientists have struggled to answer the question of how to protect sensor components from substances that naturally exist in extracted samples.

First-ever observation of quantum interference between dissimilar particles

Daniel Brandenburg and Zhangbu Xu at the STAR detector of the Relativistic Heavy Ion Collider (RHIC).
Photo Credit: Courtesy of Brookhaven National Laboratory

Nuclear physicists have found a new way to use the Relativistic Heavy Ion Collider (RHIC)—a particle collider at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory—to see the shape and details inside atomic nuclei. The method relies on particles of light that surround gold ions as they speed around the collider and a new type of quantum entanglement that’s never been seen before.

Through a series of quantum fluctuations, the particles of light (a.k.a. photons) interact with gluons—gluelike particles that hold quarks together within the protons and neutrons of nuclei. Those interactions produce an intermediate particle that quickly decays into two differently charged “pions” (π). By measuring the velocity and angles at which these π+ and π- particles strike RHIC’s STAR detector, the scientists can backtrack to get crucial information about the photon—and use that to map out the arrangement of gluons within the nucleus with higher precision than ever before.

“This technique is similar to the way doctors use positron emission tomography (PET scans) to see what’s happening inside the brain and other body parts,” said former Brookhaven Lab physicist James Daniel Brandenburg, a member of the STAR collaboration who joined The Ohio State University as an assistant professor in January 2023. “But in this case, we’re talking about mapping out features on the scale of femtometers—quadrillionths of a meter—the size of an individual proton.”

‘Veggie’ dinosaurs differed in how they ate their food

Some of the finite element models compared bite performance across the five ornithischian dinosaurs in the study, with different models showing different bite points. Cooler colors (blue) represent areas of low stress while hot colors (red and pink) indicate areas that are highly stressed.
Illustration Credit: David Button

Although most early dinosaurs were vegetarian, there were a surprising number of differences in the way that these animals tackled eating a plant-based diet, according to a new study by scientists from the Natural History Museum and the Universities of Bristol and Birmingham.

Scientists used CT scans of dinosaur skulls to track the evolution of early dinosaur herbivores - reconstructing jaw muscles and measuring the animals’ bite force to understand how dinosaur feeding evolved.

Five skulls from the plant-eating group Ornithischia provided the key to unlocking their feeding habits: Heterodontosaurus, Lesothosaurus, Scelidosaurus, Hypsilophodon and Psittacosaurus - earliest representatives of what would become the major herbivore dinosaur groups.

Later ornithischian dinosaurs, like Triceratops and Stegosaurus, show a wide range of adaptations to eating plants yet their early relatives have not been examined properly, until now.

How a CRISPR Protein Might Yield New Tests for Many Viruses

In this illustration based on cryo-electron microscope images, a Cas12a2 protein unzips a DNA double helix, allowing it to cut the single strands of DNA (blue and green).
Illustration Credit: Jack Bravo/University of Texas at Austin

In a first for the genetic toolset known as CRISPR, a recently discovered protein has been found to act as a kind of multipurpose self-destruct system for bacteria, capable of degrading single-stranded RNA, single-stranded DNA and double-stranded DNA. With its abilities to target so many types of genetic material, the discovery holds potential for the development of new inexpensive and highly sensitive at-home diagnostic tests for a wide range of infectious diseases, including COVID-19, influenza, Ebola and Zika, according to the authors of a new study in the journal Nature.

Using a high-resolution imaging technique called cryo-EM, the team discovered that when this protein, named Cas12a2, binds to a specific sequence of genetic material from a potentially dangerous virus, called a target RNA, a side portion of Cas12a2 swings out to reveal an active site, similar to a sprung-open switchblade knife. Then, the active site starts to indiscriminately cut any genetic material it comes into contact with. The researchers discovered that, with a single mutation to the Cas12a2 protein, the active site degrades only single-stranded DNA—a feature especially useful in developing new diagnostics tailored for any of a wide range of viruses.

Major Breakthrough as Scientists Sequence the Genomes of Endangered Sharks

Hammerhead Shark
Photo Credit: David Clode

The first-ever chromosome-level genome sequences completed for great hammerhead and shortfin mako sharks have shown that both species have experienced major population declines over a 250,000-year history. Low genetic diversity and signs of inbreeding add a layer of concern to the management of Critically Endangered great hammerhead sharks, whose populations have been in freefall recently due to overfishing for their highly valued fins. In contrast, with a larger effective population size (the ideal breeding population size) in the past and higher genetic diversity, shortfin mako sharks appear equipped to be more resilient to rapid environmental change: that is, if the current fishing pressure on them is substantially reduced.

“With their whole genomes deciphered at high resolution we have a much better window into the evolutionary history of these endangered species,” said Mahmood Shivji, Ph.D., professor at Nova Southeastern University’s (NSU) Halmos College of Arts and Sciences and director of the Save Our Seas Foundation Shark Research Center and NSU’s Guy Harvey Research Institute.

It’s a startling image that describes a milestone in conservation science for sharks. Shivji, Michael Stanhope, Ph.D., from Cornell University’s College of Veterinary Medicine and their collaborators have glanced back in history by sequencing to chromosome level the genomes (entire genetic blueprint) of great hammerhead and shortfin mako sharks. Their DNA timeline shows that their populations have declined substantially over 250,000 years. What the scientists have also found is worrying: great hammerhead sharks have low genetic variation, which makes them less resilient to adapting to our rapidly changing world. The species also shows signs of inbreeding, an issue that can lower the ability of its populations to survive.

Serpent in the sky captured with ESO telescope

The Sh2-54 nebula in the infrared with VISTA
This image of the spectacular Sh2-54 nebula was taken in infrared light using ESO’s VISTA telescope at Paranal Observatory in Chile. The clouds of dust and gas that are normally obvious in visible light are less evident here, and in this light, we can see the light of the stars behind the nebulae now piercing through. 
Image Credit: ESO/VVVX

A myriad of stars is revealed behind the faint orange glow of the Sh2-54 nebula in this new infrared image. Located in the constellation Serpens, this stunning stellar nursery has been captured in all its intricate detail using the Visible and Infrared Survey Telescope for Astronomy (VISTA) based at ESO’s Paranal Observatory in Chile.

When the ancients looked up at the night sky, they saw random patterns in the stars. The Greeks, for instance, named one of these “constellations” Serpens, because of its resemblance to a snake. What they wouldn’t have been able to see is that at the tail end of this constellation there is a wealth of stunning astronomical objects. These include the Eagle, the Omega and the Sh2-54 nebulae; the last of these is revealed, in a new light, in this spectacular infrared image.

Nebulae are vast clouds of gas and dust from which stars are born. Telescopes have allowed astronomers to identify and analyze these rather faint objects in exquisite detail. The nebula shown here, located about 6000 light-years away, is officially called Sh2-54; the “Sh” refers to the US astronomer Steward Sharpless, who catalogued more than 300 nebulae in the 1950s.

Common Fatty Acid Contributes to Temperature and Pain Sensitivity in Psoriasis Plaques

Photo Credit: Eszter Miller

A common fatty acid found in the Western diet breaks down into compounds that contribute to increased temperature and pain – but not itch – sensitivity in psoriatic lesions. The finding could lead to better understanding of how lipids communicate with sensory neurons, and potentially to improved pain and sensitivity treatments for psoriasis patients.

Linoleic acid is a fatty acid found in vegetable oils, nuts and seeds, and is one of the predominant fatty acids found in the Western diet. Metabolites from linoleic acid – the products formed when the body breaks it down through digestion – play a role in skin barrier function.

“We noticed high levels of two types of lipids derived from linoleic acid in psoriatic lesions,” says Santosh Mishra, associate professor of neuroscience at North Carolina State University and corresponding author of the research. “That led us to wonder whether the lipids might affect how sensory neurons in these lesions communicate. We decided to investigate whether their presence could be related to the temperature or pain hypersensitivity that many psoriasis patients report.”

Zebrafish testing identifies a gene potentially at the root of domestication

Photo Credit: Petr Kuznetsov

The research, published in iScience, looked at genetically modified zebrafish that fail to make the baz1b protein. The results suggest the gene is not only at the cornerstone of physical and behavioral changes in the fish and other domesticated species, but potentially also human beings’ social relationships.

Domesticated species - such as dogs and cats - show genetic differences compared to their wild type counterparts, including variation in the baz1b gene. These genetic changes correlate with physical and behavioral traits including smaller facial features such as skulls and teeth, as well as being more sociopositive, less aggressive, and having less fear.

However, studies have also suggested that modern humans domesticated themselves after they split from their extinct relatives, Neanderthals and Denisovans. In doing so, we experienced similar physical and behavioral changes.

Those changes have all been linked to the fact that domesticated animals have fewer of a certain type of stem cell, called neural crest stem cells.

The research led by the Queen Mary team builds on this by studying the impact of removing baz1b gene function, and the impact of doing so on neural crest development and social behavior.

Was That Explosion Chemical or Nuclear?

From left to right: Tim Johnson, Hunter Knox, and Harry Miley bring together different perspectives to better detect underground nuclear explosions. 
Composite Image Credit: by Shannon Colson | Pacific Northwest National Laboratory

If an underground explosion occurs anywhere in the world, there is a good chance that a seismologist can pinpoint it. However, they won’t necessarily be able to tell you what kind of explosion had occurred—whether it is chemical or nuclear in nature. New research from Pacific Northwest National Laboratory (PNNL) scientists makes detecting nuclear explosions easier.

“To a seismologist, chemical and nuclear explosions look identical,” said Harry Miley, Laboratory Fellow and physicist in the National Security Directorate at PNNL. “Radionuclide detection technologies, like the PNNL-developed Xenon International and Radionuclide Aerosol Sampler/Analyzer, known as RASA, can discriminate between the two by detecting radioactive atoms that are created in nuclear explosions. However, we have very little scientific understanding of the geologic containment of these atoms following an explosion.”

When an underground explosion occurs, gases travel through fractures in the ground and escape into the atmosphere. Instruments such as Xenon International and RASA can then detect radionuclide gases, but their chemical signatures may be greatly affected by rock damage that the gases must pass through.

Self-powered, printable smart sensors created from emerging semiconductors could mean cheaper, greener Internet of Things

Simon Fraser University professor Vincenzo Pecunia
Photo Credit: Courtesy of Simon Fraser University

Creating smart sensors to embed in our everyday objects and environments for the Internet of Things (IoT) would vastly improve daily life—but requires trillions of such small devices. Simon Fraser University professor Vincenzo Pecunia believes that emerging alternative semiconductors that are printable, low-cost and eco-friendly could lead the way to a cheaper and more sustainable IoT.

Leading a multinational team of top experts in various areas of printable electronics, Pecunia has identified key priorities and promising avenues for printable electronics to enable self-powered, eco-friendly smart sensors. His forward-looking insights are outlined in his paper published on Dec. 28 in Nature Electronics.

“Equipping everyday objects and environments with intelligence via smart sensors would allow us to make more informed decisions as we go about in our daily lives,” says Pecunia. “Conventional semiconductor technologies require complex, energy-intensity, and expensive processing, but printable semiconductors can deliver electronics with a much lower carbon footprint and cost, since they can be processed by printing or coating, which require much lower energy and materials consumption.”

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