It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Thursday, September 21, 2023
Dinosaur feathers reveal traces of ancient proteins
New method reveals similarities between dinosaurs and birds
IMAGE: DR TIFFANY SLATER PICTURED AT THE SCHOOL OF BIOLOGICAL, EARTH AND ENVIRONMENTAL SCIENCES AT UNIVERSITY COLLEGE CORK.view more
CREDIT: DARAGH MC SWEENEY/PROVISION
Palaeontologists at University College Cork (UCC) in Ireland have discovered X-ray evidence of proteins in fossil feathers that sheds new light on feather evolution.
Previous studies suggested that ancient feathers had a different composition to the feathers of birds today. The new research, however, reveals that the protein composition of modern-day feathers was also present in the feathers of dinosaurs and early birds, confirming that the chemistry of feathers originated much earlier than previously thought.
The research, published today in Nature Ecology and Evolution, was led by palaeontologists Dr Tiffany Slater and Prof. Maria McNamara of UCC’s School of Biological, Earth, and Environmental Science, who teamed with scientists based at Linyi University (China) and the Stanford Synchrotron Radiation Lightsource (USA).
The team analysed 125-million-year-old feathers from the dinosaur Sinornithosaurus and the early bird Confuciusornis from China, plus a 50-million-year-old feather from the USA.
“It’s really exciting to discover new similarities between dinosaurs and birds,” Dr Slater says. “To do this, we developed a new method to detect traces of ancient feather proteins. Using X-rays and infrared light we found that feathers from the dinosaur Sinornithosaurus contained lots of beta-proteins, just like feathers of birds today.”
To help interpret the chemical signals preserved in the fossil feathers, the team also ran experiments to help understand how feather proteins break down during the fossilization process.
“Modern bird feathers are rich in beta-proteins that help strengthen feathers for flight,” Dr Slater says.
“Previous tests on dinosaur feathers, though, found mostly alpha-proteins. Our experiments can now explain this weird chemistry as the result of protein degradation during the fossilization process. So although some fossil feathers do preserve traces of the original beta-proteins, other fossil feathers are damaged and tell us a false narrative about feather evolution.”
This research helps answer a long-standing debate about whether feather proteins, and proteins in general, can preserve in deep time.
Prof. Maria McNamara, senior author on the study, said
“Traces of ancient biomolecules can clearly survive for millions of years, but you can’t read the fossil record literally because even seemingly well-preserved fossil tissues have been cooked and squashed during fossilization. We’re developing new tools to understand what happens during fossilization and unlock the chemical secrets of fossils. This will give us exciting new insights into the evolution of important tissues and their biomolecules. “
ENDS
Dr Tiffany Slater and Prof. Maria McNamara pictured in the experimental fossilization laboratory at the School of Biological, Earth and Environmental Sciences at University College Cork.
CREDIT
Daragh Mc Sweeney/Provision
A graphical abstract based on paper by Slater et al., 2003
CREDIT
Science Graphic Design
Fossil feather (IMAGE)
UNIVERSITY COLLEGE CORK
Isolated fossil feather from the Green River Formation (ca. 50 million years old, USA). Specimen held in the Yale University Peabody Museum of Natural History. Scale bar indicates 100 mm
Scanning electron microscopy image of zebra finch feather. Scale bar indicates 200 µm.
A research team led by Prof. LIN Nan from the Institute of Psychology of the Chinese Academy of Sciences found that during sentence processing, the neural activity of two canonical language areas, i.e., the left ventral temporoparietal junction (vTPJ) and the lateral anterior temporal lobe (lATL), is associated with social-semantic working memory rather than language processing per se.
The study was published in Nature Human Behaviour on Sept. 21.
Language and social cognition are two deeply interrelated abilities of the human species, but have traditionally been studied as two separate domains. Both sentence processing and social tasks can evoke neural activity in the left vTPJ and lATL, suggesting that the function of these regions may link language comprehension with social cognition. However, previous studies have attributed the activity of these regions in language tasks to general semantic and/or syntactic processing, whereas their activity in social tasks is attributed to social concept activation.
In this study, the researchers tested a novel hypothesis that the activity of the left vTPJ and lATL in language and social tasks are both due to a common cognitive component—i.e., social-semantic working memory.
Using fMRI experiments, they validated that these regions were sensitive to sentences only if the sentences conveyed social meaning. In addition, these regions showed persistent social-semantic-selective activity after the linguistic stimuli disappeared and were sensitive to the sociality of nonlinguistic stimuli. Furthermore, these regions were more tightly connected to the social-semantic-processing areas than to the sentence-processing areas.
The results indicate that the left vTPJ and lATL are not specific to language processing and contribute to language comprehension through social-semantic working memory.
"Since the 1990s, it has been consistently observed that the left vTPJ and lATL are sensitive to sentence processing. Therefore, our findings were quite surprising," said Prof. LIN, corresponding author of the study.
These findings are likely to force a major reconsideration of the functional organization of the cortical language network, and they also make an important new contribution to the field of social neuroscience, according to a reviewer for Nature Human Behaviour.
This study was supported by the National Natural Science Foundation of China, the Scientific Foundation of the Institute of Psychology, and the National Science and Technology Innovation 2030 Major Program.
IMAGE: PNNL CHEMIST ISAAC ARNQUIST EXAMINES ULTRA-LOW RADIATION COPPER CABLES SPECIALLY CREATED FOR SENSITIVE PHYSICS DETECTION EXPERIMENTS.view more
CREDIT: (PHOTO BY ANDREA STARR | PACIFIC NORTHWEST NATIONAL LABORATORY)
RICHLAND, Wash.—Imagine trying to tune a radio to a single station but instead encountering static noise and interfering signals from your own equipment. That is the challenge facing research teams searching for evidence of extremely rare events that could help understand the origin and nature of matter in the universe. It turns out that when you are trying to tune into some of the universe’s weakest signals, it helps to make your instruments very quiet.
Around the world more than a dozen teams are listening for the pops and electronic sizzle that might mean they have finally tuned into the right channel. These scientists and engineers have gone to extraordinary lengths to shield their experiments from false signals created by cosmic radiation. Most such experiments are found in very inaccessible places—such as a mile underground in a nickel mine in Sudbury, Ontario, Canada, or in an abandoned gold mine in Lead, South Dakota—to shield them from naturally radioactive elements on Earth. However, one such source of fake signals comes from natural radioactivity in the very electronics that are designed to record potential signals.
Radioactive contaminants, even at concentrations as tiny as one part-per-billion, can mimic the elusive signals that scientists are seeking. Now, a research team at the Department of Energy’s Pacific Northwest National Laboratory, working with Q-Flex Inc., a small business partner in California, has produced electronic cables with ultra-pure materials. These cables are specially designed and manufactured to have such extremely low levels of the radioactive contaminants that they will not interfere with highly sensitive neutrino and dark matter experiments. The scientists report in the journal EPJ Techniques and Instrumentation that the cables have applications not only in physics experiments, but they may also be useful to reduce the effect of ionizing radiation interfering with future quantum computers.
“We have pioneered a technique to produce electronic cabling that is a hundred times lower than current commercially available options,” said PNNL principal investigator Richard Saldanha. “This manufacturing approach and product has broad application across any field that is sensitive to the presence of even very low levels of radioactive contaminants.”
An ultra-quiet choreographed ballet
Small amounts of naturally occurring radioactive elements are found everywhere: in rocks, dirt and dust floating in the air. The amount of radiation that they emit is so low that they do not pose any health hazards, but it’s still enough to cause problems for next-generation neutrino and dark matter detectors.
“We typically need to get a million or sometimes a billion times cleaner than the contamination levels you would find in just a little speck of dirt or dust,” said PNNL chemist Isaac Arnquist, who co-authored the research article and led the measurement team.
For these experiments, Saldanha, Arnquist, and PNNL colleagues Maria Laura di Vacri, Nicole Rocco and Tyler Schlieder evaluated the amount of uranium, thorium and potassium at each step of the dozen or so processing steps that ultimately produce a detector cable. The team then developed special cleaning and fabrication techniques to reduce the contamination down to insignificant levels. Working in an ultraclean, dust and contaminant-free laboratory, the PNNL researchers meticulously plan out their every move.
“I almost think of us as performance athletes because everything, every movement we make, is extremely thought out. It's almost like we're choreographed dancers,” said Arnquist. “When we handle a detector sample material, there's no wasted extraneous motion or interaction with the sample because that interaction could impart some contamination that limits how well we can measure the materials.”
After several years of work and hundreds of measurements, the resulting cables are now so free of contaminants that they will not impact the operation of next-generation dark matter and neutrino experiments such as DAMIC-M, OSCURA, and nEXO. The research team points out in their study that low-radioactivity cables can increase the sensitivity of the experiments and even allow more flexibility in detector design.
Getting closer to the a-ha moment
So, exactly what are the researchers looking for in these experiments? In the case of both dark matter and neutrinoless double beta decay, they are hoping to record extremely rare events that could solve two key mysteries of the universe. Both of these mysteries pose fundamental questions about why the universe looks the way it does. The galaxies that fill our universe would not have formed without the existence of dark matter. Dark matter makes up around 85 percent of the matter of the universe, and yet, we have never observed dark matter directly, only its gravitational imprint on the universe. Perhaps more intriguing, the question of why there is matter in the universe at all may hinge on a unique property of the smallest known particles of matter—the neutrino. Unlike all other fundamental particles, neutrinos could possibly interact as both matter and anti-matter. If true, this could result in an extremely rare nuclear decay called neutrinoless double beta decay. Scientists are building large experiments consisting of many tons of sensitive material with the hope of finding the first evidence of neutrinoless double beta decay within the next decade.
“Every step we take to eliminate interfering radioactivity gets us closer to finding evidence for dark matter or neutrinoless double beta decay,” said Saldanha.
“These flexible cables have many conductive pathways, which are needed to read out complicated signals,” added Arnquist. “When, say, dark matter interacts with the detector or a neutrinoless double beta decay occurs, it’s going to create an event that needs to be accurately recorded—read out—to make the discovery. We need to put a complex electronic part that is extremely clean of radioactive elements into the heart of the detector.”
“Next generation searches for neutrinoless double beta decay will be among the lowest radioactivity experiments ever constructed,” said David Moore, a Yale University physicist and PNNL collaborator. “These detectors use such pure materials that even a small amount of normal cabling materials would overwhelm the radioactivity from the entire rest of the detector, so developing ultra-low-background cables to read out such detectors is a major challenge. This recent work from PNNL and Q-Flex is key to enabling these detectors and will reduce the cabling background to a small fraction of what was possible with previous technologies."
Planning is already underway to upgrade the highly sensitive DAMIC-M dark matter experiment and the new ultra-pure cables are one of the key improvements scheduled for installation in the detector.
“One component that we can’t avoid in our detector are the cables that transmit the signals, which must be of very low radioactivity,” said Alvaro E Chavarria, a physicist at the University of Washington and a collaborator on the DAMIC-M project. “Prior to this recent PNNL development, the best solution was microcoax cables, which carry too few signals and would have required a significant redesign of our detector. This development is super exciting, since it enables the use of the industry-standard flex-circuit technology for low-background applications.”
Recent research findings by PNNL scientists and other collaborators indicate that the performance of some quantum computing devices can be affected by the presence of trace radioactive contaminants. While radioactivity is not currently what limits the capabilities of existing quantum computers, it is possible that quantum devices of the future might need low-radioactivity cables to enhance their performance.
“We see the potential for these cables to find applications in a wide range of sensitive radiation detectors and perhaps other applications such as quantum computing,” Saldanha said.
The research was supported by the Department of Energy, Office of Science, under its Early Career Research and Small Business Innovation Research programs.
Chemist Isaac Arnquist and post-doctoral researcher Tyler Schlieder examine a sheet of ultra-pure copper cables designed for physics experiments.
Close up of an ultra-low radiation electronic cable with dozens of conductive circuitry pathways to monitor sensitive physics experiments. This sample cable allows the research team to assess radiopurity after production and cleaning.
CREDIT
(Photo by Andrea Starr | Pacific Northwest National Laboratory)
A new form of agricultural pest control could one day take root—one that treats crop infestations deep under the ground in a targeted manner with less pesticide.
Engineers at the University of California San Diego have developed nanoparticles, fashioned from plant viruses, that can deliver pesticide molecules to soil depths that were previously unreachable. This advance could potentially help farmers effectively combat parasitic nematodes that plague the root zones of crops, all while minimizing costs, pesticide use and environmental toxicity.
Controlling infestations caused by root-damaging nematodes has long been a challenge in agriculture. One reason is that the types of pesticides used against nematodes tend to cling to the top layers of soil, making it tough to reach the root level where nematodes wreak havoc. As a result, farmers often resort to applying excessive amounts of pesticide, as well as water to wash pesticides down to the root zone. This can lead to contamination of soil and groundwater.
To find a more sustainable and effective solution, a team led by Nicole Steinmetz, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and founding director of the Center for Nano-ImmunoEngineering, developed plant virus nanoparticles that can transport pesticide molecules deep into the soil, precisely where they are needed. The work is detailed in a paper published in Nano Letters.
Steinmetz’s team drew inspiration from nanomedicine, where nanoparticles are being created for targeted drug delivery, and adapted this concept to agriculture. This idea of repurposing and redesigning biological materials for different applications is also a focus area of the UC San Diego Materials Research Science and Engineering Center (MRSEC), of which Steinmetz is a co-lead.
“We’re developing a precision farming approach where we’re creating nanoparticles for targeted pesticide delivery,” said Steinmetz, who is the study’s senior author. “This technology holds the promise of enhancing treatment effectiveness in the field without the need to increase pesticide dosage.”
The star of this approach is the tobacco mild green mosaic virus, a plant virus that has the ability to move through soil with ease. Researchers modified these virus nanoparticles, rendering them noninfectious to crops by removing their RNA. They then mixed these nanoparticles with pesticide solutions in water and heated them, creating spherical virus-like nanoparticles packed with pesticides through a simple one-pot synthesis.
This one-pot synthesis offers several advantages. First, it is cost-effective, with just a few steps and a straightforward purification process. The result is a more scalable method, paving the way toward a more affordable product for farmers, noted Steinmetz. Second, by simply packaging the pesticide inside the nanoparticles, rather than chemically binding it to the surface, this method preserves the original chemical structure of the pesticide.
“If we had used a traditional synthetic method where we link the pesticide molecules to the nanoparticles, we would have essentially created a new compound, which will need to go through a whole new registration and regulatory approval process,” said study first author Adam Caparco, a postdoctoral researcher in Steinmetz’s lab. “But since we’re just encapsulating the pesticide within the nanoparticles, we’re not changing the active ingredient, so we won’t need to get new approval for it. That could help expedite the translation of this technology to the market.”
Moreover, the tobacco mild green mosaic virus is already approved by the Environmental Protection Agency (EPA) for use as an herbicide to control an invasive plant called the tropical soda apple. This existing approval could further streamline the path from lab to market.
The researchers conducted experiments in the lab to demonstrate the efficacy of their pesticide-packed nanoparticles. The nanoparticles were watered through columns of soil and successfully transported the pesticides to depths of at least 10 centimeters. The solutions were collected from the bottom of the soil columns and were found to contain the pesticide-packed nanoparticles. When the researchers treated nematodes with these solutions, they eliminated at least half of the population in a petri dish.
While the researchers have not yet tested the nanoparticles on nematodes lurking beneath the soil, they note that this study marks a significant step forward.
“Our technology enables pesticides meant to combat nematodes to be used in the soil,” said Caparco. “These pesticides alone cannot penetrate the soil. But with our nanoparticles, they now have soil mobility, can reach the root level, and potentially kill the nematodes.”
Future research will involve testing the nanoparticles on actual infested plants to assess their effectiveness in real-world agricultural scenarios. Steinmetz’s lab will perform these follow-up studies in collaboration with the U.S. Horticultural Research Laboratory. Her team has also established plans for an industry partnership aimed at advancing the nanoparticles into a commercial product.
This work was supported in part by the U.S. Department of Agriculture (grants NIFA-2020-67021-31255 and NIFA-2022-67012-36698), the National Science Foundation (CMMI 1901713) and the UC San Diego Materials Research Science and Engineering Center (MRSEC), which is supported by the National Science Foundation (grant DMR-2011924). This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). This work was also performed in part at the UC San Diego Department of Neurosciences Microscopy Core, which is supported by the National Institutes of Health (NINDS P30NS047101).
Three independent state-of-the-art datasets reveal that the West Side has more nitrogen dioxide (NO2) pollution than the rest of the city
Depending on the month, residents in this area experience 16 to 32% higher NO2 concentrations on average
By identifying hotspots, residents and policymakers can be confident about where to prioritize immediate interventions
EVANSTON, Ill. — The western edge of Chicago — including the North and South Lawndale, East Garfield Park, Archer Heights and Brighton Park neighborhoods — experiences up to 32% higher concentrations of nitrogen dioxide (NO2) air pollution compared to the rest of the city, a new Northwestern University study has found.
In the new study, researchers developed a process to systematically identify areas of agreement and disagreement among three individual state-of-the-art air-quality datasets: satellite observations, a simulation developed at Northwestern and sensors from Microsoft Research’s Project Eclipse.
Although one or two datasets identified multiple areas as NO2 hotspots, all three datasets consistently flagged Chicago’s West Side as having elevated NO2 pollution. The West Side also has more Black, Hispanic and Latinx residents compared to the rest of the city, highlighting the disproportionate pollution and health burdens shouldered by these communities.
“The three tools that we explored sometimes identified different areas of elevated pollution from one another,” said Northwestern’s Anastasia Montgomery, who led the study. “That doesn’t necessarily mean the tools are not working. It could be that they are looking at different things. However, in areas where we found agreement between the datasets, we have greater confidence that NO2 pollution is significantly high. The three different tools we used all pointed to the West Side as an area where pollution is significantly elevated relative to the Chicago average.”
“High spatial resolution air quality data has the potential to reveal inequitable exposure to pollution by identifying localized hotspots,” said Northwestern’s Daniel Horton, the study’s senior author. “Using this science-backed evidence, residents can advocate for change, and government officials can develop more targeted policies. By combining and improving tools to identify these hotspots, we can ensure that mitigation efforts serve the most affected communities.”
To conduct the study, the researchers compared how each dataset quantified NO2. A byproduct of fossil-fuel combustion engines, NO2 is incredibly harmful to human health. Chronic exposure to these fumes can lead to bronchitis, pneumonia, asthma and even premature death. And under certain conditions, when NO2 interacts with sunlight, it can also produce ground-level ozone, which is linked to childhood asthma and other respiratory health issues.
Each tool in the study used a different method to gather data. Microsoft Research’s Project Eclipse collected real-time air-quality data by deploying 100 low-cost sensors throughout Chicago, which sampled the air every one minute. Previously developed in Horton’s laboratory, the Northwestern simulation combines emissions data with weather and chemical transport models to create neighborhood estimates of air quality. And the satellite tool takes a snapshot of Earth’s atmosphere once per day.
“Satellite tools are sensitive to different wavelengths of light,” Montgomery explained. “Nitrogen dioxide absorbs light at certain wavelengths, so satellite snapshots can reveal different levels of nitrogen dioxide concentrations across space.”
Because air pollution changes across seasons, the researchers looked at air quality data in February and August. Then, they pinpointed neighborhoods with high agreement (meaning all tools agree), medium agreement (two tools agree) and low agreement (consensus among none of the tools) regarding NO2hotspots.
All tools consistently identified the city’s West Side as a hotspot in both August and February, regardless of season or wind direction. Depending on the month, the estimated 501,000 people who live and work within this hotspot experience NO2 concentrations that are 16 to 32% higher than the city-wide average.
Data from satellites and Microsoft Research’s sensors also pinpointed an adjoining hotspot just a bit north of the consensus hotspot, encompassing the Austin, Humboldt Park and West Garfield Park neighborhoods. The Northwestern simulation, however, did not indicate a hotspot in this area.
“Our model does not simulate significantly high pollution concentrations here, but observations show otherwise,” Montgomery said. “Because the model simulations don’t agree with two observational datasets, it suggests that our model has limitations. Perhaps we need to adjust the model physics or the underlying emission estimates.”
Another area of medium agreement occurred along highways. While satellite data and the Northwestern simulation uncovered high NO2 along highways, the Microsoft Research data did not.
“We think that’s because most highways in Chicago are typically above street level,” Montgomery said. “Microsoft placed sensors at bus stops, which are always at street level, so they didn’t capture the elevated interstate corridors well.”
Even though the tools might disagree on hotspots, the causes behind the hotspots are certain. All areas with high or medium agreement are considered heavily trafficked and moderately to highly industrialized.
“Tools like those we used in this study can be used as complementary components for monitoring a city to show where targeted inventions are most needed,” Montgomery said. “We can look at the zoning there and who is being affected. Policies could be implemented to incentivize engine idling restrictions, building standards or the purchase of electric vehicles.”
The study, “Intraurban NO2 hotspot detection across multiple air quality products,” was supported by the National Science Foundation and Microsoft Research.
Organisms, including viruses, live in the deepest, darkest places on the planet
Marine virologists analyzed sediment from the Mariana Trench, the deepest place on Earth, and identified a new bacteriophage
The phage infects Halomonas bacteria, which have been found in deep-sea environments and near hydrothermal vents
The study helps probe how phages and hosts evolve together in secluded, hostile environments
Washington, D.C. — The Mariana Trench, the deepest place on Earth, plunges nearly 11,000 meters at its lowest point on the floor of the Pacific Ocean. Life persists in the deep and cold darkness, and “wherever there’s life, you can bet there are regulators at work,” said marine virologist Min Wang, Ph.D, at the Ocean University of China, in Qingdao. “Viruses, in this case.”
This week in Microbiology Spectrum, Wang and an international group of researchers report the discovery of a new virus isolated from sediment brought up from a depth of 8,900 meters. The virus is a bacteriophage, or a virus that infects and replicates inside bacteria, and bacteriophages are believed to be the most abundant life forms on the planet. “To our best knowledge, this is the deepest known isolated phage in the global ocean,” said Wang.
The newly found phage infects bacteria in the phylum Halomonas, which are often found in sediments from the deep seas and from hydrothermal vents, geyser-like openings on the seafloor that release streams of heated water. Wang said the group’s analysis of the viral genetic material points to existence of a previously unknown viral family in the deep ocean, as well as new insights into the diversity, evolution and genomic features of deep-sea phages and phage-host interactions.
In previous work, the researchers have used metagenomic analysis to study viruses that infect bacteria in the order Oceanospirallales, which includes Halomonas. For the new study, Wang’s team looked for viruses in bacterial strains collected and isolated by a team led by marine virologist Yu-Zhong Zhang, Ph.D, also at the Ocean University of China, in Qingdao. Zhang’s research explores microbial life in extreme environments, including polar regions and the Mariana Trench.
The genomic analysis of the new virus, identified as vB_HmeY_H4907, suggests that it is distributed widely in the ocean and has a similar structure to its host. Wang said the study points to new questions and research areas focused on the survival strategies of viruses in harsh, secluded environments—and how they co-evolve with their hosts. The new virus is lysogenic, which means it invades and replicates inside its host, but usually without killing the bacterial cell. As the cell divides, the viral genetic material is also copied and passed on.
In future studies, Wang said, the group plans to investigate the molecular machinery that drives interactions between deep-sea viruses and their hosts. They’re also searching for other new viruses in extreme places, “which would contribute to broadening our comprehension of the virosphere,” Wang said. “Extreme environments offer optimal prospects for unearthing novel viruses.”
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