NOT PRODUCED IN A LAB

Samples from Huanan Seafood Market provide further evidence of COVID-19 animal origins

A new analysis co-authored by University of Arizona virus expert Michael Worobey provides additional evidence that wildlife sold illegally at a Chinese market were "ground zero" for the COVID pandemic.

University of Arizona

 

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Professional sterilization teams can be seen outside the main entrance of the Huanan Seafood Wholesale Market in Wuhan, China in March 2020, shortly after its closure. 

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Credit: China News Service/Wikipedia

A new international study provides a shortlist of the wildlife species present at the market from which SARS-CoV-2, the virus responsible for the COVID-19 pandemic, most likely arose in late 2019.

The study, published Thursday in the journal Cell, is based on an analysis of genetic data released by the Chinese Center for Disease Control and Prevention. The data comes from more than 800 samples collected in and around the Huanan Seafood Wholesale market in Wuhan, China, beginning on Jan. 1, 2020, and from viral genomes from early COVID-19 patients.

"This may be the last big, new set of data directly from the market, and in a way, it's like finishing the last piece of a puzzle showing a picture that has been pretty clear already," said Michael Worobey, one of three co-corresponding authors on the paper and head of the Department of Ecology and Evolutionary Biology at the University of Arizona. "We present a thorough and rigorous analysis of the data and how it fits in with the rest of the huge body of evidence we have about how the pandemic started."

On Jan. 1, 2020, just hours after the market closed, investigators from the Chinese CDC went to the market to collect samples. Although they encountered little in the way of live wildlife, they swabbed the floors, walls and other surfaces of many stalls. They came back days later to focus on surfaces in stalls where wildlife was sold, such as a cages and carts used to move animals, and also collected samples from drains and sewers.

They performed metatranscriptomic sequencing of the samples, a technique used to obtain RNA sequences (and which can pick up DNA as well) from all organisms present in the samples – viruses, bacteria, plants, animals and humans. The Chinese CDC team, led by Liu Jun, published its data and results in 2023 in the journal Nature. However, the article left unresolved the exact identities of the animal species found in the data. The Chinese CDC shared the sequencing data on public and open repositories.

According to the latest analysis of the data, SARS-CoV-2 was present in some of the same stalls where wildlife was sold at the market. That wildlife included raccoon dogs – small foxlike animals with markings similar to raccoons – and civet cats – small carnivorous mammals related to mongooses and hyenas. In some cases, genetic material from the SARS-CoV-2 virus and these animals were found on the same swabs.

"Many of the key animal species had been cleared out before the Chinese CDC teams arrived, so we can't have direct proof that the animals were infected," said co-corresponding author Florence Débarre of the French National Centre for Scientific Research. "We are seeing the DNA and RNA ghosts of these animals in the environmental samples, and some are in stalls where SARS-CoV-2 was found, too. This is what you would expect under a scenario in which there were infected animals in the market."

'Spark in a tinderbox'

Putting wild animals with viruses in contact with humans in the heart of big cities, where population densities make it easy for these viruses to take hold, is one of the most risky things humans can do, Worobey said.

"Not all of those viruses have the potential to start a pandemic, but when you do bring them in, it's like a spark in a tinderbox," he said.

The researchers also performed evolutionary analysis of the earliest viral genomes reported in the pandemic. The results imply that there were very few, if any, humans infected prior to the market outbreak. This is consistent with spillovers from animals to humans within the market, then subsequent spread throughout Wuhan and, eventually, the whole world, Worobey said.

While the data cannot prove whether one or more of these animals were infected, the analyses provide a clear list of the species that most likely could have carried the virus.

The study also presents the most complete record of animal species and specific populations within those species that could have acted as intermediate hosts at the market, Worobey said.

"It gives us clues about the populations that were represented there for each species," he said. "Where in Southeast Asia did they live? Where might they have come from? How many were farmed versus wild-caught and then moved into the transportation networks of illegal wildlife?"

Although there has been an increased focus on lab safety since the pandemic began more than four years ago, Worobey says "surprisingly little has been done to decrease the risk of a virus jumping from wildlife into humans again."

"We need to start putting the evidence of how this pandemic started into action by taking serious, concrete action to stop the perilous practice of bringing live animals with potential pandemic pathogens into densely populated urban areas," he said.

Michael Worobey, one of three co-corresponding authors on the paper, heads the Department of Ecology and Evolutionary Biology at the University of Arizona. 

Credit

Beatriz Verdugo/University of Arizona

Journal

Cell

DOI

10.1016/j.cell.2024.08.010 

Method of Research

Data/statistical analysis

Subject of Research

Animals

Article Title

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Article Publication Date

19-Sep-2024

Genetic tracing at the Huanan Seafood market further supports COVID animal origins

Cell Press

A new international collaborative study provides a list of the wildlife species present at the market from which SARS-CoV-2, the virus responsible for the COVID-19 pandemic, most likely arose in late 2019. The study is based on a new analysis of metatranscriptomic data released by the Chinese Center for Disease Control and Prevention (CDC). The data come from more than 800 samples collected in and around the Huanan Seafood Wholesale market beginning on January 1, 2020, and from viral genomes reported from early COVID-19 patients. The research appears September 19 in the journal Cell.

“This is one of the most important datasets that exists on the origin of the COVID-19 pandemic,” says co-corresponding author Florence Débarre of the French National Centre for Scientific Research (CNRS). “We’re extremely grateful that the data exist and were shared.”

“This paper adds another layer to the accumulating evidence that all points to the same scenario: that infected animals were introduced into the market in mid- to late November 2019, which sparked the pandemic,” says co-corresponding author Kristian Andersen of Scripps Research.

“We have analyzed, in new and rigorous ways, the vitally important data that the Chinese CDC team collected,” says co-corresponding author Michael Worobey of the University of Arizona. “This is an authoritative analysis of that data and how it fits in with the rest of the huge body of evidence we have about how the pandemic started.”

On January 1, 2020, after the animals were removed and just hours after the market was closed, investigators from the Chinese CDC went to the market to collect samples. They swabbed the floors, walls, and other surfaces of the stalls; they came back days later to focus on surfaces in stalls selling wildlife, such as a cage and carts used to move animals, and then also collected samples from the drains and sewers.

They performed metatranscriptomic sequencing of the samples, a technique aiming to obtain all RNA sequences (and which can pick up DNA as well) from all organisms present in the samples—viruses, bacteria, plants, animals, humans. The Chinese CDC team, led by Liu Jun, published their data and results in 2023 in the journal Nature. However, the article left unresolved the exact identities of the animal species found in the data that could represent plausible intermediate hosts. The Chinese CDC shared their sequencing data on public and open repositories.

According to the latest analysis of these data being published in Cell, SARS-CoV-2 was present in some of the same stalls as wildlife sold at the market—including raccoon dogs (small fox-like animals with markings similar to raccoons) and civet cats (small carnivorous mammals related to mongooses and hyenas). In some cases, genetic material from the SARS-CoV-2 virus and these animals was even found on the same swabs. The exact animal species were identified by genotyping their mitochondrial genomes in the samples.

“Many of the key animal species had been cleared out before the Chinese CDC teams arrived, so we can’t have direct proof that the animals were infected,” Débarre says. “We are seeing the DNA and RNA ghosts of these animals in the environmental samples, and some are in stalls where SARS-CoV-2 was found too. This is what you would expect under a scenario in which there were infected animals in the market.”

“These are the same sorts of animals that we know facilitated the original SARS coronavirus jumping into humans in 2002,” Worobey adds. “This is the most risky thing we can do—take wild animals that are teeming with viruses and then play with fire by bringing them into contact with humans living in the heart of big cities, whose population densities make it easy for these viruses to take hold.”

The international team also performed evolutionary analysis of the earliest viral genomes reported in the pandemic, including these environmental sequences, and inferred the most likely progenitor genotypes of the virus that infected humans and led to the COVID-19 pandemic. The results imply that there were very few, if any, humans infected prior to the market outbreak. This is consistent with spillovers from animals to humans within the market. There may also have been spillovers of limited impact in the immediate upstream animal trade.

“In this paper, we show that the sequences linked to the market are consistent with a market emergence,” Débarre says. “The main diversity of SARS-CoV-2 was in the market from the very beginning.”

The new study landed on a short list of animal species in the wet market found co-occurring or close to viral samples that could represent the most likely intermediate hosts for SARS-CoV-2. The common raccoon dog, a species susceptible to SARS-CoV-2 and that carried SARS-CoV in 2003, was found to be the most genetically abundant animal in the samples from market wildlife stalls. Genetic material from masked palm civets, which were also associated with the earlier outbreak of SARS-CoV, was also found in a stall with SARS-CoV-2 RNA. Other species such as the Hoary bamboo rat and Malayan porcupines were also found to be present in SARS-CoV-2-positive samples, as well as a multitude of other species.

While the data cannot prove whether one or more of these animals may have been infected, the team’s analyses provide a clear list of the species that most plausibly could have carried the virus and genetic information that could be used to help trace where they originated.

The investigators stress the importance of understanding the origins of the COVID-19 pandemic, especially in light of other recent spillovers, such as the spread of avian flu viruses in cattle in the United States. “There has been a lot of disinformation and misinformation about where SARS-CoV-2 originated,” Worobey says. “The reason it’s so important to find out is that this affects national security and public health, not just in the United States but around the world. And the truth is, since the pandemic started more than four years ago, although there has been an increased focus on lab safety, not much has been done to decrease the chance of a zoonotic scenario like this happening again.”

###

Funding information can be found in the text of the paper.

Cell, Crits-Christoph et al. “Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic” https://cell.com/cell/fulltext/S0092-8674(24)00901-2

Cell (@CellCellPress), the flagship journal of Cell Press, is a bimonthly journal that publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology, molecular biology, neuroscience, immunology, virology and microbiology, cancer, human genetics, systems biology, signaling, and disease mechanisms and therapeutics. Visit http://www.cell.com/cell. To receive Cell Press media alerts, contact press@cell.com.

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Journal

Cell

DOI

10.1016/j.cell.2024.08.010 

Method of Research

Data/statistical analysis

Subject of Research

Not applicable

Article Title

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Article Publication Date

19-Sep-2024

 BILLIONAIRES BY ANY OTHER NAME

National Academies add philanthropists to their long-standing brain trust of government, university, and industry leaders

National Academies of Sciences, Engineering, and Medicine

Sept. 18, 2024

FOR IMMEDIATE RELEASE

National Academies Add Philanthropists to Their Long-Standing Brain Trust of Government, University, and Industry Leaders

WASHINGTON — The National Academies of Sciences, Engineering, and Medicine’s Government-University-Industry Research Roundtable (GUIRR) — a forum for leaders to discuss the U.S. scientific research enterprise — has announced the inclusion of philanthropy leadership in the long-standing group. The roundtable’s new name is the Government-University-Industry-Philanthropy Research Roundtable (GUIPRR).

“When GUIRR was formed in 1984, it was lauded as being ahead of its time by identifying the need for government, universities, and industry institutions to liaise and develop innovative partnerships,” said Marcia McNutt, president of the National Academy of Sciences. “We are following this same trailblazing path by formally recognizing the role philanthropy will play in building innovation and the future U.S. research ecosystem.”

Funding for basic science and applied research is critical to scientists and researchers as well as the public. Scientific innovation drives advancements that improve quality of life, such as medical breakthroughs. It fosters economic growth by creating new industries and job opportunities while also exploring unique pathways to address challenges. Supporting basic science and applied research also encourages a culture of curiosity and learning, empowering individuals to contribute to, and benefit from, societal progress. Philanthropic funding for scientific research has increased significantly, doubling in the past 70 years through support of higher education and nonprofit institutions.

“Philanthropic investment provides new models for advancing research from the bench to the market, balancing risk-taking and societal needs,” said France Córdova, president of the Science Philanthropy Alliance and GUIPRR Council member. “We have seen philanthropists’ interest in funding science increase, and they have an undeniable role in shaping the U.S. scientific enterprise. Philanthropy can make bets on discoveries that will benefit society, perhaps far in the future, and it can scale that support through partnerships with other private and public funders. Philanthropists will bring great insights and different perspectives to the roundtable.”

GUIPRR is charged with improving the nation’s research enterprise by resolving cross-sector issues that prevent the U.S. research community from reaching its full potential. This mission is achieved by convening senior-most representatives from government, universities, industry, and philanthropy to frame the critical issues, followed by — when appropriate — the execution of activities designed to address specific impediments to achieving a healthy, vibrant research enterprise. The roundtable is led by GUIPRR Council co-chairs Darryll Pines and Danelle Merfeld, and convenes its 60 members three times a year with outside experts to explore unique perspectives and promote cross-sector dialogue on how to build new collaborations and work more effectively to enhance the competitiveness and effectiveness of U.S. science and technology and its application to national goals.

“Philanthropy represents a major funding source for the high-risk, high-reward research needed to keep our research and innovation ecosystem productive and competitive into the future,” said Michael W. Nestor, the National Academies’ board director for GUIPRR. “We are thrilled with this new direction and look forward to valuable discussions and collective action to keep our scientific enterprise vibrant.”

The National Academies of Sciences, Engineering, and Medicine are private, nonprofit institutions that provide independent, objective analysis and advice to the nation to solve complex problems and inform public policy decisions related to science, engineering, and medicine. They operate under an 1863 congressional charter to the National Academy of Sciences, signed by President Lincoln.

 

AI model can reveal the structures of crystalline materials

By analyzing X-ray crystallography data, the model could help researchers develop new materials for many applications, including batteries and magnets.

Massachusetts Institute of Technology

For more than 100 years, scientists have been using X-ray crystallography to determine the structure of crystalline materials such as metals, rocks, and ceramics.

This technique works best when the crystal is intact, but in many cases, scientists have only a powdered version of the material, which contains random fragments of the crystal. This makes it more challenging to piece together the overall structure.

MIT chemists have now come up with a new generative AI model that can make it much easier to determine the structures of these powdered crystals. The prediction model could help researchers characterize materials for use in batteries, magnets, and many other applications. 

“Structure is the first thing that you need to know for any material. It's important for superconductivity, it's important for magnets, it's important for knowing what photovoltaic you created. It's important for any application that you can think of which is materials-centric,” says Danna Freedman, the Frederick George Keyes Professor of Chemistry at MIT.

Freedman and Jure Leskovec, a professor of computer science at Stanford University, are the senior authors of the new study, which appears in the Journal of the American Chemical Society. MIT graduate student Eric Riesel and Yale University undergraduate Tsach Mackey are the lead authors of the paper.

Distinctive patterns

Crystalline materials, which include metals and most other inorganic solid materials, are made of lattices that consist of many identical, repeating units. These units can be thought of as “boxes” with a distinctive shape and size, with atoms arranged precisely within them.

When X-rays are beamed at these lattices, they diffract off atoms with different angles and intensities, revealing information about the positions of the atoms and the bonds between them. Since the early 1900s, this technique has been used to analyze materials, including biological molecules that have a crystalline structure, such as DNA and some proteins.

For materials that exist only as a powdered crystal, solving these structures becomes much more difficult because the fragments don’t carry the full 3D structure of the original crystal.

“The precise lattice still exists, because what we call a powder is really a collection of microcrystals. So, you have the same lattice as a large crystal, but they’re in a fully randomized orientation,” Freedman says.

For thousands of these materials, X-ray diffraction patterns exist but remain unsolved. To try to crack the structures of these materials, Freedman and her colleagues trained a machine-learning model on data from a database called the Materials Project, which contains more than 150,000 materials. First, they fed tens of thousands of these materials into an existing model that can simulate what the X-ray diffraction patterns would look like. Then, they used those patterns to train their AI model, which they call Crystalyze, to predict structures based on the X-ray patterns.

The model breaks the process of predicting structures into several subtasks. First, it determines the size and shape of the lattice “box” and which atoms will go into it. Then, it predicts the arrangement of atoms within the box. For each diffraction pattern, the model generates several possible structures, which can be tested by feeding the structures into a model that determines diffraction patterns for a given structure.

“Our model is generative AI, meaning that it generates something that it hasn't seen before, and that allows us to generate several different guesses,” Riesel says. “We can make a hundred guesses, and then we can predict what the powder pattern should look like for our guesses. And then if the input looks exactly like the output, then we know we got it right.”

Solving unknown structures

The researchers tested the model on several thousand simulated diffraction patterns from the Materials Project. They also tested it on more than 100 experimental diffraction patterns from the RRUFF database, which contains powdered X-ray diffraction data for nearly 14,000 natural crystalline minerals, that they had held out of the training data. On these data, the model was accurate about 67 percent of the time. Then, they began testing the model on diffraction patterns that hadn’t been solved before. This data came from the Powder Diffraction File, which contains diffraction data for more than 400,000 solved and unsolved materials.

Using their model, the researchers came up with structures for more than 100 of these previously unsolved patterns. They also used their model to discover structures for three materials that Freedman’s lab created by forcing elements that do not react at atmospheric pressure to form compounds under high pressure. This approach can be used to generate new materials that have radically different crystal structures and physical properties, even though their chemical composition is the same. 

Graphite and diamond — both made of pure carbon — are examples of such materials. The materials that Freedman has developed, which each contain bismuth and one other element, could be useful in the design of new materials for permanent magnets.

“We found a lot of new materials from existing data, and most importantly, solved three unknown structures from our lab that comprise the first new binary phases of those combinations of elements,” Freedman says.

Being able to determine the structures of powdered crystalline materials could help researchers working in nearly any materials-related field, according to the MIT team, which has posted a web interface for the model at crystalyze.org. 

The research was funded by the U.S. Department of Energy and the National Science Foundation.

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Written by Anne Trafton, MIT News

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Journal

Journal of the American Chemical Society

Article Title

"Crystal Structure Determination from Powder Diffraction Patterns with Generative Machine Learning"

 

Engineers 3D print sturdy glass bricks for building structures

The interlocking bricks, which can be repurposed many times over, can withstand similar pressures as their concrete counterparts.

Peer-Reviewed Publication

Massachusetts Institute of Technology

 

image: 

The manufactured glass bricks are assembled together in a wall configuration in Killian Court at MIT. 

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Credit: Ethan Townsend

What if construction materials could be put together and taken apart as easily as LEGO bricks? Such reconfigurable masonry would be disassembled at the end of a building’s lifetime and reassembled into a new structure, in a sustainable cycle that could supply generations of buildings using the same physical building blocks. 

That’s the idea behind circular construction, which aims to reuse and repurpose a building’s materials whenever possible, to minimize the manufacturing of new materials and reduce the construction industry’s “embodied carbon,” which refers to the greenhouse gas emissions associated with every process throughout a building’s construction, from manufacturing to demolition. 

Now MIT engineers, motivated by circular construction’s eco potential, are developing a new kind of reconfigurable masonry made from 3D-printed, recycled glass. Using a custom 3D glass printing technology provided by MIT spinoff Evenline, the team has made strong, multilayered glass bricks, each in the shape of a figure eight, that are designed to interlock, much like LEGO bricks. 

In mechanical testing, a single glass brick withstood pressures similar to that of a concrete block. As a structural demonstration, the researchers constructed a wall of interlocking glass bricks. They envision that 3D-printable glass masonry could be reused many times over as recyclable bricks for building facades and internal walls. 

“Glass is a highly recyclable material,” says Kaitlyn Becker, assistant professor of mechanical engineering at MIT. “We’re taking glass and turning it into masonry that, at the end of a structure’s life, can be disassembled and reassembled into a new structure, or can be stuck back into the printer and turned into a completely different shape. All this builds into our idea of a sustainable, circular building material.”

“Glass as a structural material kind of breaks people’s brains a little bit,” says Michael Stern, a former MIT graduate student and researcher in both MIT’s Media Lab and Lincoln Laboratory, who is also founder and director of Evenline. “We’re showing this is an opportunity to push the limits of what’s been done in architecture.”

Becker and Stern, with their colleagues, detail their glass brick design in a study appearing in the journal Glass Structures and Engineering. Their MIT co-authors include lead author Daniel Massimino and Charlotte Folinus, along with Ethan Townsend at Evenline.

Lock step

The inspiration for the new circular masonry design arose partly in MIT’s Glass Lab, where Becker and Stern, then undergraduate students, first learned the art and science of blowing glass.  

“I found the material fascinating,” says Stern, who later designed a 3D printer capable of printing molten recycled glass — a project he took on while studying in the mechanical engineering department. “I started thinking of how glass printing can find its place and do interesting things, construction being one possible route.”

Meanwhile, Becker, who accepted a faculty position at MIT, began exploring the intersection of manufacturing and design, and ways to develop new processes that enable innovative designs. 

“I get excited about expanding design and manfucaturing spaces for challenging materials with interesting characteristics, like glass and its optical properties and recyclability,” Becker says. “As long as it’s not contaminated, you can recycle glass almost infinitely.”

She and Stern teamed up to see whether and how 3D-printable glass could be made into a structural masonry unit as sturdy and stackable as traditional bricks. For their new study, the team used the Glass 3D Printer 3 (G3DP3), the latest version of Evenline’s glass printer, which pairs with a furnace to melt crushed glass bottles into a molten, printable form that the printer then deposits in layered patterns. 

The team printed prototype glass bricks using soda-lime glass that is typically used in a glassblowing studio. They incorporated two round pegs onto each printed brick, similar to the studs on a LEGO brick. Like the toy blocks, the pegs enable bricks to interlock and assemble into larger structures. Another material placed between the bricks prevent scratches or cracks between glass surfaces but can be removed if a brick structure were to be dismantled and recycled, also allowing bricks to be remelted in the printer and formed into new shapes. The team decided to make the blocks into a figure-eight shape. 

“With the figure-eight shape, we can constrain the bricks while also assembling them into walls that have some curvature,” Massimino says. 

Stepping stones

The team printed glass bricks and tested their mechanical strength in an industrial hydraulic press that squeezed the bricks until they began to fracture. The researchers found that the strongest bricks were able to hold up to pressures that are comparable to what concrete blocks can withstand. Those strongest bricks were made mostly from printed glass, with a separately manufactured interlocking feature that attached to the bottom of the brick. These results suggest that most of a masonry brick could be made from printed glass, with an interlocking feature that could be printed, cast, or separately manufactured from a different material. 

“Glass is a complicated material to work with,” Becker says. “The interlocking elements, made from a different material, showed the most promise at this stage.”

The group is looking into whether more of a brick’s interlocking feature could be made from printed glass, but doesn’t see this as a dealbreaker in moving forward to scale up the design. To demonstrate glass masonry’s potential, they constructed a curved wall of interlocking glass bricks. Next, they aim to build progressively bigger, self-supporting glass structures. 

“We have more understanding of what the material’s limits are, and how to scale,” Stern says. “We’re thinking of stepping stones to buildings, and want to start with something like a pavilion — a temporary structure that humans can interact with, and that you could then reconfigure into a second design. And you could imagine that these blocks could go through a lot of lives.”

This research was supported, in part, by the Bose Research Grant Program and MIT’s Research Support Committee.

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Written by Jennifer Chu, MIT News

Paper: “Additive Manufacturing of Interlocking Glass Masonry Units”

https://link.springer.com/article/10.1007/s40940-024-00279-8

  

The team made strong, multilayered glass bricks, each in the shape of a figure eight, that are designed to interlock, much like LEGO bricks. Pictured is a glass brick being printed with custom 3D glass printing technology. 

Credit

Ethan Townsend

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Journal

Glass Structures & Engineering

DOI

10.1007/s40940-024-00279-8 

Article Title

“Additive Manufacturing of Interlocking Glass Masonry Units”

 

What’s for dinner? Scientists unearth key clues to cuisine of resident killer whales

University of Washington

 

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A resident killer whale chasing a coho salmon to the surface. Image taken under permit.

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Credit: Candice Emmons/NOAA Fisheries

Link to release:

https://www.washington.edu/news/2024/09/19/killer-whale-cuisine/

 

A team led by researchers at the University of Washington and the National Oceanic and Atmospheric Administration has uncovered key information about what resident killer whale populations are eating. Researchers had long known that resident killer whales — also known as resident orcas — prefer to hunt fish, particularly salmon. But some populations thrive, while others have struggled. Scientists have long sought to understand the role that diet plays in these divergent fates.

“Killer whales are incredibly intelligent, and learn foraging strategies from their matriarchs, who know where to find the richest prey resources in their regions,” said Amy Van Cise, UW assistant professor of aquatic and fishery sciences, who began this study as a postdoctoral researcher with NOAA’s Northwest Fisheries Science Center. “So we wanted to know: Does all of that social learning affect diet preferences in different populations of resident killer whales, or in pods within populations?”

In a paper published Sept. 18 in the journal Royal Society Open Science, Van Cise and her colleagues report the cuisine preferences of two resident killer whale populations: the Alaska residents and the southern residents, which reside primarily in the Salish Sea and off the coast of Washington, British Columbia, Oregon and northern California. The two populations show broad preference for salmon, particularly Chinook, chum and coho. But they differ in when they switch to hunting and eating different salmon species, as well as the other fish species they pursue to supplement their diets.

Southern resident killer whales are critically endangered, while other populations are growing. This new study will inform conservation efforts for resident killer whales from northern California to the Gulf of Alaska.

”We know that lack of food is one of the main threats facing the endangered southern resident killer whales,” said Van Cise. “We figured that if we could compare their diet to the dietary habits of a healthy and growing population, it might help us better understand how we can steward and protect this vulnerable population.”

While the rivers of Alaska, British Columbia and the Pacific Northwest have historically provided resident killer whales with abundant levels of salmon, humans have recently disrupted this food supply — both directly by polluting waters and building dams that reduce salmon runs, and indirectly by generating noise pollution that interferes with hunting. In addition, in the latter half of the 20th century, resident killer whales — particularly southern residents — were captured and penned in amusement parks, which disrupted their social structure and further reduced their numbers.

This anthropogenic impact has left its mark. While Alaska resident killer whales number in the thousands and the northern resident killer whale population is growing steadily, southern resident killer whale numbers have plateaued at approximately 75 individuals. Recent research has implicated noise pollution from cargo vessels and higher rates of pregnancy failure as factors.

For this study, the team from 2011 to 2021 collected fecal samples from both southern resident and Alaska resident killer whales at various points during the year. The researchers analyzed DNA in the fecal samples to determine what the killer whales were eating. They discovered that the summer diet of Alaska residents included more chum and coho salmon, in contrast to the Chinook-heavy summer diet of a southern resident killer whale.

“Chinook are clearly an important resource for resident killer whales in any population. They’re large and energy-rich, which makes them a delicious and nutritious meal,” said Van Cise. “But what we’ve learned from the Alaska residents is that stable sources of other fishes — chum and coho salmon, even flatfishes like arrowtooth flounder — may be an important nutritional supplement helping this population thrive.”

In recent years the team has obtained more fecal samples outside of the summer months. Those samples revealed an unexpectedly diverse diet for resident killer whales. Sablefish, arrowtooth flounder, lingcod, Pacific halibut and big skate all feature in the diets of these whales, which were previously thought to eat salmon exclusively. The two populations differ in the non-salmon species they choose to supplement their diet, and when they switch among species. These dietary patterns reflect a delicate balance between regional abundance of different fish species, as well as a matriarch’s knowledge of reliable foraging locations.

“The survival of her family depends on whether the foraging sites she knows are reliable from year to year,” said Van Cise.

In both the United States and Canada, resident killer whales have gained fame, particularly the very public plight of southern residents. The team believes that their findings and follow-up dietary studies are key to aiding their recovery.

”While protecting key populations of Chinook salmon will always be vital to supporting the recovery of the endangered southern resident killer whale population, this study has taught us that we might need to think more holistically about how we can conserve the whole ecosystem of fishes that together make up the annual diet of predator populations like this one,” said Van Cise.

Co-authors on the study are M. Bradley Hanson, Candice Emmons and Kim Parsons of NOAA’s Northwest Fishery Science Center; Dan Olsen and Craig Matkin of the Alaska-based North Gulf Oceanic Society; and Abigail Wells of Lynker Technologies. The research was funded by the North Gulf Oceanic Society, the National Fish and Wildlife Federation, Shell, SeaWorld, NOAA, the Exxon Valdez Trustee Council and the U.S. Marine Mammal Commission.

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For more information, contact Van Cise at avancise@uw.edu. 

 

Related coverage from NOAA:
Sept. 19, 2024: “Comparing killer whale cuisine”

 

Related UW coverage:

Sept. 10, 2024: “Thanks to humans, Salish Sea waters are too noisy for resident orcas to hunt successfully”

March 10, 2023: “Northern and southern resident orcas hunt differently, which may help explain the decline of southern orcas”

Dec. 16, 2019: “Resident orcas’ appetite likely reason for decline of big Chinook salmon”

June 29, 2017: “Study shows high pregnancy failure in southern resident killer whales; links to nutritional stress and low salmon abundance”

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Journal

Royal Society Open Science

DOI

10.1098/rsos.240445 

Method of Research

Observational study

Subject of Research

Animals

Article Title

Spatial and seasonal foraging patterns drive diet differences among north Pacific resident killer whale populations

Article Publication Date

18-Sep-2024

 

Killing weeds and nurturing crops: sustainable agriculture at its finest

Supported by a new USDA National Institute of Food and Agriculture grant, Lehigh Univ. researcher Jonas Baltrusaitis is developing nutrient-containing biodegradable polymers for mulch films, addressing environmental challenges and improving soil health

Lehigh University

 

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Jonas Baltrusaitis, an associate professor in the Department of Chemical and Biomolecular Engineering at Lehigh University, is at the forefront of developing sustainable nutrient-delivery materials, including composite nutrient-containing degradable polymers for mulch films. His pioneering work in this area aims to create sustainable alternatives to traditional plastic mulch films, addressing significant environmental challenges in agriculture.

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Credit: Lehigh University

Weeds. Not only do they strangle your aunt’s petunias at the roots, they also have the entire agricultural industry in a $33 billion headlock.

That is the estimated annual cost of dealing with invasive plants that compete with cultivated crops for water, nutrients, light, and space.

These days, mulch films are widely used in agriculture to suppress these pesky plants, retain soil moisture, and regulate soil temperature, thereby enhancing crop yields. However, conventional plastic mulch films pose severe environmental issues, as they do not decompose and thus contribute mightily to our planet’s plastic pollution.

Jonas Baltrusaitis, an associate professor in the Department of Chemical and Biomolecular Engineering at Lehigh University, is at the forefront of developing sustainable nutrient-delivery materials, including composite nutrient-containing degradable polymers for mulch films. His pioneering work in this area aims to create sustainable alternatives to traditional plastic mulch films, addressing significant environmental challenges in agriculture.

Recently, this work has earned the support of the United States Department of Agriculture (USDA) and its National Institute of Food and Agriculture through a new multi-year research grant entitled PARTNERSHIP: Engineering Nutrient-Enhanced Mulch Film to Improve Degradation and Soil Health. The $744,000 project, which formally kicked off July 1, 2024, runs through June 30, 2028. Baltrusaitis, the lead researcher, is teaming up with colleagues from the University of Massachusetts Lowell; USDA Agricultural Research Service (ARS) in Maricopa, Arizona; and Ben Gurion University in Israel, who are contributing diverse and critical expertise to the project.

A farmer’s dream

Baltrusaitis’ research is focused on creating sustainable nutrient delivery systems by incorporating them into biodegradable polymers that can perform the same functions as traditional plastics, with an ecologically inspired twist. The films would break down naturally and safely, while adding nutrients to the soil to benefit crops.

Baltrusaitis’ team employs a multidisciplinary approach, combining expertise in sustainable chemical engineering and materials design, environmental engineering, and agricultural practices. They are designing nitrogen-efficient materials, urea cocrystals, to provide nutrients to the mulch films.

The team is collaborating with Margaret Sobkowicz-Kline, a professor in the Plastics Engineering Department at UMass Lowell, leveraging her work with biopolymers such as polylactic acid (PLA) and polyhydroxyalkanoates (PHA), which are derived from renewable resources and can decompose into nontoxic components under specific environmental conditions. Sobkowicz-Kline will combine the cocrystals with commercial bioplastics that are already suited for degradation in soil conditions, but which have unknown impacts on the longer-term soil health. Her team will create films with these bioplastic-cocrystal compounds for testing in laboratory and real agricultural environments.

“Our work with urea cocrystals that provide a convenient vehicle of nutrient delivery into degradable polymers aims to develop sustainable solutions for agricultural practices,” Baltrusaitis explains. “Traditional plastic mulch films have a detrimental impact on the environment. By developing biodegradable alternatives, we can help reduce plastic pollution, improve soil health, and promote sustainable farming practices.”

One of the key challenges Baltrusaitis and his team face is ensuring that the biodegradable mulch films maintain their structural integrity and effectiveness throughout the growing season. To address this, they are investigating various formulations and processing techniques to enhance the durability and performance of the bioplastics. This involves rigorous testing under different soil and climate conditions to ensure that the films meet the practical needs of farmers while decomposing effectively after use.

“We are constantly refining our formulations to strike the right balance between durability and biodegradability,” he says. “It’s crucial that the films remain effective throughout the crop cycle and then degrade without leaving harmful residues. This requires a deep understanding of both material science and agricultural needs.”

In addition to the technical aspects, Baltrusaitis is also focused on the economic viability of biodegradable mulch films. Traditional plastic films are relatively inexpensive, and transitioning to biodegradable alternatives must be cost-effective for widespread adoption. His team is working on optimizing production processes and sourcing sustainable raw materials to make the biodegradable films competitive in the market.

Baltrusaitis emphasizes the broader implications of his research. “Sustainability in agriculture is not just about protecting the environment; it’s also about ensuring economic viability for farmers,” he notes. “Our goal is to develop solutions that are affordable and practical, so farmers can adopt them without compromising their livelihoods.”

Baltrusaitis’ work has garnered attention and support from various stakeholders, including environmental groups, agricultural communities, and policymakers. His research aligns with global efforts to promote sustainable agriculture and reduce plastic pollution, making it highly relevant in today’s context of increasing environmental awareness.

Looking ahead, Baltrusaitis is optimistic about the potential impact of his research. “We are making significant strides in developing nutrient-containing biodegradable mulch films that can transform agricultural practices,” he said. “The ultimate success of our work lies in its adoption by farmers and its contribution to a more sustainable agricultural system. I am excited about the future and the positive changes we can bring about to create a more sustainable and resilient future.”

About Jonas Baltrusaitis

Jonas Baltrusaitis is an associate professor of chemical and biomolecular engineering in Lehigh University’s P.C. Rossin College of Engineering and Applied Science. Baltrusaitis conducts groundbreaking research in catalysis, clean energy, and sustainable agriculture and has dedicated his career to addressing pressing environmental challenges through innovative engineering solutions.

At Lehigh, Baltrusaitis leads a dynamic research group centered around catalysis and nanoengineering for a wide variety of environmentally friendly applications. His work is characterized by a multidisciplinary approach, integrating principles of chemistry, materials science, and environmental engineering. He collaborates extensively with industry partners and academic institutions to translate his research into practical applications.

In addition to his research, Baltrusaitis is a dedicated educator, and serves as Lehigh’s director of distance education in chemical engineering. He also serves as editor-in chief of the new academic journal Sustainability in Science and Technology from IOP Publishing.

Related Links: 

• Faculty Profile: Jonas Baltrusaitis
• USDA grant abstract: "PARTNERSHIP: Engineering Nutrient-Enhanced Mulch Film to Improve Degradation and Soil Health"
• USDA National Institute of Food and Agriculture
• UMass Lowell: Margaret Sobkowicz-Kline

 

PTSD symptoms can be reduced through treatment including a video game

Uppsala University

 

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Illustration Mental Image and video games

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Credit: Michael Watson

A single treatment session, which includes the video game Tetris, can reduce symptoms of post-traumatic stress disorder (PTSD). This has been shown in a new study carried out with healthcare professionals working during the COVID-19 pandemic. The study is led by researchers at Uppsala University and is published in BMC Medicine.

“It is possible to reduce the frequence of unpleasant and intrusive memories of trauma, and thereby also alleviate other PTSD symptoms. With just one guided treatment session, we saw positive effects that persisted after five weeks and even six months after treatment. Trauma can affect anyone. If this effect can be achieved with an everyday tool that includes video gaming, it could be an accessible way to help many people,” explains Emily Holmes, Professor at Uppsala University who led the study.

The hallmark symptom of PTSD is unpleasant and intrusive memories of a traumatic event in the form of mental images – typically known as flashbacks. Other symptoms may include avoidance, excessive tension and problems such as difficulty sleeping and concentrating. Holmes and her colleagues have been researching how to prevent PTSD for a long time. In the current study, the researchers focused on getting rid of flashbacks. By replacing intrusive memories using a visual task, other PTSD symptoms can also be reduced.  

Mental rotation using Tetris

The treatment is based on what is known as mental rotation, which lies at the heart of Tetris. When you look at an object from one angle, you can imagine what it would look like if it were rotated to a different position and could be seen from a different angle.

The study involved 164 participants (see fact box). All participants monitored their intrusive memories of trauma for a week. After that they were randomised to one of two conditions. Half the group were asked to play Tetris with mental rotation. The other half, the control group, was given a non-visual task: listening to the radio. All participants kept a diary about their flashbacks. At the start of the study, participants were experiencing an average of 15 flashbacks a week. At a five-week follow-up, participants in the control group had an average of five episodes a week, but those in the gaming group had an average of just one.

At a follow-up six months after treatment, participants in the gamling group had less severe symptoms of PTSD. In an assessment using a recognised questionnaire (PCL-5) often used to assess all PTSD symptoms, the gaming group experienced around half as many as problems as the control group.

 “It was surprising to us that the treatment method was so effective and that the improvement in symptoms lasted for six months. I realise that it may seem unlikely that such a short intervention, which includes video games but doesn’t include an in-depth discussion of trauma with a therapist, could help. But the study provides scientifically controlled evidence that a single guided digital treatment session can reduce the number of intrusive memories, and that it can be used safely by participants,” she continues.

“Cognitive vaccination”

“My vision is that one day we will be able to provide a tool for people such as healthcare professionals after traumatic events to  help prevent and treat early PTSD symptoms,that is  a 'cognitive vaccine', in a similar way that we currently vaccinate against some infectious physical diseases” explains Holmes.

The research was conducted in collaboration with colleagues at Uppsala Clinical Research and Karolinska Trials Alliance, Karolinska Institutet, Karolinska University Hospital, Dalarna University, Sophiahemmet University, Ambulance Services in Region Västerbotten, the University of Münster (Germany), P1Vital (UK) and the University of New South Wales, UNSW (Australia). 

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Journal

BMC Medicine

DOI

10.1186/s12916-024-03569-8 

Method of Research

Randomized controlled/clinical trial

Subject of Research

People

Article Title

’A guided single session intervention to reduce intrusive memories of work-related trauma: a randomised controlled trial with healthcare workers in the COVID-19 pandemic’

Article Publication Date

19-Sep-2024