According to the researchers, Pennsylvania’s ruffed grouse populations have declined by up to 70% since the early 1960s, with birds in the southern part of the state particularly affected by West Nile virus, which is spread by mosquitoes, and by habitat fragmentation due to development.

“By all typical metrics, the ruffed grouse is in a state of rapid decline,” said Julian Avery, associate research professor of wildlife conservation at Penn State and co-author of the paper. “Yet, until now, no one had used genetic tools to investigate the effects of this decline at a deeper level. By applying whole-genome sequencing, we have found that the bird is genetically better off than we suspected, which means that habitat protection and other management interventions can work to protect this species.”

Leilton Luna, postdoctoral researcher at Penn State and corresponding author of the paper, explained that when an organism’s population size drops too low because of disease or habitat loss, inbreeding can occur, which can lead to a decline in genetic diversity over time.

“Populations with low genetic diversity have a harder time evolving in response to changing environmental conditions and are at greater risk of extinction,” Luna said. “In the case of the Pennsylvania ruffed grouse, due to the sharp population decline, it certainly doesn’t have the same healthy genetic conditions as it did in the past. Even so, the current levels of genetic diversity and connectivity give us great hope for the preservation of this species.”

As an initial step, the team produced the first high-quality reference genome for ruffed grouse. A reference genome, Luna said, is a representative example of a particular organism’s genes.

“This reference genome serves as a standardized genetic baseline, facilitating accurate comparisons of genome-wide diversity between individuals and populations,” Luna said. “Additionally, this genomic resource will enable us to investigate important questions, such as whether specific genetic components, like adapted genes, contribute to varying population responses to West Nile virus in different ruffed grouse populations.”

To investigate the population health of the ruffed grouse in Pennsylvania, the research team sequenced 54 individual bird genomes within habitats that were both fragmented by development and intact. The researchers examined the sequence data for evidence of gene flow, which indicates that genetic material is readily exchanged among migrating populations.

“We compared each individual to every other individual that we sampled,” Luna said. “By doing this, we were able to tell if the birds all belong to a single geographic population or to different populations, as well as how environmental factors such as habitat fragmentation and terrain elevation shape the effective dispersal of birds and, therefore, the exchange of genes.”

He said the team’s DNA analysis provided weak evidence of population subdivision across the state, although the researchers identified reduced genetic connectivity in the south, where the bird’s habitat is fragmented by human development.

“This tells us that the population may not be doing as bad as we expected,” Luna said. “It also helped us to inform wildlife managers which areas would most benefit from the development of habitat corridors. However, it is just a snapshot of the population at this particular moment. In the future, we hope to analyze the DNA of museum specimens so we can compare the genetic diversity and connectivity of today’s populations with those from before West Nile virus was present and before the habitat was so fragmented.”

Surprisingly, the team said, it also stumbled onto the presence of two genetic “anomalies,” called chromosomal inversions. These occur when a segment of DNA breaks off and then reattaches in reverse order.

“We found chromosomal inversions within some of the individuals we sampled, and these were found in individuals from across the Commonwealth,” said co-author David Toews, assistant professor of biology at Penn State.

“The data are very clear,” he said. “There are these two large chunks of the ruffed grouse genome that are highly differentiated from the rest of the genome, and they are not associated with any obvious geographic pattern among the birds. It adds a fun ruffle to the story.”

Toews noted that chromosomal inversions previously were found in other bird species and were expressed via different plumage patterns or more aggressive behaviors, for example. He said the team does not yet know how the inversions might affect the ruffed grouse. It’s a topic the team plans to further investigate.

In the meantime, Toews said, the chromosomal inversions have important implications for conservation.

“On the surface, all ruffed grouse look fairly similar, but they actually have deep genetic differences,” he said. “In the context of conservation, it may be important to think beyond the species overall to consider protecting individuals with these genetic variations.”

Avery noted that Penn State has a long history of working with state agencies — such as the Pennsylvania Game Commission, Pennsylvania Fish and Boat Commission and Pennsylvania Department of Conservation and Natural Resources — to collect and analyze scientific data that can help inform conservation strategies. He said the team’s findings suggest that certain management interventions may help the bird to maintain healthy populations. These include:

• Creating and maintaining habitats that functionally connect forested regions and populations
• Evaluating the impact of hunting to ensure harvest is not contributing to the decline of more vulnerable populations
• Implementing periodic genetic monitoring to track changes and assess whether habitat interventions lead to positive genetic changes

“Not only do ruffed grouse play an important role in the ecosystem, but they are also really interesting,” Avery said. “The males make this drumming sound in the spring to attract mates. You can physically feel the bass when they’re drumming in the woods. They also pair the drumming with a flashy display of ornamental feathers and a spread tail, similar to the over-the-top performance of a male peacock. To top it off, during the fall, ruffed grouse grow these fascinating extensions of their toe scales that may help to increase surface area during the winter months. They’re just beautiful and bizarre, and they deserve our conservation attention.”

Other authors on the paper include Lisa Williams, wildlife biologist; Kenneth Duren, game bird section supervisor; and Reina Tyl, wildlife biologist, all at the Pennsylvania Game Commission.

The Pennsylvania Game Commission supported this research.

Known as MXene and MBene compounds, these substances are only a few atoms thick, making them two-dimensional. Because of their large surface area, the materials have the potential to absorb carbon dioxide molecules from the atmosphere, which could help reduce the harmful effects of climate change by safely sequestering carbon dioxide.

In a paper published Oct. 4 in the journal Chem, UC Riverside professor Mihri Ozkan and her co-authors explain the potential of MXenes and MBenes in carbon capture technologies.

“In this review, we conducted an exhaustive analysis and proposed strategies for the widespread implementation of these materials in large-scale applications,” said Ozkan, a climate action professor in UCR’s Electrical and Computer Engineering Department at the Bourns College of Engineering.

“Their unique properties make them excellent candidates for capturing carbon dioxide.”

According to Ozkan, these two-dimensional materials can be engineered to selectively capture carbondioxide. One of their key advantages is their high selectivity towards carbon dioxide, which can be attributed to a process called interlayer distance engineering. Additionally, the materials are mechanically stable and maintain their structural integrity even after multiple cycles of carbon capture and release.

graphic As human-caused carbon dioxide emissions continue to increase, developing carbon-capture technologies has become a top priority. It is projected that the planet’s temperature could rise by 1.5°C above pre-industrial levels within the next decade, leading to more frequent severe weather events, worsening drought, crop failures, increased levels of human migration, and political instability. These negative impacts highlight the urgent need for action to curb carbon emissions and mitigate the effects of climate change.

Scientists at Drexel University in Philadelphia, Pa., discovered MXenes and MBenes in the early 2010s. MXene is an inorganic compound made up of atomically thin layers of transition metal carbides, nitrides or carbonitrides. On the other hand, MBenes are dimensional transition metal borides made from boron. These compounds are produced through chemical etching techniques and have crystalline lattices with repeating orthorhombic and hexagonal structures.

Ozkan explained that these materials can be used in conjunction with existing technologies, such as those developed by the Swiss company Climework AS. These systems extract carbon dioxide directly from the atmosphere and sequester it for safe and long-term storage.

Before these compounds can be used in carbon capture devices, several technical issues need to be resolved, according to Ozkan. First and foremost, scientists must address the bottlenecks associated with synthesis-related challenges in large-volume production. Other obstacles to large-scale manufacturing include non-uniform mixing, temperature gradients, and problems with heat transfer, among others.

Still, these hurdles can be overcome.

A top-down approach is ideal for large-scale MXene synthesis by scaling up wet etching methods or developing new ones, according to Ozkan.

The paper’s co-authors are UCR’s Kathrine A.M. Quiros, Jordyn M. Watkins, Talyah M. Nelson, Navindra D. Singh, Mahbub Chowdhury, Thrayesh Namboodiri, Kamal R. Talluri, and Emma Yuan.

Associate Professor Manisha Pandey, Professor Michael Good, and their team from Griffith University’s Institute for Glycomics, are leading the development of a Strep A vaccine which is currently in Phase 1 clinical trials in Canada and quickly advancing to Phase 2 efficacy trials.

The team’s new preclinical research, recently published in Nature Communications, shows an experimental liposome-based vaccine approach incorporating a conserved M-protein epitope from Strep A and an immunostimulatory glycolipid (3D(6-acyl) PHAD) administered via the nasal passage, can provide long-term mucosal protection against Strep A.

Lead author Dr Victoria Ozberk said studies have shown most pathogens enter or colonise via the soft tissue in the upper respiratory tract, which is essentially the highway to the rest of the body.

“This has the potential to be a world-first as there are currently no subunit vaccines that target the upper respiratory tract due to a lack of licenced immunostimulants suitable for human use,” Dr Ozberk said.

“We demonstrated that a liposomal mucosal vaccination strategy can induce robust local protective immunity.”

Associate Professor Pandey said the team found PHAD plays an augmenting role in inducing enduring humoral and cellular immunity, which was evident for at least one-year post-vaccination.

“The longevity of immune response is a critical hallmark of successful vaccination and therefore the findings from this study are highly significant,” she said.

Professor Good said: “In the future, this vaccine platform could pave the way for other mucosal pathogens.”

Group A Streptococcus is a global human pathogen that leads to a wide range of infections from illnesses such as mild pharyngitis and impetigo to invasive diseases such as toxic shock syndrome, necrotising fasciitis, and cellulitis.

Professor Mark von Itzstein AO, Director of the Institute for Glycomics, welcomed these research findings.

“This platform provides a real shot at developing a new direction for vaccine discovery against significant infectious pathogens that cause serious and life-threatening diseases,” he said.

Immunity to Strep A takes several years to develop, and currently, there is no vaccine available.

Moreover, repeated infections can lead to the post-streptococcal sequelae of rheumatic fever and rheumatic heart disease, for which the Australian Indigenous population bears the highest disease burden globally.

Strep A causes 700 million human infections each year and there are more than 500,000 deaths globally.

The team has developed a Strep A vaccine which is currently being tested in a human clinical trial in Canada.

The paper ‘A Glycolipidated-liposomal peptide vaccine confers long-term mucosal protection against Streptococcus pyogenes via IL-17, macrophages and neutrophils’ has been published in Nature Communications.

The team of University of Illinois and Princeton University researchers created a cost-effective, end-to-end pipeline for this valuable organic acid by engineering a tough, acid-tolerant yeast as the fermenting agent, avoiding costly steps in downstream processing. Succinic acid is a widely used additive for food and beverages and has diverse applications in agricultural and pharmaceutical products.

This same pipeline can be used to produce other industrially important organic acids targeted by CABBI in its work to develop sustainable biofuels and biochemicals from crops, said co-author Huimin Zhao, CABBI’s Conversion Theme Leader and Professor of Chemical and Biomolecular Engineering (ChBE) at Illinois. To reduce reliance on fossil fuels, Conversion researchers are deploying microbes to convert plant biomass into chemicals used in everyday products as an alternative to conventional petroleum-based production.

“This will serve as a blueprint for all the other metabolic engineering products in CABBI,” said Zhao, one of several CABBI principal investigators on the project. Other PIs included Vijay Singh, CABBI’s Deputy Director for Science & Technology, Distinguished and Founder Professor of Agricultural and Biological Engineering (ABE), and Executive Director of the Integrated Bioprocessing Research Laboratory (IBRL) at Illinois; Jeremy Guest, Associate Professor of Civil & Environmental Engineering (CEE) at Illinois and part of CABBI’s Sustainability Theme; and Conversion Deputy Theme Leader Joshua Rabinowitz, Professor of Chemistry and the Lewis-Sigler Institute for Integrative Genomics at Princeton.

The study, published in Nature Communications, is led by CABBI — a U.S. Department of Energy Bioenergy Research Center — and funded by BioMADE, a Manufacturing Innovation Institute with more than 230 member organizations around the country, including companies, universities, and nonprofit organizations. BioMADE was catalyzed by the U.S. Department of Defense and works to secure America’s future through bioindustrial manufacturing innovation, education, and collaboration.

The work builds on years of research on succinic acid production by Zhao and his colleagues using Issatchenkia orientalis, an unconventional yeast ideal for making organic acids.

I. orientalis has the unique ability to thrive in low-pH, or acidic, conditions. Most organisms require a neutral pH environment to survive, including Saccharomyces cerevisiae, a more conventional yeast, or Escherichia coli bacteria. Both have been used by companies and labs to produce succinic acid but proved to be too costly, so efforts to scale up production have failed, Zhao said.

Those microorganisms require the addition of a base to neutralize the toxic acidic conditions so they can continue making succinic acid. But that generates side products, such as gypsum or calcium sulfate, which have to be separated out at the end of the pipeline to purify the product, driving up downstream processing costs.

“One of the bottlenecks in the production of organic acids is the separation cost,” Zhao said. “We have to add a lot of base to keep the pH near neutral, between 6 to 7.”

With I. orientalis, however, “the organism lives happily at a pH of 3 to 4,” so the additives are not required, Zhao said. “In the end, that significantly reduces costs.”

The CABBI researchers also did extensive metabolic engineering to rewire I. orientalis to produce robust levels of succinic acid — higher than either S. cerevisiae or E. coli, he said. Using metabolic flux analysis from Rabinowitz’s lab, they identified the steps in the yeast’s metabolism that limited the production of succinic acid. One key roadblock: Native I. orientalis can’t utilize the sucrose from sugarcane. So an enzyme was added that could break down sucrose from the sugarcane juice into glucose and fructose to make succinic acid. Other genes were introduced to overproduce succinic acid.

Working with Singh’s group at IBRL, the team then scaled up succinic acid production using industrially relevant equipment to conduct an end-to-end integration of the process. The pilot-scale work showed the new strains could produce up to 110 g/L of succinic acid and, after batch fermentation and downstream processing, an overall yield of 64% — impressive results having commercial significance, Singh said.

The combination of higher production levels through genetic engineering and lower costs from the elimination of downstream separation makes the process “very attractive,” Zhao said. “That’s why the pipeline is so economical, at least at this pilot scale.”

The final step was working with Guest to simulate a full end-to-end, low-pH succinic acid production pipeline, using the open-source software platform BioSTEAM developed by his group. The techno-economic analysis (TEA) and life cycle assessment showed the process was financially viable and could reduce greenhouse gas emissions by 34% to 90% relative to fossil fuel-based production processes.

“These advancements in metabolic engineering could have large-scale benefits, simultaneously driving down costs and environmental impacts in support of a circular bioeconomy,” Guest said.

The process emits less carbon dioxide (CO₂) than conventional petroleum-based chemical processing. Plants like sugarcane also soak up carbon, and CO₂ can be used as a substrate for the process, further reducing its carbon footprint.

“It’s definitely more environmentally friendly. That’s the premise for all the research in CABBI: using renewable resources to make chemicals and fuels,” Zhao said.

Researchers plan further scale-up studies soon to support commercialization of the succinic acid production process.

The work will also be a template for production of other CABBI products using I. orientalis, including 3-hydroxypropionic acid (3-HP). The market for 3-HP, used in components of disposable diapers and sealants, exceeds $1 billion, and research to date shows huge promise, Zhao said.

“We expect I. orientalis can serve as a general industrial platform for the production of a wide variety of organic acids,” said Vinh Tran, primary author on the paper and a Ph.D. student in ChBE.

The project involved several lab groups and contributions from all three themes of CABBI’s research — using sugarcane juice from the Feedstock Production research team, metabolic research and bioprocessing facilities from the Conversion team, and economic and environmental analysis from the Sustainability team.

Co-authors included CABBI researchers Sarang Bhagwat of CEE and Yihui Shen of the Department of Chemistry at Princeton; Somesh Mishra of ABE; Saman Shafaei, Shih-I Tan, Zia Fatma, and Benjamin Crosly of ChBE; and Jayne Allen of CEE.

That’s the assertion made by an international group of scientists in one of four related research papers, all appearing in the journal Science Open: Airbursts and Cratering Impacts. The papers are the latest results in the investigation of the Younger Dryas Impact Hypothesis, the idea that an anomalous cooling of the Earth almost 13 millennia ago was the result of a cosmic impact.

“In this general region, there was a change from more humid conditions that were forested and with diverse sources of food for hunter-gatherers, to drier, cooler conditions when they could no longer subsist only as hunter-gatherers,” said Earth scientist James Kennett, a professor emeritus of UC Santa Barbara . The settlement at Abu Hureyra is famous among archaeologists for its evidence of the earliest known transition from foraging to farming. “The villagers started to cultivate barley, wheat and legumes,” he noted. “This is what the evidence clearly shows.”

These days, Abu Hureyra and its rich archaeological record lie under Lake Assad, a reservoir created by construction of the Taqba Dam on the Euphrates River in the 1970s. But before this flood, archaeologists managed to extract loads of material to study. “The village occupants,” the researchers state in the paper, “left an abundant and continuous record of seeds, legumes and other foods.” By studying these layers of remains, the scientists were able to discern the types of plants that were being collected in the warmer, humid days before the climate changed and in the cooler, drier days after the onset of what we know now as the Younger Dryas cool period.

Before the impact, the researchers found, the inhabitants’ prehistoric diet involved wild legumes and wild-type grains, and “small but significant amounts of wild fruits and berries.” In the layers corresponding to the time after cooling, fruits and berries disappeared and their diet shifted toward more domestic-type grains and lentils, as the people experimented with early cultivation methods. By about 1,000 years later, all of the Neolithic “founder crops” — emmer wheat, einkorn wheat, hulled barley, rye, peas, lentils, bitter vetch, chickpeas and flax — were being cultivated in what is now called the Fertile Crescent. Drought-resistant plants, both edible and inedible, become more prominent in the record as well, reflecting a drier climate that followed the sudden impact winter at the onset of the Younger Dryas.

The evidence also indicates a significant drop in the area’s population, and changes in the settlement’s architecture to reflect a more agrarian lifestyle, including the initial penning of livestock and other markers of animal domestication.

To be clear, Kennett said, agriculture eventually arose in several places on Earth in the Neolithic Era, but it arose first in the Levant (present-day Syria, Jordan, Lebanon, Palestine, Israel and parts of Turkey) initiated by the severe climate conditions that followed the impact.

And what an impact it must have been.

In the 12,800-year-old layers corresponding to the shift between hunting and gathering and agriculture, the record at Abu Hureyra shows evidence of massive burning. The evidence includes a carbon-rich “black mat” layer with high concentrations of platinum, nanodiamonds and tiny metallic spherules that could only have been formed under extremely high temperatures — higher than any that could have been produced by man’s technology at the time. The airburst flattened trees and straw huts, splashing meltglass onto cereals and grains, as well as on the early buildings, tools and animal bones found in the mound — and most likely on people, too.

This event is not the only such evidence of a cosmic airburst on a human settlement. The authors previously reported a smaller but similar event which destroyed the biblical city at Tall el-Hammam in the Jordan Valley about 1600 BCE.

The black mat layer, nanodiamonds and melted minerals have also been found at about 50 other sites across North and South America and Europe, the collection of which has been called the Younger Dryas strewnfield. According to the researchers, it’s evidence of a widespread simultaneous destructive event, consistent with a fragmented comet that slammed into the Earth’s atmosphere. The explosions, fires and subsequent impact winter, they say, caused the extinction of most large animals, including the mammoths, saber-toothed cats, American horses, and American camels, as well as the collapse of the North American Clovis culture.

Because the impact appears to have produced an aerial explosion there is no evidence of craters in the ground. “But a crater is not required,” Kennett said. “Many accepted impacts have no visible crater.” The scientists continue to compile evidence of relatively lower-pressure cosmic explosions — the kind that occur when the shockwave originates in the air and travels downward to the Earth’s surface.

“Shocked quartz is well known and is probably the most robust proxy for a cosmic impact,” he continued. Only forces on par with cosmic-level explosions could have produced the microscopic deformations within quartz sand grains at the time of the impacts, and these deformations have been found in abundance in the minerals gathered from impact craters.

This “crème de la crème” of cosmic impact evidence has also been identified at Abu Hureyra and at other Younger Dryas Boundary (YDB) sites, despite an absence of craters. However, it has been argued that the kind of shock-fractured quartz found in the YDB sites is not equivalent to that found in the large crater-forming sites, so the researchers worked to link these deformations to lower-pressure cosmic events.

To do so, they turned to humanmade explosions of the magnitude of cosmic airbursts: nuclear tests conducted at the Alamogordo Bombing Range in New Mexico in 1945 and in Kazakhstan, in 1949 and 1953. Similar to cosmic airbursts, the nuclear explosions occurred above ground, sending shockwaves toward Earth.

“In the papers, we characterize what the morphologies are of these shock fractures in these lower-pressure events,” Kennett said. “And we did this because we wanted to compare it with what we have in the shock-fractured quartz in the Younger Dryas Boundary, to see if there was any comparison or similarities between what we see at the Trinity atomic test site and other atomic bomb explosions.” Between the shocked quartz at the nuclear test sites and the quartz found at Abu Hureyra, the scientists found close associations in their characteristics, namely glass-filled shock fractures, indicative of temperatures greater than 2,000 degrees Celsius, above the melting point of quartz.

“For the first time, we propose that shock metamorphism in quartz grains exposed to an atomic detonation is essentially the same as during a low-altitude, lower-pressure cosmic airburst,” Kennett said. However, the so-called “lower pressure” is still very high — probably greater than 3 GPa or about 400,000 pounds per square inch, equivalent to about five 737 airplanes stacked on a small coin. The novel protocol the researchers developed for identifying shock fractures in quartz grains will be useful in identifying previously unknown airbursts that are estimated to recur every few centuries to millennia.

Taken together, the evidence presented by these papers, according to the scientists, “implies a novel causative link among extraterrestrial impacts, hemispheric environmental and climatic change, and transformative shifts in human societies and culture, including agricultural development.”