Category: 7. Science

A team of scientists led by Prof. GAO Caixia at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, has developed two innovative genome editing platforms known as Programmable Chromosome Engineering (PCE) and RePCE. These technologies enable highly precise DNA manipulations at scales ranging from kilobases to megabases in plants and other eukaryotic cells.

Published online in Cell on August 4, the study overcomes longstanding challenges associated with the widely used Cre-Lox recombinase system, according to a press relerase. While Cre-Lox has great potential for precise chromosomal editing, its broader application has been limited by three key issues: reversible recombination due to symmetric Lox sites, the complex tetrameric structure of Cre recombinase that hampers engineering, and leftover Lox sites that reduce editing accuracy.

To address these challenges, the researchers introduced three major innovations:

• Asymmetric Lox sites: Through a high-throughput platform for recombination site modification, the team designed novel Lox variants that reduce unwanted reversible recombination by over 10-fold while maintaining high forward recombination efficiency.
• AiCErec: Leveraging an AI-informed protein engineering system, the team optimized the multimerization interface of Cre recombinase, creating a variant with 3.5 times greater recombination efficiency than the wild type.
• Re-pegRNA: Combining the precision of prime editing with recombinase technology, this scarless editing method uses specially designed pegRNAs to replace residual Lox sites with the original genomic sequence, ensuring seamless genome modifications.

The integration of these advances led to the creation of PCE and RePCE platforms that allow flexible programming of insertion sites and orientations. This enables precise, scarless manipulation of DNA fragments ranging from a few kilobases up to several megabases in both plant and animal cells. Achievements include targeted insertion of DNA fragments up to 18.8 kb, complete replacement of 5-kb sequences, chromosomal inversions spanning 12 megabases, deletions of 4 megabases, and even whole-chromosome translocations.

As a demonstration of the technology’s power, the team successfully engineered herbicide-resistant rice with a precise 315-kb chromosomal inversion, highlighting its transformative potential for genetic engineering and crop improvement.This pioneering work not only resolves the historical limitations of Cre-Lox technology but also opens new avenues for high-precision genome engineering across a broad range of organisms, promising significant advances in agric

Each spring, a grizzly bear emerges from its den after months of deep hibernation — having eaten nothing, barely moved and slowed its heart and metabolism to a crawl. Yet it wakes up strong, alert and healthy.

Its muscles remain intact. Its organs are unharmed. And any signs of metabolic stress seem to vanish as if they were never there.

What if humans had access to the same biological resilience?

That is the question scientists at the University of Utah asked, and they now believe they might have an answer. Their latest research, stemming from two studies, suggests that the genetic tool kit that enables animals like bears to survive hibernation could also exist in humans, lying dormant within their DNA. If scientists can learn to activate it, it could transform the treatment of chronic diseases like Type 2 diabetes, stroke and Alzheimer’s.

“Humans already have the genetic framework,” said Dr. Susan Steinwand, lead author in one of the studies. “We just need to identify the control switches for these hibernator traits.”

According to the research published in Science, some of the same genetic switches that enable hibernation may already exist in humans, they’ve just never been used.

“There’s potentially an opportunity — by understanding these hibernation-linked mechanisms in the genome — to find strategies to intervene and help with age-related diseases,” said Dr. Chris Gregg, senior author of the studies and professor of neurobiology and human genetics at University of Utah Health.

The DNA link

The study focused on a familiar part of the genome: the FTO locus, known as a major risk factor for obesity in humans. Surprisingly, this same region also plays a central role in hibernating animals’ ability to slow metabolism and survive extreme conditions. By instead studying the genes directly, the Utah team zoomed in on noncoding regions of DNA, specifically stretches of DNA called cis-regulatory elements, or CREs. These elements act like “dimmer switches,” controlling how much or how little nearby genes are expressed.

“What’s striking about this region is that it is the strongest genetic risk factor for human obesity,” Gregg noted.

The researchers likened finding these genetic regions to searching for needles in a “a massive DNA haystack.”

To test their effects, scientists mutated hibernator-specific DNA regions in mice and tracked the results. They saw changes in weight, metabolic rate and even the ability to regulate body temperature, responses similar to those seen in hibernating animals.

“When you knock out one of these elements — this one tiny, seemingly insignificant DNA region — the activity of hundreds of genes changes,” Steinwand said. “It’s pretty amazing.”

In fact, the regions highlighted weren’t genes at all, but control elements, similar to traffic signals directing the flow of genetic activity.

“This means that mutating a single hibernator-specific region has wide-ranging effects extending far beyond the FTO locus,” Steinwand added.

What this could mean for medicine

These findings hope to revolutionize treatments for metabolic and neurological conditions. Understanding hibernators’ metabolic flexibility could lead to better treatments for human metabolic disorders like Type 2 diabetes, the researchers say.

“If we could regulate our genes a bit more like hibernators,” said Elliott Ferris, bioinformatician at U of U Health and first author on the second study, “maybe we could overcome Type 2 diabetes the same way that a hibernator returns from hibernation back to a normal metabolic state.”

A complementary study from Oregon

Scientists at Oregon Health and Science University are also exploring ways to replicate hibernation-like states in humans. In a recent study, researchers identified a brain-based mechanism called thermoregulatory inversion, a process that allows animals to lower their core body temperature without triggering the usual warming responses like shivering or burning a specific type of fat in the body, brown fat. Essentially, it flips the body’s natural survival settings.

“The idea is to reduce the body temperature to a lower level so that tissues like the brain or heart don’t need as much oxygen,” Dr. Domenico Tupone, senior author of the OHSU study, explained. “That could improve outcomes from strokes or heart attacks.”

In typical mammals, exposure to cold triggers heat generation. But in hibernators, that response is flipped — allowing them to survive long periods with little energy use.

“If we had a mechanism that allows us to transform humans into hibernating animals,” Tupone added, “we could achieve and control therapeutic hypothermia much better.”

This could one day allow doctors to safely lower a person’s body temperature during medical emergencies like heart attacks or strokes, giving vital organs more time to survive reduced oxygen flow.

By learning how to activate or mimic these gene switches, researchers from both universities hope to unlock hibernation’s secrets — not to help sleep through winter, but to transform how diseases, injury and aging itself are treated.

“If that’s hidden in the genome that we’ve already got,” Gregg says, “we could learn from hibernators to improve our own health.”

Fraudulent scientific research is now being produced and published on a large scale, with some unethical researchers colluding with unethical editors to attain the prestige that comes with publication, according to a new study in the Proceedings of the National Academy of Sciences.

Large groups of editors and authors appear to have cooperated in what it called “the tide of fraudulent science.”

The researchers who conducted the study obtained retracted articles. They collected reports of the same image used in multiple publications. Making use of the fact that editors’ names are public at some science publishers, they looked at whether some editors handled disproportionate numbers of problematic scientific papers, ones that were later retracted or noted negatively by other scientists.

At the journal PLOS One, they were able to identify 45 editors who worked on 30.2% of retracted articles. Of these 45 editors, 25 had their own papers retracted. The 45 editors represented 0.25% of the total number of editors at the journal. PLOS One did not respond to a request for comment.

Researchers also found clusters of articles accepted in less than a month, often involving the same editors and authors.

“They found cases where people submitted papers and those papers got accepted extremely fast, and when you looked at the editors, they were just sending them to each other,” said Luís Amaral, a systems biologist at Northwestern University and senior author of the study.

“There are people who believe that there is widespread fraud,” said Reese Richardson, a postdoctoral researcher in the Amaral Lab at Northwestern and lead author of the study. “What this paper does is give a method and a starting point and the data to show that this is actually happening, and that the current mechanisms are not equipped to stop it.”

The study’s findings confirm the suspicions of many researchers, including Elisabeth Bik, a microbiologist and independent scientific integrity consultant who has spent years identifying fraudulent research.

In one case, she found 125 papers that reused parts of the same image. “It was the same photo, but different crops of the same image,” she said. “They didn’t generate the photos themselves. They got the photos from a third party — a broker, a paper mill.”

Researchers have been using the term “paper mill” to describe organizations that sell mass-produced low quality and fabricated research articles.

Many of these fraudulent papers, Bik added, seem to come from doctors or researchers in countries where promotions are tied to publication metrics. They see it as an investment, she explained, where a couple of thousand dollars gets them a paper, and a fast track up the promotional ladder.

This institutional pressure is especially common in China and India, where promotions, medical licensing or graduation are linked by policy to publication counts, several experts said. Although the “publish or perish” culture is also common in the U.S., it manifests more in expectations around prestige, funding and tenure, rather than fixed quotas.

India and China are the world’s most populous nations and both are scientific powerhouses. The paper notes that science fraud can happen anywhere.

The accumulation of fake literature has turned some scientific fields — RNA biology, for example — into what Richardson called an academic “minefield,” making it difficult for researchers to identify which studies are reliable. Some fraudulent studies have even made it into meta-analyses that shape the way doctors treat patients. They found evidence that this field of research has been targeted by bad actors.

Experts say growing awareness of fraud could feed broader skepticism of science, especially if institutional action doesn’t keep up.

“The more polluted the record becomes, the harder it is to clean up, and the harder it is to rebuild trust inside and outside the scientific community,” said Stephanie Kinnan, a longtime member of the Committee on Publication Ethics (COPE).

The scientific community has tools to fight back. It fines and excludes researchers and universities. Journals retract articles. Aggregators can sideline problematic journals. But the authors of the paper found the amount of “research” from suspected paper mills has been doubling roughly every 1½ years. The actions are not keeping up.

For Amaral, and many other scientists, the implications are deeply personal. “I dreamed of being a scientist since I was 12,” he said. “Seeing the thing that I’ve dreamt of being a part of, that I cherish, being potentially destroyed is really enraging.”

All research is built on previous research, Amaral explained. That collapses without trust.

“This is the great fear — that the entire scientific enterprise that gave us vaccines, that gave us medicine for cancer, that gave us, X-ray machines, computer scanning devices — would just disappear,” he said.

Newswise — North America has lost an estimated 3 billion birds since 1970—a nearly 30% drop across species—mostly due to habitat loss and degradation. So when a team of researchers repeated a bird population study they did 30 years earlier in a very large commercial forest landscape in Maine, they were stunned to find more birds than before.

“When we started this project, we expected to add to the pile of bad news,” says Michael Reed, a professor of biology in the School of Arts and Sciences at Tufts University and co-author of the study. “So we were very pleasantly surprised to find that, for most of the bird species in our study, things were actually looking up.”

The research team wanted to see if bird populations and habitat use had changed over the decades, particularly given a shifting forest landscape. “Forest management practices in Maine have changed significantly since the early 1990s,” says Reed. Due to social pressure, clearcutting has become much less common in Maine. Today, most logging operations remove fewer trees per acre—returning to spots every decade or so—and spread their activity across a broader area

The study, published in Biological Conservation, found that 26—or more than half—of 47 species counted by the researchers had significantly increased in numbers since the early 1990s, while populations for 13 species (or 28%) had remained stable. That’s contrary to what happened across much of the continent, with the North American Breeding Bird Survey showing that 35—or 75%—of the same species analyzed had seen their numbers decline, both regionally and continentally, for the same timeframe.

But what makes the commercial forests of Maine so different from other forests in the northern Atlantic states and North America? And can we learn anything from them to bolster bird populations regionally and nationally?

“Numerous factors are likely behind the abundance of bird populations we see in northcentral Maine,” says Reed. “We can’t know what they all are, but we know at least one: It’s all forest up there.”

The original and current study took place in a 588,000-acre commercial forest nestled within 10 million acres of commercial, public, and protected forest landscape. Together, these woodlands create the largest contiguous tract of non-developed forest east of the Mississippi. The habitat is recognized worldwide as an Important Bird Area, an area officially recognized as critical for protecting bird species and biodiversity by a coalition of international bird conservation groups.

The remote forestland is also one of the darkest places left on the East Coast. “Most bird species migrate at night, orienting by the stars,” says John Hagan, the study’s senior author and the founder and president of Our Climate Common. “So it may be when birds flying at night get tired, they look down, spot a vast patch of darkness, and decide it’s a good place to land and raise young.”

Many of the bird species observed seemed more flexible in their habitat use than previously thought; the researchers have another paper on these findings in the works. This suggests that high-quality forest next to more average forest may still be appealing enough to attract and support more birds over time. Individual birds often return to breed where they were hatched, and many migratory species are drawn to areas where others of their kind are already present. As Reed puts it, this may mean that “the rich get richer” when it comes to birds in Maine’s commercial forests.

Much of the population growth came from more birds per acre, not more habitat. “You’d expect bird numbers to go up if there’s more habitat,” says Reed. “But we actually saw increased numbers for some species whose main habitat acreage stayed the same size or even decreased from the 1990s. For example, in places where we previously counted two ovenbirds singing before, we now counted four.”

Data from one species—the golden-crowned kinglet—suggests that how forests are managed may affect species’ ability to thrive. These tiny, round songbirds are declining sharply across much of North America, including in the commercial forests of New Brunswick, Canada. But just over the border in Maine, their numbers are rising.

In Canada, commercial forests are commonly replanted in neat plantation-style rows, creating simpler forests, with less understory and trees that are all the same age. In contrast, Maine’s commercial forests rely on natural regrowth, creating denser forests with a broader mix of tree species and ages. Reed and Hagan hypothesize this more natural approach may offer better shelter or support more of the insects that kinglets need to raise their young.

Despite the widespread increases, bird numbers for 14 species—about 30%—still declined in the study area. The researchers hope to more closely examine the pressures faced by these decreasing bird species, including species like the winter wren and the Canada warbler, to see if commercial forestry could do something differently to better support them. They are particularly worried about steep declines in mature trees—some more than 200 years old—and its impact on the bird populations. Hagan is now leading additional research to assess this conservation threat. The threat could be on their migration or overwintering grounds, in which case little can be done in Maine to improve their numbers.

Even though about two-thirds of U.S. forestland is available or used to produce industrial wood products, the research team believes theirs is the first bird survey to compare species population numbers in a commercial forest over a long period of time. And given the 521 million acres of commercial U.S. forestland, they hope it certainly will not be the last.

In the face of ongoing human habitat expansion and continental declines in bird populations, the team says it’s important to understand how all types of forest ownership may help create important sanctuaries for birds. “Birds also may be thriving in commercial forests in Michigan, Wisconsin, and Minnesota, which are managed similarly to those in Maine,” Hagan says. “Hopefully, someone will look to see.”

“Many people don’t expect places where you harvest wood to serve as valuable habitat because they are cutting trees down,” adds Reed. “But nobody thinks the goal of a farm is to cut down corn—it’s to grow it. And commercial forests grow trees.”

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How to Help the Birds at Home

You may not own an acre of land—never mind hundreds of acres—but you can still bring some qualities of Maine forestland to your own yard.

• Plant a tree that is native to your area.
• Add native shrubs, which provide vital food and shelter for birds while offering multi-season visual appeal for you.
• “Leave the leaves” in the parts of your yard where you are creating understory. Nature abhors a leaf blower—and it means less yardwork and free mulch for you.
• Fight light pollution by reducing outdoor lighting to what’s truly necessary.
• Where safe to do so, leave dead trees standing. “Snags” provide valuable habitat for owls, woodpeckers, and cavity-nesting birds.
• Replace part of your lawn with native plants. Check out Douglas Tallamy’s book Nature’s Best Hope for ideas.

 

About 56 million years ago, Earth slipped into the Paleocene-Eocene Thermal Maximum (PETM), a sudden global warming pulse that pushed temperatures up by at least 5°C (9°F). In the badlands of what is now Wyoming, one mid-sized predator, Dissacus praenuntius, found itself confronting a landscape in flux.

A new study led by Rutgers University suggests the animal’s solution was unexpected: when prey became scarce, it started crunching bones.

“What happened during the PETM very much mirrors what’s happening today and what will happen in the future,” said Andrew Schwartz, the Rutgers anthropology doctoral student who led the research.

The work combines field excavations in the Bighorn Basin with a forensic technique called dental microwear texture analysis (DMTA).

By reading microscopic pits and scratches on fossil teeth, the team reconstructed what the animal was chewing in the weeks before it died; tougher, deeper marks usually point to hard items such as bone.

Dissacus praenuntius ate bones

Dissacus praenuntius was roughly the size of a modern coyote and, at first glance, looked like a lanky wolf. But it walked on tiny hooves and belonged to an archaic lineage known as mesonychids.

“They looked superficially like wolves with oversized heads,” Schwartz said, describing them as super weird mammals “Their teeth were kind of like hyenas. But they had little tiny hooves on each of their toes.”

Before the planet heated up, DMTA shows the predator had a diet which resembled that of today’s cheetahs: mostly soft but sinewy meat. Once the PETM began, everything changed.

“We found that their dental microwear looked more like that of lions and hyenas,” Schwartz said. “That suggests they were eating more brittle food, which were probably bones, because their usual prey was smaller or less available.”

The microwear evidence dovetails with other signs of environmental stress. Earlier work has shown many mammal species shrank during the PETM, and Dissacus appears to have followed that trend – smaller bodies need less food.

While scientists once blamed this shrinkage solely on heat, the new findings strengthen the case that limited nutrition was a major driver.

Adaptability drove survival success

“One of the best ways to know what’s going to happen in the future is to look back at the past,” Schwartz said. “How did animals change? How did ecosystems respond?”

For Schwartz, the PETM offers a natural experiment on how warming reshapes food webs. The lesson, he argues, is that dietary flexibility can make or break a species.

“In the short term, it’s great to be the best at what you do,” he said. “But in the long term, it’s risky. Generalists, meaning animals that are good at a lot of things, are more likely to survive when the environment changes.”

That principle is visible today. “We already see this happening,” Schwartz said. “In my earlier research, jackals in Africa started eating more bones and insects over time, probably because of habitat loss and climate stress.”

Pandas, koalas, and other extreme specialists lack that wiggle room and could therefore be more vulnerable as habitats fragment or shift.

Wyoming’s ancient badlands

To trace Dissacus praenuntius through time, the team zeroed in on the Bighorn Basin, one of the rare places where sedimentary layers preserve an almost year-by-year record across the PETM.

Field crews collected dozens of jaws and isolated teeth from successive strata, then scanned their chewing surfaces under high-resolution confocal microscopes.

Sophisticated software converted the textures into numerical values capturing roughness, complexity, and orientation – clues to the animal’s final meals.

Professor Robert Scott, a co-author on the paper, notes that DMTA is revolutionizing paleontology because it captures dietary snapshots just weeks or months before death, unlike isotope analyses that average years.

The method revealed a clear pattern: before the thermal maximum, tooth surfaces carried long, shallow scratches characteristic of slicing flesh; during and after, they showed deeper pits and gouges typical of bone fragmentation.

Dissacus praenuntius faded away

Despite this adaptive flair for bones, Dissacus praenuntius did not make it through the next 15 million years. Bigger, better-equipped carnivores eventually displaced it, and the shifting vegetation of post-PETM North America favored more agile hunters.

Still, its bone-crunching episode underscores how rapidly predators can recalibrate their behavior when climate jolts prey supply.

Schwartz hopes insights like these will aid modern conservation biology by spotlighting which species could be climate winners or losers.

The study also signals the importance of preserving continuous fossil sites: without the Bighorn Basin’s layered rocks, the dietary flip would have remained invisible.

Local fossils, global lessons

Schwartz traces his fascination with fossils to childhood trips along New Jersey’s waterways with his father, an amateur collector. Now close to completing his Ph.D., he is eager to show the broader public how deep time research can illuminate future challenges.

 “If I see a kid in a museum looking at a dinosaur, I say, ‘Hey, I’m a paleontologist. You can do this, too.’”

That encouragement matters because, as Earth barrels toward PETM-like CO₂ levels, society will need scientists who can decode past crises to steer us through the next one.

The tale of a jackal-sized mammal gnawing harder fare in a hothouse world is more than a curiosity; it is a mirror held up to our own warming century.

The study is published in the journal Palaeogeography, Palaeoclimatology, Palaeoecology

Image Credit: ДиБгд, CC BY 4.0 , via Wikimedia Commons

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