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Scientists stunned to discover plants beneath mile-deep Greenland ice: Long-lost ice core provides direct evidence that giant ice sheet melted off within the last million years and is highly vulnerable to a warming climate



Scientists stunned to discover plants beneath mile-deep Greenland ice: Long-lost ice core provides direct evidence that giant ice sheet melted off within the last million years and is highly vulnerable to a warming climate

In 1966, US Army scientists drilled down through nearly a mile of ice in northwestern Greenland — and pulled up a fifteen-foot-long tube of dirt from the bottom. Then this frozen sediment was lost in a freezer for decades. It was accidentally rediscovered in 2017.

In 2019, University of Vermont scientist Andrew Christ looked at it through his microscope — and couldn’t believe what he was seeing: twigs and leaves instead of just sand and rock. That suggested that the ice was gone in the recent geologic past — and that a vegetated landscape, perhaps a boreal forest, stood where a mile-deep ice sheet as big as Alaska stands today.Over the last year, Christ and an international team of scientists — led by Paul Bierman at UVM, Joerg Schaefer at Columbia University and Dorthe Dahl-Jensen at the University of Copenhagen — have studied these one-of-a-kind fossil plants and sediment from the bottom of Greenland. Their results show that most, or all, of Greenland must have been ice-free within the last million years, perhaps even the last few hundred-thousand years.”Ice sheets typically pulverize and destroy everything in their path,” says Christ, “but what we discovered was delicate plant structures — perfectly preserved. They’re fossils, but they look like they died yesterday. It’s a time capsule of what used to live on Greenland that we wouldn’t be able to find anywhere else.””

The discovery helps confirm a new and troubling understanding that the Greenland ice has melted off entirely during recent warm periods in Earth’s history — periods like the one we are now creating with human-caused climate change.

Understanding the Greenland Ice Sheet in the past is critical for predicting how it will respond to climate warming in the future and how quickly it will melt. Since some twenty feet of sea-level rise is tied up in Greenland’s ice, every coastal city in the world is at risk. The new study provides the strongest evidence yet that Greenland is more fragile and sensitive to climate change than previously understood — and at grave risk of irreversibly melting off.“”This is not a twenty-generation problem,” says Paul Bierman, a geoscientist at UVM in the College of Arts & Sciences, Rubenstein School of Environment & Natural Resources, and fellow in the Gund Institute for Environment. “This is an urgent problem for the next 50 years.”

The new research was published March 15 in the Proceedings of the National Academy of Sciences.


The material for the new PNAS study came from Camp Century, a Cold War military base dug inside the ice sheet far above the Arctic Circle in the 1960s. The real purpose of the camp was a super-secret effort, called Project Iceworm, to hide 600 nuclear missiles under the ice close to the Soviet Union. As cover, the Army presented the camp as a polar science station.

The military mission failed, but the science team did complete important research, including drilling a 4560-foot-deep ice core. The Camp Century scientists were focused on the ice itself — part of the burgeoning effort at the time to understand the deep history of Earth’s ice ages. They, apparently, took less interest in a bit of dirt gathered from beneath the ice core. Then, in a truly cinematic set of strange plot twists, the ice core was moved from an Army freezer to the University of Buffalo in the 1970s, to another freezer in Copenhagen, Denmark, in the 1990s, where it languished for decades — until it surfaced when the cores were being moved to a new freezer.

For much of the Pleistocene — the icy period covering the last 2.6 million years — portions of the ice on Greenland persisted even during warmer spells called “interglacials.” But most of this general story has been pieced together from indirect evidence in mud and rock that washed off the island and was gathered by offshore ocean drilling. The extent of Greenland’s ice sheet and what kinds of ecosystems existed there before the last interglacial warm period — that ended about 120,000 years ago — have been hotly debated and poorly understood.

The new study makes clear that the deep ice at Camp Century — some 75 miles inland from the coast and only 800 miles from the North Pole — entirely melted at least once within the last million years and was covered with vegetation, including moss and perhaps trees. The new research, supported by the National Science Foundation, lines up with data from two other ice cores from the center of Greenland, collected in 1990s. Sediment from the bottom of these cores also indicate that the ice sheet was gone for some time in the recent geologic past. The combination of these cores from the center of Greenland with the new insight from Camp Century in the far northwest give researchers an unprecedented view of the shifting fate of the entire Greenland ice sheet.

The team of scientists used a series of advanced analytical techniques — none of which were available to researchers fifty years ago — to probe the sediment, fossils, and the waxy coating of leaves found at the bottom of the Camp Century ice core. For example, they measured ratios of rare forms — isotopes — of both aluminum and the element beryllium that form in quartz only when the ground is exposed to the sky and can be hit by cosmic rays. These ratios gave the scientists a window onto how long rocks at the surface were exposed vs. buried under layers of ice. This analysis gives the scientists a kind of clock for measuring what was happening on Greenland in the past. Another test used rare forms of oxygen, found in the ice within the sediment, to reveal that precipitation must have fallen at much lower elevations than the height of the current ice sheet, “demonstrating ice sheet absence,” the team writes. Combining these techniques with studies of luminescence that estimate the amount of time since sediment was exposed to light, radiocarbon-dating of bits of wood in the ice, and analysis of how layers of ice and debris were arranged — allowed the team to be clear that most, if not all, of Greenland melted at least once during the past million years — making Greenland green with moss and lichen, and perhaps with spruce and fir trees.

And the new study shows that ecosystems of the past were not scoured into oblivion by ages of glaciers and ice sheets bulldozing overtop. Instead, the story of these living landscapes remains captured under the relatively young ice that formed on top of the ground, frozen in place, and holds them still.

In a 1960’s movie about Camp Century created by the Army, the narrator notes that “more than ninety percent of Greenland is permanently frozen under a polar ice cap.” This new study makes clear that it’s not as permanent as we once thought. “Our study shows that Greenland is much more sensitive to natural climate warming than we used to think — and we already know that humanity’s out-of-control warming of the planet hugely exceeds the natural rate,” says Christ.

“Greenland may seem far away,” says UVM’s Paul Bierman, “but it can quickly melt, pouring enough into the oceans that New York, Miami, Dhaka — pick your city — will go underwater.”

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Editing without ‘cutting’: Molecular mechanisms of new gene-editing tool revealed




Scientists stunned to discover plants beneath mile-deep Greenland ice: Long-lost ice core provides direct evidence that giant ice sheet melted off within the last million years and is highly vulnerable to a warming climate

Joint research led by Yutaro Shuto, Ryoya Nakagawa, and Osamu Nureki of the University of Tokyo determined the spatial structure of various processes of a novel gene-editing tool called “prime editor.” Functional analysis based on these structures also revealed how a “prime editor” could achieve reverse transcription, synthesizing DNA from RNA, without “cutting” both strands of the double helix. Clarifying these molecular mechanisms contributes greatly to designing gene-editing tools accurate enough for gene therapy treatments. The findings were published in the journal Nature.

The 2020 Nobel Prize in Chemistry was awarded to Jennifer Doudna and Emmanuelle Charpentier for developing a groundbreaking yet simple way to edit DNA, the “blueprint” of living organisms. While their discovery opened new avenues for research, the accuracy of the method and safety concerns about “cutting” both strands of DNA limited its use for gene therapy treatments. As such, research has been underway to develop tools that do not have these drawbacks.

The prime editing system is one such tool, a molecule complex consisting of two components. One component is the prime editor, which combines a SpCas9 protein, used in the first CRISPR-Cas gene editing technology, and a reverse transcriptase, an enzyme that transcribes RNA into DNA. The second component is the prime editing guide RNA (pegRNA), a modified guide RNA that identifies the target sequence within the DNA and encodes the desired edit. In this complex, the prime editor works like a “word processor,” accurately replacing genomic information. The tool has already been successfully implemented in living cells of organisms such as plants, zebrafish, and mice. However, precisely how this molecule complex executes each step of the editing process has not been clear, mostly due to a lack of information on its spatial structure.

“We became curious about how the unnatural combination of proteins Cas9 and reverse transcriptase work together,” says Shuto, the first author of the paper.

The research team used cryogenic electron microscopy, an imaging technique that makes observations possible at a near-atomic scale. The method required samples to be in glassy ice to protect them from the potential damage by the electron beams, posing some additional challenges.

“We found the prime editor complex to be unstable under experimental conditions,” explains Shuto. “So, it was very challenging to optimize the conditions for the complex to stay stable. For a long time, we could only determine the structure of Cas9.”

Finally overcoming the challenges, the researchers succeeded in determining the three-dimensional structure of the prime editor complex in multiple states during reverse transcription on the target DNA. The structures revealed that the reverse transcriptase bound to the RNA-DNA complex that formed along the “part” of the Cas9 protein associated with DNA cleavage, the splitting of a single strand of the double helix. While performing the reverse transcription, the reverse transcriptase maintained its position relative to the Cas9 protein. The structural and biochemical analyses also indicated that the reverse transcriptase could lead to additional, undesired insertions.

These findings have opened new avenues for both basic and applied research. So, Shuto lays out the next steps.

“Our structure determination strategy in this study can also be applied to prime editors composed of a different Cas9 protein and reverse transcriptase. We want to utilize the newly obtained structural information to lead to the development of improved prime editors.”

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Acute sense of touch helps hummingbirds hover near a flower without bumping into it




Scientists stunned to discover plants beneath mile-deep Greenland ice: Long-lost ice core provides direct evidence that giant ice sheet melted off within the last million years and is highly vulnerable to a warming climate

Hummingbirds seem like a marvel of nature and engineering: a living creature that can hover near a flower with surgical precision. How do they do this?

Though hummingbirds’ flight mechanics have been well studied, far less is known about how their sense of touch helps these tiny, energetic birds sip nectar from a flower without bumping into it. Most of what scientists know about how touch is processed in the brain comes from studies on mammals, but bird brains are very different from mammal brains.

UCLA-led research published in Current Biology shows that hummingbirds create a 3D map of their body when neurons in two specific spots of the forebrain fire — as gusts of air touch feathers on the leading edge of their wings and skin of their legs. Receptors on their bill, face and head also work toward this end. The air pressure’s intensity, influenced by factors including proximity to an object, is picked up by nerve cells at the base of the feathers and in the leg skin and transmitted to the brain, which gauges the body’s orientation relative to an object.

Zebra finches, also studied by the researchers, have the same general organization with slightly less sensitivity in some areas than hummingbirds, suggesting that these areas help with highly specialized hummingbird flight dynamics. The work adds to knowledge of how animals perceive and navigate in their worlds and can help identify ways to treat them more humanely.

Humans produce a tactile map of the body that progresses from the toes at the center of the brain, down to the legs, back and a much larger area that represents touch to the face and hands. These areas, used for touching and touch tasks, are enlarged in the human brain.

“In mammals, we know that touch is processed across the outer surface of the forebrain in the cortex,” said Duncan Leitch, corresponding author and a professor of integrative biology at UCLA. “But birds have a brain without a layered cortex structure, so it was a wide-open question how touch is represented in their brains. We showed exactly where different kinds of touch activate specific neurons in these regions and how touch is organized in their forebrains.”

Previous studies in which birds were injected with dye showed their brains have one region in the forebrain to process touch to the face and head, and one for touch anywhere else on the body. In owls, for example, touch centers that typically correspond to face touch are devoted solely to talons. But since hummingbirds live very different lives than owls, it didn’t seem likely this would hold true for them.

Leitch and co-authors at Royal Veterinary College and the University of British Columbia were able to observe neurons firing in real time by placing electrodes on hummingbirds and finches, and touching them gently with cotton swabs or puffs of air. A computer amplified the signals from the electrodes and converted them to sound for easier analysis.

The experiments confirmed that touch for the head and body is mapped in different regions of the forebrain and showed for the first time that air pressure activates specific clusters of neurons in these regions. Examination of the wings showed a network of nerve cells that likely sent a signal to the brain when activated by puffs of air on the feathers.

The researchers found particularly large clusters of brain cells that reacted to stimulation of the edges of wings, which they think help the birds adjust flight in a nuanced way. They also discovered that the feet are acutely sensitive to touch and this touch had a large representation in the brain, presumably to help with perching. The researchers speculate these areas may be even larger in parrots and other birds that use their feet to grasp and move objects.

In their study, the researchers identified receptive fields on the birds, in which a touch would trigger a neuron to fire. In hummingbirds, some of these fields — especially on the bill, face and head — were very small, meaning they could sense the lightest touch. Zebra finches had the same but larger receptive fields, suggesting these regions in finches are not quite as sensitive and  probably of greater relevance to hummingbirds that rely on constant, steady precision flight.

“Hummingbirds were often reacting to the slightest thresholds we could give them,” Leitch said.

Learning more about how diverse animals map touch across their body could lead to advances in technologies that use sensors to move about or perform a task, such as prosthetic limbs or autonomous devices. But improvements to animal welfare are perhaps a more immediate outcome of the research.

“If we can understand how animals perceive their sense of touch, we can develop practices that are less disturbing to them,” Leitch said.

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Complete X and Y chromosome sequences of living great ape species determined




Scientists stunned to discover plants beneath mile-deep Greenland ice: Long-lost ice core provides direct evidence that giant ice sheet melted off within the last million years and is highly vulnerable to a warming climate

Newly generated, complete “end-to-end” reference genomes for the sex chromosomes of five great ape species and one lesser ape species — produced by an international collaborative team led by researchers at Penn State, the National Human Genome Research Institute and the University of Washington — highlight extremely rapid changes on the male-specific Y chromosome among ape species. These findings shed light on the evolution of sex chromosomes and inform understanding of diseases related to genes on these chromosomes in both apes and humans.

“The Y chromosome is important for human fertility, and the X chromosome harbors genes critical for reproduction, cognition and immunity,” said Kateryna Makova, Verne M. Willaman Chair of Life Sciences, professor of biology at Penn State and leader of the research team. “Our study opens doors for many future investigations of sex chromosomes, how they evolved, and diseases associated with them. The living non-human great ape species we studied are all endangered. The availability of their complete sex chromosome sequences will facilitate studies of their sex-specific dispersal in the wild and of their genes important for reproduction and fertility.”

Such reference genomes act as a representative example that are useful for future studies of these species. The team found that, compared to the X chromosome, the Y chromosome varies greatly across ape species and harbors many species-specific sequences. However, it is still subject to purifying natural selection — an evolutionary force that protects its genetic information by removing harmful mutations.

The new study appears May 29 in the journal Nature.

“Researchers sequenced the human genome in 2001, but it wasn’t actually complete,” Makova said. “The technology available at the time meant that certain gaps weren’t filled in until a renewed effort led by the Telomere-to-Telomere, or T2T, Consortium in 2022-23. We leveraged the experimental and computational methods developed by the Human T2T Consortium to determine the complete sequences for the sex chromosomes of our closest living relatives — great apes.”

The team produced complete sex chromosome sequences for five species of great apes — chimpanzee, bonobo, gorilla, Bornean orangutan and Sumatran orangutan, which comprise most great ape species living today — as well as a lesser ape, siamang. They generated sequences for one individual of each species. The resulting reference genomes act as a map of genes and other chromosomal regions, which can help researchers sequence and assemble the genomes of other individuals of that species. Previous sex chromosome sequences for these species were incomplete or — for the Bornean orangutan and siamang — did not exist.

“The Y chromosome has been challenging to sequence because it contains many repetitive regions, and, because traditional short-read sequencing technology decodes sequences in short bursts, it is difficult to put the resulting segments in the correct order,” said Karol Pál, postdoctoral researcher at Penn State and a co-first author of the study. “T2T methods use long-read sequencing technologies that overcome this challenge. Combined with advances in computational analysis, on which we collaborated with Adam Phillippy’s group at the NHGRI, this allowed us to completely resolve repetitive regions that were previously difficult to sequence and assemble. By comparing the X and Y chromosomes to each other and among species, including to the previously generated human T2T sequences of the X and the Y, we learned many new things about their evolution.”

High variability on the Y chromosome

“Sex chromosomes started like any other chromosome pair, but the Y has been unique in accumulating many deletions, other mutations and repetitive elements because it does not exchange genetic information with other chromosomes over most of its length,” said Makova, who is also the director of the Center for Medical Genomics at Penn State.

As a result, across the six ape species, the research team found that the Y chromosome was much more variable than the X over a variety of characteristics, including size. Among the studied apes, the X chromosome ranges in size from 154 million letters of the ACTG alphabet — representing the nucleotides that make up DNA — in chimpanzee and human to 178 million letters in gorilla. In contrast, the Y chromosome ranges from 30 million DNA letters in siamang to 68 million letters in Sumatran orangutan.

The amount of DNA sequence shared between species was also more variable on the Y. For example, about 98% of the X chromosome aligns between human and chimpanzee, but only about a third of the Y aligns between them. The researchers found that this is in part because the Y chromosome is more likely to be rearranged or have portions of its genetic material duplicated.

Additionally, the percentage of the chromosome occupied by sequences that are repeated is highly variable on the Y. Whereas, depending on the species, 62% to 66% of the X chromosomes are occupied by repetitive elements, 71% to 85% of the Y chromosomes are occupied by them. These percentages are higher on both the X and the Y than in other chromosomes in the human genome.

How the Y has survived

“We found the ape Y to be shrinking, accumulating many mutations and repeats, and losing genes,” Makova said. “So why hasn’t the Y chromosome disappeared, as some previous hypotheses suggested? In collaboration with Sergei Kosakovsky Pond from Temple University and others, we found that the Y chromosome still has a number of genes evolving under purifying selection — a type of natural selection that keeps gene sequences intact. Many of these genes are important for spermatogenesis. This means that the Y chromosome is unlikely to disappear any time soon.”

The researchers found that many genes on the Y chromosome seem to use two strategies to survive. The first takes advantage of genetic redundancy — the presence of multiple copies of the same gene on a chromosome — so that intact copies of the gene can compensate for copies that might acquire mutations. The team quantified this genetic redundancy by completing the landscape of multi-copy gene families on ape sex chromosomes for the first time.

The second survival strategy takes advantage of palindromes, where the sequence of letters in the DNA alphabet is followed by the same, but inverted sequence, for example, ACTG-GTCA. When located within a palindrome, genes benefit from the palindrome’s ability to correct mutations.

“We found that the Y chromosome can exchange genetic information with itself between the repeated sequences of the two palindrome arms, which fold so that the inverted sequences align,” Pál said. “When two copies of the same gene are located within palindromes, and one copy is hit by a mutation, the mutation can be rescued by the genetic exchange with another copy. This can compensate for the Y’s lack of genetic information exchange with the other chromosomes.”

The research team obtained the complete sequences of palindromes on ape sex chromosomes also for the first time, as they were previously difficult to sequence and study. They found that palindromes are particularly abundant and long on the ape Y chromosome, yet they are usually only shared among closely related species.

In collaboration with Michael Schatz and his team at Johns Hopkins University, the researchers also studied the sex chromosomes of 129 individual gorillas and chimpanzees to better understand the genetic variation within each species and search for evidence of natural selection and other evolutionary forces acting on them.

“We obtained substantial new information from previously studied gorilla and chimpanzee individuals by aligning their sex chromosome sequencing reads to our new reference sequences,” said Zachary Szpiech, assistant professor of biology at Penn State and an author of the paper. “While increasing the sample size in the future will be very helpful to improve our ability to detect signatures of different evolutionary forces, this can be ethically and logistically challenging when working with endangered species, so it is critical that we can get the most out of the data we do have.”

The researchers explored a variety of factors that could explain variation on the Y chromosome within gorillas and within chimpanzees, and this analysis revealed additional signatures of purifying selection on the Y. This confirms the role of this type of natural selection on the Y, as was discovered in their previous analyses of genes.

“The powerful combination of bioinformatic techniques and evolutionary analyses that we used allows us to better explain the evolutionary processes acting on sex chromosomes in our closest living relatives, great apes,” said Christian Huber, assistant professor of biology at Penn State and an author of the paper. “Additionally, the reference genomes we produced will be instrumental for future studies of primate evolution and human diseases.”

In addition to Makova, Pál, Szpiech and Huber, the research team at Penn State includes Kaivan Kamali, computational scientist in the departments of biology and of biochemistry and molecular biology; Troy LaPolice, graduate student in bioinformatics and genomics; Paul Medvedev, professor of computer science and engineering and of biochemistry and molecular biology; Sweetalana, research assistant in the department of biology; Huiqing Zeng, research technologist in biology; Xinru Zhang, graduate student in bioinformatics and genomics; Robert Harris, assistant research professor of biology, now retired; Barbara McGrath, associate research professor of biology, now retired; and Sarah Craig, associate research professor of biology, currently a program officer at the National Institutes of Health. The co-authors also included Penn State alumni Monika Cechova, currently a postdoctoral fellow at the University of California Santa Cruz, and Melissa Wilson, currently an associate professor at Arizona State University.

In addition to Makova, the team was co-led by co-corresponding study authors Adam Phillippy, senior investigator at NHGRI, and Evan Eichler, professor of Genome Sciences at the University of Washington. A full list of authors for this paper is available here.

Funding from the National Institutes of Health supported this research.

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