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Brightest gamma-ray burst of all time came from the collapse of a massive star

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Brightest gamma-ray burst of all time came from the collapse of a massive star


In October 2022, an international team of researchers, including Northwestern University astrophysicists, observed the brightest gamma-ray burst (GRB) ever recorded, GRB 221009A.

Now, a Northwestern-led team has confirmed that the phenomenon responsible for the historic burst — dubbed the B.O.A.T. (“brightest of all time”) — is the collapse and subsequent explosion of a massive star. The team discovered the explosion, or supernova, using NASA’s James Webb Space Telescope (JWST).

While this discovery solves one mystery, another mystery deepens.

The researchers speculated that evidence of heavy elements, such as platinum and gold, might reside within the newly uncovered supernova. The extensive search, however, did not find the signature that accompanies such elements. The origin of heavy elements in the universe continues to remain as one of astronomy’s biggest open questions.

The research will be published on Friday (April 12) in the journal Nature Astronomy.

“When we confirmed that the GRB was generated by the collapse of a massive star, that gave us the opportunity to test a hypothesis for how some of the heaviest elements in the universe are formed,” said Northwestern’s Peter Blanchard, who led the study. “We did not see signatures of these heavy elements, suggesting that extremely energetic GRBs like the B.O.A.T. do not produce these elements. That doesn’t mean that all GRBs do not produce them, but it’s a key piece of information as we continue to understand where these heavy elements come from. Future observations with JWST will determine if the B.O.A.T.’s ‘normal’ cousins produce these elements.”

Blanchard is a postdoctoral fellow at Northwestern’s Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), where he studies superluminous supernovae and GRBs. The study includes co-authors from the Center for Astrophysics | Harvard & Smithsonian; University of Utah; Penn State; University of California, Berkeley; Radbound University in the Netherlands; Space Telescope Science Institute; University of Arizona/Steward Observatory; University of California, Santa Barbara; Columbia University; Flatiron Institute; University of Greifswald and the University of Guelph.

Birth of the B.O.A.T.

When its light washed over Earth on Oct. 9, 2022, the B.O.A.T. was so bright that it saturated most of the world’s gamma-ray detectors. The powerful explosion occurred approximately 2.4 billion light-years away from Earth, in the direction of the constellation Sagitta and lasted a few hundred seconds in duration. As astronomers scrambled to observe the origin of this incredibly bright phenomenon, they were immediately hit with a sense of awe.

“As long as we have been able to detect GRBs, there is no question that this GRB is the brightest we have ever witnessed by a factor of 10 or more,” Wen-fai Fong, an associate professor of physics and astronomy at Northwestern’s Weinberg College of Arts and Sciences and member of CIERA, said at the time.

“The event produced some of the highest-energy photons ever recorded by satellites designed to detect gamma rays,” Blanchard said. “This was an event that Earth sees only once every 10,000 years. We are fortunate to live in a time when we have the technology to detect these bursts happening across the universe. It’s so exciting to observe such a rare astronomical phenomenon as the B.O.A.T. and work to understand the physics behind this exceptional event.”

A ‘normal’ supernova

Rather than observe the event immediately, Blanchard, his close collaborator Ashley Villar of Harvard University and their team wanted to view the GRB during its later phases. About six months after the GRB was initially detected, Blanchard used the JWST to examine its aftermath.

“The GRB was so bright that it obscured any potential supernova signature in the first weeks and months after the burst,” Blanchard said. “At these times, the so-called afterglow of the GRB was like the headlights of a car coming straight at you, preventing you from seeing the car itself. So, we had to wait for it to fade significantly to give us a chance of seeing the supernova.”

Blanchard used the JWST’s Near Infrared Spectrograph to observe the object’s light at infrared wavelengths. That’s when he saw the characteristic signature of elements like calcium and oxygen typically found within a supernova. Surprisingly, it wasn’t exceptionally bright — like the incredibly bright GRB that it accompanied.

“It’s not any brighter than previous supernovae,” Blanchard said. “It looks fairly normal in the context of other supernovae associated with less energetic GRBs. You might expect that the same collapsing star producing a very energetic and bright GRB would also produce a very energetic and bright supernova. But it turns out that’s not the case. We have this extremely luminous GRB, but a normal supernova.”

Missing: Heavy elements

After confirming — for the first time — the presence of the supernova, Blanchard and his collaborators then searched for evidence of heavy elements within it. Currently, astrophysicists have an incomplete picture of all the mechanisms in the universe that can produce elements heavier than iron.

The primary mechanism for producing heavy elements, the rapid neutron capture process, requires a high concentration of neutrons. So far, astrophysicists have only confirmed the production of heavy elements via this process in the merger of two neutron stars, a collision detected by the Laser Interferometer Gravitational-Wave Observatory (LIGO) in 2017. But scientists say there must be other ways to produce these elusive materials. There are simply too many heavy elements in the universe and too few neutron-star mergers.

“There is likely another source,” Blanchard said. “It takes a very long time for binary neutron stars to merge. Two stars in a binary system first have to explode to leave behind neutron stars. Then, it can take billions and billions of years for the two neutron stars to slowly get closer and closer and finally merge. But observations of very old stars indicate that parts of the universe were enriched with heavy metals before most binary neutron stars would have had time to merge. That’s pointing us to an alternative channel.”

Astrophysicists have hypothesized that heavy elements also might be produced by the collapse of a rapidly spinning, massive star — the exact type of star that generated the B.O.A.T. Using the infrared spectrum obtained by the JWST, Blanchard studied the inner layers of the supernova, where the heavy elements should be formed.

“The exploded material of the star is opaque at early times, so you can only see the outer layers,” Blanchard said. “But once it expands and cools, it becomes transparent. Then you can see the photons coming from the inner layer of the supernova.”

“Moreover, different elements absorb and emit photons at different wavelengths, depending on their atomic structure, giving each element a unique spectral signature,” Blanchard explained. “Therefore, looking at an object’s spectrum can tell us what elements are present. Upon examining the B.O.A.T.’s spectrum, we did not see any signature of heavy elements, suggesting extreme events like GRB 221009A are not primary sources. This is crucial information as we continue to try to pin down where the heaviest elements are formed.”

Why so bright?

To tease apart the light of the supernova from that of the bright afterglow that came before it, the researchers paired the JWST data with observations from the Atacama Large Millimeter/Submillimeter Array (ALMA) in Chile.

“Even several months after the burst was discovered, the afterglow was bright enough to contribute a lot of light in the JWST spectra,” said Tanmoy Laskar, an assistant professor of physics and astronomy at the University of Utah and a co-author on the study. “Combining data from the two telescopes helped us measure exactly how bright the afterglow was at the time of our JWST observations and allow us to carefully extract the spectrum of the supernova.”

Although astrophysicists have yet to uncover how a “normal” supernova and a record-breaking GRB were produced by the same collapsed star, Laskar said it might be related to the shape and structure of the relativistic jets. When rapidly spinning, massive stars collapse into black holes, they produce jets of material that launch at rates close to the speed of light. If these jets are narrow, they produce a more focused — and brighter — beam of light.

“It’s like focusing a flashlight’s beam into a narrow column, as opposed to a broad beam that washes across a whole wall,” Laskar said. “In fact, this was one of the narrowest jets seen for a gamma-ray burst so far, which gives us a hint as to why the afterglow appeared as bright as it did. There may be other factors responsible as well, a question that researchers will be studying for years to come.”

Additional clues also may come from future studies of the galaxy in which the B.O.A.T. occurred. “In addition to a spectrum of the B.O.A.T. itself, we also obtained a spectrum of its ‘host’ galaxy,” Blanchard said. “The spectrum shows signs of intense star formation, hinting that the birth environment of the original star may be different than previous events.”

Team member Yijia Li, a graduate student at Penn State, modeled the spectrum of the galaxy, finding that the B.O.A.T.’s host galaxy has the lowest metallicity, a measure of the abundance of elements heavier than hydrogen and helium, of all previous GRB host galaxies. “This is another unique aspect of the B.O.A.T. that may help explain its properties,” Li said.

The study, “JWST detection of a supernova associated with GRB 221009A without an r-process signature,” was supported by NASA (award number JWST-GO-2784) and the National Science Foundation (award numbers AST-2108676 and AST-2002577). This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope.



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

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


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

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


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

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


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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