TOP SCEINCE
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.
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.
TOP SCEINCE
Early dark energy could resolve cosmology’s two biggest puzzles
A new study by MIT physicists proposes that a mysterious force known as early dark energy could solve two of the biggest puzzles in cosmology and fill in some major gaps in our understanding of how the early universe evolved.
Now, the MIT team has found that both puzzles could be resolved if the early universe had one extra, fleeting ingredient: early dark energy. Dark energy is an unknown form of energy that physicists suspect is driving the expansion of the universe today. Early dark energy is a similar, hypothetical phenomenon that may have made only a brief appearance, influencing the expansion of the universe in its first moments before disappearing entirely.
Some physicists have suspected that early dark energy could be the key to solving the Hubble tension, as the mysterious force could accelerate the early expansion of the universe by an amount that would resolve the measurement mismatch.
The MIT researchers have now found that early dark energy could also explain the baffling number of bright galaxies that astronomers have observed in the early universe. In their new study, reported in the Monthly Notices of the Royal Astronomical Society, the team modeled the formation of galaxies in the universe’s first few hundred million years. When they incorporated a dark energy component only in that earliest sliver of time, they found the number of galaxies that arose from the primordial environment bloomed to fit astronomers’ observations.
“You have these two looming open-ended puzzles,” says study co-author Rohan Naidu, a postdoc in MIT’s Kavli Institute for Astrophysics and Space Research. “We find that in fact, early dark energy is a very elegant and sparse solution to two of the most pressing problems in cosmology.”
The study’s co-authors include lead author and Kavli postdoc Xuejian (Jacob) Shen, and MIT professor of physics Mark Vogelsberger, along with Michael Boylan-Kolchin at the University of Texas at Austin, and Sandro Tacchella at the University of Cambridge.
Big city lights
Based on standard cosmological and galaxy formation models, the universe should have taken its time spinning up the first galaxies. It would have taken billions of years for primordial gas to coalesce into galaxies as large and bright as the Milky Way.
But in 2023, NASA’s James Webb Space Telescope (JWST) made a startling observation. With an ability to peer farther back in time than any observatory to date, the telescope uncovered a surprising number of bright galaxies as large as the modern Milky Way within the first 500 million years, when the universe was just 3 percent of its current age.
“The bright galaxies that JWST saw would be like seeing a clustering of lights around big cities, whereas theory predicts something like the light around more rural settings like Yellowstone National Park,” Shen says. “And we don’t expect that clustering of light so early on.”
For physicists, the observations imply that there is either something fundamentally wrong with the physics underlying the models or a missing ingredient in the early universe that scientists have not accounted for. The MIT team explored the possibility of the latter, and whether the missing ingredient might be early dark energy.
Physicists have proposed that early dark energy is a sort of antigravitational force that is turned on only at very early times. This force would counteract gravity’s inward pull and accelerate the early expansion of the universe, in a way that would resolve the mismatch in measurements. Early dark energy, therefore, is considered the most likely solution to the Hubble tension.
Galaxy skeleton
The MIT team explored whether early dark energy could also be the key to explaining the unexpected population of large, bright galaxies detected by JWST. In their new study, the physicists considered how early dark energy might affect the early structure of the universe that gave rise to the first galaxies. They focused on the formation of dark matter halos — regions of space where gravity happens to be stronger, and where matter begins to accumulate.
“We believe that dark matter halos are the invisible skeleton of the universe,” Shen explains. “Dark matter structures form first, and then galaxies form within these structures. So, we expect the number of bright galaxies should be proportional to the number of big dark matter halos.”
The team developed an empirical framework for early galaxy formation, which predicts the number, luminosity, and size of galaxies that should form in the early universe, given some measures of “cosmological parameters.” Cosmological parameters are the basic ingredients, or mathematical terms, that describe the evolution of the universe.
Physicists have determined that there are at least six main cosmological parameters, one of which is the Hubble constant — a term that describes the universe’s rate of expansion. Other parameters describe density fluctuations in the primordial soup, immediately after the Big Bang, from which dark matter halos eventually form.
The MIT team reasoned that if early dark energy affects the universe’s early expansion rate, in a way that resolves the Hubble tension, then it could affect the balance of the other cosmological parameters, in a way that might increase the number of bright galaxies that appear at early times. To test their theory, they incorporated a model of early dark energy (the same one that happens to resolve the Hubble tension) into an empirical galaxy formation framework to see how the earliest dark matter structures evolve and give rise to the first galaxies.
“What we show is, the skeletal structure of the early universe is altered in a subtle way where the amplitude of fluctuations goes up, and you get bigger halos, and brighter galaxies that are in place at earlier times, more so than in our more vanilla models,” Naidu says. “It means things were more abundant, and more clustered in the early universe.”
“A priori, I would not have expected the abundance of JWST’s early bright galaxies to have anything to do with early dark energy, but their observation that EDE pushes cosmological parameters in a direction that boosts the early-galaxy abundance is interesting,” says Marc Kamionkowski, professor of theoretical physics at Johns Hopkins University, who was not involved with the study. “I think more work will need to be done to establish a link between early galaxies and EDE, but regardless of how things turn out, it’s a clever — and hopefully ultimately fruitful — thing to try.”
“We demonstrated the potential of early dark energy as a unified solution to the two major issues faced by cosmology. This might be an evidence for its existence if the observational findings of JWST get further consolidated,” Vogelsberger concludes. “In the future, we can incorporate this into large cosmological simulations to see what detailed predictions we get.”
This research was supported, in part, by NASA and the National Science Foundation.
TOP SCEINCE
Plant-derived secondary organic aerosols can act as mediators of plant-plant interactions
A new study published in Science reveals that plant-derived secondary organic aerosols (SOAs) can act as mediators of plant-plant interactions. This research was conducted through the cooperation of chemical ecologists, plant ecophysiologists and atmospheric physicists at the University of Eastern Finland.
The study showed that Scots pine seedlings, when damaged by large pine weevils, release VOCs that activate defences in nearby plants of the same species. Interestingly, the biological activity persisted after VOCs were oxidized to form SOAs. The results indicated that the elemental composition and quantity of SOAs likely determines their biological functions.
“A key novelty of the study is the finding that plants adopt subtly different defence strategies when receiving signals as VOCs or as SOAs, yet they exhibit similar degrees of resistance to herbivore feeding,” said Professor James Blande, head of the Environmental Ecology Research Group. This observation opens up the possibility that plants have sophisticated sensing systems that enable them to tailor their defences to information derived from different types of chemical cue.
“Considering the formation rate of SOAs from their precursor VOCs, their longer lifetime compared to VOCs, and the atmospheric air mass transport, we expect that the ecologically effective distance for interactions mediated by SOAs is longer than that for plant interactions mediated by VOCs,” said Professor Annele Virtanen, head of the Aerosol Physics Research Group. This could be interpreted as plants being able to detect cues representing close versus distant threats from herbivores.
The study is expected to open up a whole new complex research area to environmental ecologists and their collaborators, which could lead to new insights on the chemical cues structuring interactions between plants.
TOP SCEINCE
Folded or cut, this lithium-sulfur battery keeps going
Most rechargeable batteries that power portable devices, such as toys, handheld vacuums and e-bikes, use lithium-ion technology. But these batteries can have short lifetimes and may catch fire when damaged. To address stability and safety issues, researchers reporting in ACS Energy Letters have designed a lithium-sulfur (Li-S) battery that features an improved iron sulfide cathode. One prototype remains highly stable over 300 charge-discharge cycles, and another provides power even after being folded or cut.
The team coated iron sulfide cathodes in different polymers and found in initial electrochemical performance tests that polyacrylic acid (PAA) performed best, retaining the electrode’s discharge capacity after 300 charge-discharge cycles. Next, the researchers incorporated a PAA-coated iron sulfide cathode into a prototype battery design, which also included a carbonate-based electrolyte, a lithium metal foil as an ion source, and a graphite-based anode. They produced and then tested both pouch cell and coin cell battery prototypes.
After more than 100 charge-discharge cycles, Wang and colleagues observed no substantial capacity decay in the pouch cell. Additional experiments showed that the pouch cell still worked after being folded and cut in half. The coin cell retained 72% of its capacity after 300 charge-discharge cycles. They next applied the polymer coating to cathodes made from other metals, creating lithium-molybdenum and lithium-vanadium batteries. These cells also had stable capacity over 300 charge-discharge cycles. Overall, the results indicate that coated cathodes could produce not only safer Li-S batteries with long lifespans, but also efficient batteries with other metal sulfides, according to Wang’s team.
The authors acknowledge funding from the National Natural Science Foundation of China; the Natural Science Foundation of Sichuan, China; and the Beijing National Laboratory for Condensed Matter Physics.
-
Solar Energy3 years ago
DLR testing the use of molten salt in a solar power plant in Portugal
-
world news11 months ago
Gulf, France aid Gaza, Russia evacuates citizens
-
Camera11 months ago
DJI Air 3 vs. Mini 4 Pro: which compact drone is best?
-
Solar Energy11 months ago
Glencore eyes options on battery recycling project
-
Camera3 years ago
Charles ‘Chuck’ Geschke, co-founder of Adobe and inventor of the PDF, dies at 81
-
world news11 months ago
Strong majority of Americans support Israel-Hamas hostage deal
-
Camera11 months ago
Sony a9 III: what you need to know
-
TOP SCEINCE6 months ago
Can animals count?