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A new perspective on the genomes of archaic humans

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A new perspective on the genomes of archaic humans

A genome by itself is like a recipe without a chef — full of important information, but in need of interpretation. So, even though we have sequenced genomes of our nearest extinct relatives — the Neanderthals and the Denisovans — there remain many unknowns regarding how differences in our genomes actually lead to differences in physical traits.

“When we’re looking at archaic genomes, we don’t have all the layers and marks that we usually have in samples from present-day individuals that help us interpret regulation in the genome, like RNA or cell structure,” said David Gokhman, a postdoctoral fellow in biology at Stanford University.

“We just have the naked DNA sequence, and all we can really do is stare at it and hope one day we’d be able to understand what it means,” he said.

Motivated by such hopes, a team of researchers at Stanford and the University of California, San Francisco (UCSF), have devised a new method to harvest more information from the genomes of archaic humans to potentially reveal the physical consequences of genomic differences between us and them.

Their work, published April 22 in eLife, focused on sequences related to gene expression — the process by which genes are activated or silenced, which determines when, how and where DNA’s instructions are followed. Gene expression tends to be the genetic detail that determines physical differences between closely related groups.

Starting with 14,042 genetic variants unique to modern humans, the researchers found 407 that specifically contribute to differences in gene expression between modern and archaic humans. In further analysis, they determined that the differences were more likely to be associated with the vocal tract and the cerebellum, which is the part of our brain that receives sensory information and controls voluntary movement, including walking, coordination, balance and speech.


“It just seems so implausible that you could make a call like, ‘I think the voice box evolved,’ from the information we have,” said Dmitri Petrov, the Michelle and Kevin Douglas Professor in the School of Humanities and Sciences, who is co-senior author of the paper with Gokhman and Nadav Ahituv, a professor of bioengineering at UCSF. “The predictions are almost science fiction. If five years ago, somebody told me that this would be possible, I would not have put much money on it.”

The path to modern humans

With such a large number of variants to examine, the researchers relied on a technique called a “massively parallel reporter assay” to test which sequences actually affect gene regulation. Their version of this technique, which was developed by Ahituv, involves packaging the DNA sequence variant into a “reporter gene” inside a virus. That virus is then put into a cell. If that variant affects gene expression, the reporter gene produces a barcoded molecule that identifies what DNA sequence it came from. The barcode allows the researchers to scan the products of a large number of variants at once.

Essentially, the whole process imitates an abridged version of how each variant would play out in a cell in real life and reports the results.

Lana Harshman, a graduate student at UCSF and co-lead author of the paper, infected three types of cells with the team’s variant packages. These cells were related to the brain, skeleton and early development — subjects that are most likely to reveal evolutionary differences between us and our most recent ancestors. Carly Weiss, a postdoctoral scholar in the Petrov lab and co-lead author of the paper, analyzed the results of these experiments.


In total, the researchers found 407 sequences that represented a change in expression in modern humans compared to our predecessors. Among that list, genes that affect the cerebellum and genes that affect the voice box, pharynx, larynx and vocal cords seem to be overrepresented.

“This would suggest some kind of rapid evolution of those organs or some kind of a path that is specific to modern humans,” said Gokhman. The next step, he added, would be trying to understand more about these sequences and the roles they played in the evolution of modern humans.

Even with those unknowns, this technique by itself is a significant advance for evolutionary research, said Petrov.

“This goes beyond the sequencing of the DNA from the Neanderthal and Denisovan bones. This begins to put meaning on those differences,” said Petrov. “It’s an important conceptual step from just the sequence — no tissue, no cells — to biological information and will enable many future studies.”

Hunter Fraser, associate professor of biology at Stanford, and Fumitaka Inoue (UCSF) are also co-authors of the paper. Fraser is also a member of Stanford Bio-X, the Maternal & Child Health Research Institute (MCHRI) and the Stanford Cancer Institute. Petrov is also a member of Stanford Bio-X and the Maternal & Child Health Research Institute (MCHRI), and an affiliate of the Stanford Woods Institute for the Environment.

This research was funded by Human Frontier, Rothschild and Zuckerman fellowships; the National Human Genome Research Institute; the National Institute of Mental Health; the Uehara Memorial Foundation; and the Stanford Center for Computational, Evolutionary and Human Genomics (CEHG).

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Early dark energy could resolve cosmology’s two biggest puzzles

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A new perspective on the genomes of archaic humans


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.

One puzzle in question is the “Hubble tension,” which refers to a mismatch in measurements of how fast the universe is expanding. The other involves observations of numerous early, bright galaxies that existed at a time when the early universe should have been much less populated.

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.



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Plant-derived secondary organic aerosols can act as mediators of plant-plant interactions

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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.

It is well known that plants release volatile organic compounds (VOCs) into the atmosphere when damaged by herbivores. These VOCs play a crucial role in plant-plant interactions, whereby undamaged plants may detect warning signals from their damaged neighbours and prepare their defences. “Reactive plant VOCs undergo oxidative chemical reactions, resulting in the formation of secondary organic aerosols (SOAs). We wondered whether the ecological functions mediated by VOCs persist after they are oxidated to form SOAs,” said Dr. Hao Yu, formerly a PhD student at UEF, but now at the University of Bern.

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.



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Folded or cut, this lithium-sulfur battery keeps going

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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.

Sulfur has been suggested as a material for lithium-ion batteries because of its low cost and potential to hold more energy than lithium-metal oxides and other materials used in traditional ion-based versions. To make Li-S batteries stable at high temperatures, researchers have previously proposed using a carbonate-based electrolyte to separate the two electrodes (an iron sulfide cathode and a lithium metal-containing anode). However, as the sulfide in the cathode dissolves into the electrolyte, it forms an impenetrable precipitate, causing the cell to quickly lose capacity. Liping Wang and colleagues wondered if they could add a layer between the cathode and electrolyte to reduce this corrosion without reducing functionality and rechargeability.

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.



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