TOP SCEINCE
Agriculture accelerated human genome evolution to capture energy from starchy foods
Over the past 12,000 years, humans in Europe have dramatically increased their ability to digest carbohydrates, expanding the number of genes they have for enzymes that break down starch from an average of eight to more than 11, according to a new study by researchers from the U.S., Italy and United Kingdom.
The study, published today (Sept. 4) in the journal Nature, also provides a new method for identifying the causes of diseases that involve genes with multiple copies in the human genome, such as the genes for amylase.
The research was led by Peter Sudmant, assistant professor of integrative biology at the University of California, Berkeley, and Erik Garrison of the University of Tennessee Health Science Center in Memphis.
“If you take a piece of dry pasta and put it in your mouth, eventually it’ll get a little bit sweet,” Sudmant said. “That’s your salivary amylase enzyme breaking the starches down into sugars. That happens in all humans, as well as in other primates.”
Chimpanzee, bonobo and Neanderthal genomes all have a single copy of the gene on chromosome 1 that codes for the salivary amylase, referred to as AMY1. The same is true for the two pancreatic amylase genes, AMY2A and AMY2B. These three genes are located close to one another in a region of the primate genome known as the amylase locus.
Human genomes, however, harbor vastly different numbers of each amylase gene.
“Our study found that each copy of the human genome harbors one to 11 copies of AMY1, zero to three copies of AMY2A, and one to four copies of AMY2B,” said UC Berkeley postdoctoral fellow Runyang Nicolas Lou, one of five first authors of the paper. “Copy number is correlated with gene expression and protein level and thus the ability to digest starch.”
The researchers discovered that, while around 12,000 years ago humans across Europe had an average of about four copies of the salivary amylase gene, that number has increased to about seven. The combined number of copies of the two pancreatic amylase genes also increased by half a gene (0.5) on average over this time in Europe.
Survival advantage of multiple amylase genes
Overall, the incidence of chromosomes with multiple copies of amylase genes (that is, more total copies than chimpanzees and Neanderthals) increased sevenfold over the last 12,000 years, suggesting that this provided a survival advantage for our ancestors.
The researchers also found evidence for an increase in amylase genes in other agricultural populations around the world, and that the region of the chromosomes where these amylase genes are located looks similar in all these populations, no matter what specific starchy plant that culture domesticated. The findings demonstrate that as agriculture arose independently around the world, it seems to have rapidly altered the human genome in nearly identical ways in different populations to deal with increased carbohydrates in the diet.
In fact, the researchers found that the rate of evolution leading to changes in amylase gene copy number was 10,000 times faster than that of single DNA base pair changes in the human genome.
“It has long been hypothesized that the copy number of amylase genes had increased in Europeans since the dawn of agriculture, but we had never been able to sequence this locus fully before. It is extremely repetitive and complex,” Sudmant said. “Now, we’re finally able to fully capture these structurally complex regions, and with that, investigate the history of selection of the region, the timing of evolution and the diversity across worldwide populations. Now, we can start thinking about associations with human disease.”
One suspected association is with tooth decay. Previous studies have suggested that having more copies of AMY1 is associated with more cavities, perhaps because the saliva does a better job of converting starch in chewed food into sugar, which feeds bacteria that eat away at teeth.
The research also provides a method for exploring other areas of the genome — those involving the immune system, skin pigmentation and the production of mucus, for example — that have undergone rapid gene duplication in recent human history, Garrison said.
“One of the exciting things we were able to do here is probe both modern and ancient genomes to dissect the history of structural evolution at this locus,” he said.
These methods can also be applied to other species. Previous studies have shown that animals that hang out around humans — dogs, pigs, rats and mice — have more copies of the amylase gene than their wilder relatives, apparently to take advantage of the food we throw away.
“This is really the frontier, in my opinion,” Garrison said. “We can, for the first time, look at all of these regions that we could never look at before, and not just in humans — other species, too. Human disease studies have really struggled in identifying associations at complex loci, like amylase. Because the mutation rate is so high, traditional association methods can fail. We’re really excited how far we can push our new methods to identify new genetic causes of disease.”
From hunter-gatherer to agrarian
Scientists have long suspected that humans’ ability to digest starch may have increased after our ancestors transitioned from a hunter-gatherer lifestyle to a settled, agricultural lifestyle. This shift was shown to be associated with more copies of the amylase genes in people from societies that domesticated plants.
But the area of the human genome where these copies reside has been difficult to study because traditional sequencing — so-called short-read sequencing techniques that cut the genome into chunks of about 100 base pairs, sequence the millions of pieces and then reassemble them into a genome — was unable to distinguish gene copies from one another. Complicating matters, some copies are inverted, that is, they are flipped and read from the opposite strand of DNA.
Long-read sequencing allows scientists to resolve this region, reading DNA sequences thousands of base pairs long to accurately capture repetitive stretches. At the time of the study, the Human Pangenome Reference Consortium (HPRC) had collected long-read sequences of 94 human haploid genomes, which Sudmant and colleagues used to assess the variety of contemporary amylase regions, called haplotypes. The team then assessed the same region in 519 ancient European genomes. The HPRC data helped avoid a common bias in comparative genomic studies, which have used a single, averaged human genome as a reference. The genomes from the HPRC, referred to as a pangenome, provide a more inclusive reference that more accurately captures human diversity.
Joana Rocha, a UC Berkeley postdoctoral fellow and co-first author of the paper, compared the region where amylase genes cluster to what she called “sculptures made of different Lego bricks. Those are the haplotype structures. Previous work had to take down the sculpture first and infer from a pile of bricks what the sculpture may have looked like. Long-read sequencing and pangenomic methods now allow us to directly examine the sculpture and thus offer us unprecedented power to study the evolutionary history and selective impact of different haplotype structures.”
Using specially developed mathematical modeling, the researchers identified 28 different haplotype structures among the 94 long-read genomes and thousands of realigned short-read human genomes, all of which cluster into 11 groups, each with a unique combination of AMY1, AMY2A and AMY2B copy numbers.
“These remarkably complex, crazy structures — regions of gene duplication, inversion and deletion in the human genome — have evolved independently in different human populations over and over again, even before the rise of agriculture,” Sudmant said.
Analysis of the many contemporary human genomes also pointed to an origin 280,000 years ago of an initial duplication event that added two copies of AMY1 to the human genome.
“That particular structure, which is predisposed to high mutation rates, emerged 280,000 years ago, setting the stage for later on, when we developed agriculture, for people who had more copies to have increased fitness, and then for these copy numbers to be selected for,” Sudmant said. “Using our methods, for the first time we could really date the initial duplication event.”
Alma Halgren, a UC Berkeley graduate student in bioengineering, and Davide Bolognini and Alessandro Raveane of Human Technopole in Milan, Italy, are also first authors of the paper. Other co-authors are Andrea Guarracino of UTHSC, Nicole Soranzo of Human Technopole and the University of Cambridge in the United Kingdom, and Jason Chin of the Foundation for Biological Data Science in Belmont, California. Sudmant’s research is funded by the Institute of General Medical Sciences of the U.S. National Institutes of Health (R35GM142916).
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
-
Camera1 year ago
DJI Air 3 vs. Mini 4 Pro: which compact drone is best?
-
world news1 year ago
Gulf, France aid Gaza, Russia evacuates citizens
-
Camera1 year ago
Sony a9 III: what you need to know
-
world news1 year ago
Strong majority of Americans support Israel-Hamas hostage deal
-
Camera4 years ago
Charles ‘Chuck’ Geschke, co-founder of Adobe and inventor of the PDF, dies at 81
-
Solar Energy1 year ago
Glencore eyes options on battery recycling project
-
Indian Defense3 years ago
Israeli Radar Company Signs MoU To Cooperate With India’s Alpha Design Technologies