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‘Jumping genes’ repeatedly form new genes over evolution

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‘Jumping genes’ repeatedly form new genes over evolution

In the same way that Lego pieces can be arranged in new ways to build a variety of structures, genetic elements can be mixed and matched to create new genes, according to new research.

A long-proposed mechanism for creating genes, called exon shuffling, works by shuffling functional blocks of DNA sequences into new genes that express proteins.

A study, “Recurrent Evolution of Vertebrate Transcription Factors by Transposase Capture,” published Feb. 19 in Science, investigates how genetic elements called transposons, or “jumping genes,” are added into the mix during evolution to assemble new genes through exon shuffling.

Transposons, first discovered in the 1940s by Cornell alum and Nobel Prize-winner Barbara McClintock ’23, M.A. ’25, Ph.D. ”27, are abundant components of genomes — they make up half of human DNA — and have the ability to hop and replicate selfishly in the genome. Some transposons contain their own genes that code for enzymes called transposase proteins, which cut and paste genetic material from one chromosomal location to another.

The study, which focused on tetrapods (four-limbed vertebrates), is important because it shows that transposons represent an important force in the creation of new genes during evolution. The work also explains how genes critical for human development were born.

“We think it’s very likely this mechanism may extend beyond vertebrates and could be more of a fundamental mechanism that occurs in non-vertebrates as well,” said first author Rachel Cosby, Ph.D. ’19, a postdoctoral researcher at the National Institutes of Health. Cosby is a former graduate student in the lab of senior author Cedric Feschotte, professor in the Department of Molecular Biology and Genetics in the College of Agriculture and Life Sciences.


“You are putting the bricks in in a different way and you construct a whole new thing,” Feschotte said. “We are looking at the question of how genes are born. The originality is that we are looking at the role of transposons in creating proteins with novel function in evolution.””

In the study, the researchers first mined existing databases for genomes of tetrapods, because genomes for more than 500 species have been fully sequenced. Cosby and colleagues searched for combinations of DNA sequences known to be characteristic of transposons fused to host sequences to find good candidates for study. They then chose genes that evolved relatively recently — within tens of millions of years ago — so they could trace the history of the gene’s development through the vertebrate tree of life.

Though genes fused with these transposases are relatively rare, the researchers found them all over the vertebrate tree of life. The researchers identified more than 100 distinct genes fused with transposases born in the past 350 million years along different species lineages, including genes in birds, reptiles, frogs, bats and koalas, and a total of 44 genes born this way in the human genome.

Cosby and colleagues selected four recently evolved genes and performed a wide range of experiments in cell culture to understand their functions. They found the proteins derived from these genes are able to bind to specific DNA sequences and turn off gene expression. Such genes are known as transcription factors and act as master regulator genes for development and basic physiology. One such gene, PAX6, is well studied, plays a key role as a master regulator in the formation of eyes in all animals and is highly conserved throughout evolution.

“If you put a PAX6 gene from a mouse into a Drosophila [fruit fly], it works,” Feschotte said. Though others have proposed before that PAX6 is derived from a transposase fusion, the researchers in this study further validated the hypothesis.

Cosby and colleagues isolated one of these recently evolved genes in bats, called KRABINER, and then used CRISPR gene-editing technology to delete it from the bat genome and see what genes were affected, before adding it back in. The experiment revealed that when KRABINER was removed, hundreds of genes were dysregulated, and when they restored it, normal functioning returned. The protein expressed by the KRABINER gene bound to other related transposons in the bat genome, Cosby said.

“The experiment revealed that it controls a large network of other genes wired through the past dispersion of related transposons throughout the bat genome — creating not just a gene but what is known as a gene regulatory network,” Feschotte said.

Current and former Feschotte lab members Julius Judd, Ruiling Zhang ’20, Alan Zhong ’19, Nathaniel Garry ’21 and collaborator Ellen Pritham are co-authors of the paper.

The study was funded by the National Institutes of Health.

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The unintended consequences of success against malaria

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‘Jumping genes’ repeatedly form new genes over evolution


For decades, insecticide-treated bed nets and indoor insecticide spraying regimens have been important — and widely successful — treatments against mosquitoes that transmit malaria, a dangerous global disease. Yet these treatments also — for a time — suppressed undesirable household insects like bed bugs, cockroaches and flies.

Now, a new North Carolina State University study reviewing the academic literature on indoor pest control shows that as the household insects developed resistance to the insecticides targeting mosquitoes, the return of these bed bugs, cockroaches and flies into homes has led to community distrust and often abandonment of these treatments — and to rising rates of malaria.

In short, the bed nets and insecticide treatments that were so effective in preventing mosquito bites — and therefore malaria — are increasingly viewed as the causes of household pest resurgence.

“These insecticide-treated bed nets were not intended to kill household pests like bed bugs, but they were really good at it,” said Chris Hayes, an NC State Ph.D. student and co-corresponding author of a paper describing the work. “It’s what people really liked, but the insecticides are not working as effectively on household pests anymore.”

“Non-target effects are usually harmful, but in this case they were beneficial,” said Coby Schal, Blanton J. Whitmire Distinguished Professor of Entomology at NC State and co-corresponding author of the paper.

“The value to people wasn’t necessarily in reducing malaria, but was in killing other pests,” Hayes added. “There’s probably a link between use of these nets and widespread insecticide resistance in these house pests, at least in Africa.”

The researchers add that other factors — famine, war, the rural/city divide, and population displacement, for example — also could contribute to rising rates of malaria.

To produce the review, Hayes combed through the academic literature to find research on indoor pests like bed bugs, cockroaches and fleas, as well as papers on malaria, bed nets, pesticides and indoor pest control. The search yielded more than 1,200 papers, which, after an exhaustive review process, was whittled down to a final count of 28 peer-reviewed papers fulfilling the necessary criteria.

One paper — a 2022 survey of 1,000 households in Botswana — found that while 58% were most concerned with mosquitoes in homes, more than 40% were most concerned with cockroaches and flies.

Hayes said a recent paper — published after this NC State review was concluded — showed that people blamed the presence of bed bugs on bed nets.

“There is some evidence that people stop using bed nets when they don’t control pests,” Hayes said.

The researchers say that all hope is not lost, though.

“There are, ideally, two routes,” Schal said. “One would be a two-pronged approach with both mosquito treatment and a separate urban pest management treatment that targets pests. The other would be the discovery of new malaria-control tools that also target these household pests at the same time. For example, the bottom portion of a bed net could be a different chemistry that targets cockroaches and bed bugs.

“If you offer something in bed nets that suppresses pests, you might reduce the vilification of bed nets.”

The study appears in Proceedings of the Royal Society B. The review was supported in part by the Blanton J. Whitmire Endowment at NC State, and grants from the U.S. Department of Housing and Urban Development Healthy Homes program (NCHHU0053-19), the Department of the Army, U.S. Army Contracting Command, Aberdeen Proving Ground, Natick Contracting Division, Ft. Detrick, Maryland (W911QY1910011), and the Triangle Center for Evolutionary Medicine (257367).



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Drawing water from dry air

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‘Jumping genes’ repeatedly form new genes over evolution


Earth’s atmosphere holds an ocean of water, enough liquid to fill Utah’s Great Salt Lake 800 times.

Extracting some of that moisture is seen as a potential way to provide clean drinking water to billions of people globally who face chronic shortages.

Existing technologies for atmospheric water harvesting (AWH) are saddled with numerous downsides associated with size, cost and efficiency. But new research from University of Utah engineering researchers has yielded insights that could improve efficiencies and bring the world one step closer to tapping the air as a culinary water source in arid places.

The study unveils the first-of-its-kind compact rapid cycling fuel-fired AWH device. This two-step prototype relies on adsorbent materials that draw water molecules out of non-humid air, then applies heat to release those molecules into liquid form, according to Sameer Rao, senior author of the study published Monday and an assistant professor of mechanical engineering.

“Hygroscopic materials intrinsically have affinity to water. They soak up water wherever you go. One of the best examples is the stuff inside diapers,” said Rao, who happens to be the father of an infant son. “We work with a specific type of hygroscopic material called a metal organic framework.”

Rao likened metal organic frameworks to Lego blocks, which can be rearranged to build all sorts of structures. It this case they are arranged to create a molecule ideal for gas separation.

“They can make it specific to adsorb water vapor from the air and nothing else. They’re really selective,” Rao said. Developed with graduate student Nathan Ortiz, the study’s lead author, this prototype uses aluminum fumarate that was fashioned into panels that collect the water as air is drawn through.

“The water molecules themselves get trapped on the surfaces of our material, and that’s a reversible process. And so instead of becoming ingrained into the material itself, it sits on the walls,” Ortiz said. “What’s special about these absorbent materials is they have just an immense amount of internal surface area. There’s so many sites for water molecules to get stuck.”

Just a gram of this material holds as much surface area as two football fields, according to Rao. So just a little material can capture a lot of water.

“All of this surface area is at the molecular scale,” Rao said. “And that’s awesome for us because we want to trap water vapor onto that surface area within the pores of this material.”

Funding for the research came from the DEVCOM Soldier Center, a program run by the Department of Defense to facilitate technology transfer that supports Army modernization. The Army’s interest in the project stems from the need to keep soldiers hydrated while operating in remote areas with few water sources.

“We specifically looked at this for defense applications so that soldiers have a small compact water generation unit and don’t need to lug around a large canteen filled with water,” Rao said. “This would literally produce water on demand.”

Rao and Ortiz have filed for a preliminary patent based on the technology, which addresses non-military needs as well.

“As we were designing the system, I think we also had perspective of the broader water problem. It’s not just a defense issue, it’s very much a civilian issue,” Rao said. “We think in terms water consumption of a household for drinking water per day. That’s about 15 to 20 liters per day.”

In this proof of concept, the prototype achieved its target of producing 5 liters of water per day per kilogram of adsorbent material. In a matter of three days in the field, this devise would outperform packing water, according to Ortiz.

In the device’s second step, the water is precipitated into liquid by applying heat using a standard-issue Army camping stove. This works because of the exothermic nature of its water collecting process.

“As it collects water, it’s releasing little bits of heat. And then to reverse that, we add heat,” Ortiz said. “We just put a flame right under here, anything to get this temperature up. And then as we increase the temperature, we rapidly release the water molecules. Once we have a really humid airstream, that makes condensation at ambient temperature much easier.”

Nascent technologies abound for atmospheric water harvesting, which is more easily accomplished when the air is humid, but none has resulted in equipment that can be put to practical use in arid environments. Ortiz believes his device can be the first, mainly because it is powered with energy-dense fuel like the white gasoline used in camping stoves.

The team decided against using photovoltaics.

“If you’re reliant on solar panels, you’re limited to daytime operation or you need batteries, which is just more weight. You keep stacking challenges. It just takes up so much space,” Ortiz said. “This technology is superior in arid conditions, while refrigeration is best in high humidity.”



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3D-printed microstructure forest facilitates solar steam generator desalination

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‘Jumping genes’ repeatedly form new genes over evolution


Faced with the world’s impending freshwater scarcity, a team of researchers in Singapore turned to solar steam generators (SSGs), which are emerging as a promising device for seawater desalination. Desalination can be a costly, energy-intensive solution to water scarcity. This renewable-powered approach mimics the natural water cycle by using the sun’s energy to evaporate and isolate water. However, the technology is limited by the need to fabricate complex topologies to increase the surface area necessary to achieve high water evaporation efficiency.

To overcome this barrier, the team sought design inspiration from trees and harnessed the potential of 3D printing. In Applied Physics Reviews, the team presents a state-of-the-art technology for producing efficient SSGs for desalination and introduces a novel method for printing functional nanocomposites for multi-jet fusion (MJF).

“We created SSGs with exceptional photothermal performance and self-cleaning properties,” said Kun Zhou, a professor of mechanical engineering at Nanyang Technological University. “Using a treelike porous structure significantly enhances water evaporation rates and ensures continuous operation by preventing salt accumulation — its performance remains relatively stable even after prolonged testing.”

The physics behind their approach involves light-to-thermal energy conversion, where the SSGs absorb solar energy, convert it to heat, and evaporate the water/seawater. The SSG’s porous structure helps improve self-cleaning by removing accumulated salt to ensure sustained desalination performance.

“By using an effective photothermal fusing agent, MJF printing technology can rapidly create parts with intricate designs,” he said. “To improve the photothermal conversion efficiency of fusing agents and printed parts, we developed a novel type of fusing agent derived from metal-organic frameworks.”

Their SSGs were inspired by plant transpiration and are composed of miniature tree-shaped microstructures, forming an efficient, heat-distributing forest.

“Our bioinspired design increases the surface area of the SSG,” said Zhou. “Using a treelike design increases the surface area of the SSG, which enhances the water transport and boosts evaporation efficiency.”

One big surprise was the high rate of water evaporation observed in both simulated environments and field trials. The desalinated water consistently met standards for drinking water — even after a long-time test.

“This demonstrates the practicality and efficiency of our approach,” Zhou said. “And it can be quickly and easily mass-produced via MJF commercial printers.”

The team’s work shows significant potential for addressing freshwater scarcity.

“Our SSGs can be used in regions with limited access to freshwater to provide a sustainable and efficient desalination solution,” said Zhou. “Beyond desalination, it can be adapted for other applications that require efficient solar energy conversion and water purification.”



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