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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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How 3D printers can give robots a soft touch

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‘Jumping genes’ repeatedly form new genes over evolution


Soft skin coverings and touch sensors have emerged as a promising feature for robots that are both safer and more intuitive for human interaction, but they are expensive and difficult to make. A recent study demonstrates that soft skin pads doubling as sensors made from thermoplastic urethane can be efficiently manufactured using 3D printers.

“Robotic hardware can involve large forces and torques, so it needs to be made quite safe if it’s going to either directly interact with humans or be used in human environments,” said project lead Joohyung Kim, a professor of electrical & computer engineering at the University of Illinois Urbana-Champaign. “It’s expected that soft skin will play an important role in this regard since it can be used for both mechanical safety compliance and tactile sensing.

As reported in the journal IEEE Transactions on Robotics, the 3D-printed pads function as both soft skin for a robotic arm and pressure-based mechanical sensors. The pads have airtight seals and connect to pressure sensors. Like a squeezed balloon, the pad deforms when it touches something, and the displaced air activates the pressure sensor.

Kim explained, “Tactile robotic sensors usually contain very complicated arrays of electronics and are quite expensive, but we have shown that functional, durable alternatives can be made very cheaply. Moreover, since it’s just a question of reprogramming a 3D printer, the same technique can be easily customized to different robotic systems.”

The researchers demonstrated that this functionality can be naturally used for safety: if the pads detect anything near a dangerous area such as a joint, the arm automatically stops. They can also be used for operational functionality with the robot interpreting touches and taps as instructions.

Since 3D-printed parts are comparatively simple and inexpensive to manufacture, they can be easily adapted to new robotic systems and replaced. Kim noted that this feature is desirable in applications where cleaning and maintaining parts is expensive or infeasible.

“Imagine you want to use soft-skinned robots to assist in a hospital setting,” he said. “They would need to be regularly sanitized, or the skin would need to be regularly replaced. Either way,there’s a huge cost. However, 3D printing is a very scalable process, so interchangeable parts can be inexpensively made and easily snapped on and off the robot body.”

Tactile inputs like the kind provided by the new pads are a relatively unexplored facet of robotic sensing and control. Kim hopes that the ease of this new manufacturing technique will inspire more interest.

“Right now, computer vision and language models are the two major ways that humans can interact with robotic systems, but there is a need for more data on physical interactions, or ‘force-level’ data,” he said. “From the robot’s point of view, this information is the most direct interaction with its environment, but there are very few users — mostly researchers — who think about this. Collecting this force-level data is a target task for me and my group.



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Honey bees experience multiple health stressors out-in-the-field

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‘Jumping genes’ repeatedly form new genes over evolution


It’s not a single pesticide or virus stressing honey bees, and affecting their health, but exposure to a complex web of multiple interacting stressors encountered while at work pollinating crops, found new research out of York University.

Scientists have been unable to explain increasing colony mortality, even after decades of research examining the role of specific pesticides, parasitic mites, viruses or genetics. This led the research team to wonder if previous studies were missing something by focussing on one stressor at a time.

“Our study is the first to apply systems level or network analyses to honey bee stressors at a massive scale. I think this represents a paradigm shift in the field because we have been so focussed on finding the one big thing, the smoking gun,” says corresponding author of the new paper York Faculty of Science Professor Amro Zayed, York Research Chair in Genomics. “But we are finding that bees are exposed to a very complicated network of stressors that change quickly over time and space. It’s a level of complexity that we haven’t thought about before. To me, that’s the big surprise of this study.”

The paper, Honey bee stressor networks are complex and dependent on crop and region, published today in Current Biology, takes a much broader look at the interplay of stressors and their effects. The study team also included researchers from the University of British Columbia, Agriculture and Agri-Food Canada, the University of Victoria, the University of Lethbridge, the University of Manitoba, l’Université Laval, the University of Guelph, and the Ontario Beekeepers’ Association.

Not all stressors are the same, however. Some stressors are more influential than others — what researchers call the social media influencers of the bee world — having an outsized impact on the architecture of a highly complex network and their co-stressors. They also found that most of these influencer stressors are viruses and pesticides that regularly show up in combination with specific other stressors, compounding the negative effects through their interactions.

“Understanding which stressors co-occur and are likely to interact is profoundly important to unravelling how they are impacting the health and mortality of honey bee colonies,” says lead author, York Postdoctoral Fellow Sarah French of the Faculty of Science.

“There have been a lot of studies about major pesticides, but in this research, we also saw a lot of minor pesticides that we don’t usually think about or study. We also found a lot of viruses that beekeepers don’t typically test for or manage. Seeing the influencer stressors interact with all these other stressors, whether it be mites, other pesticides or viruses, was not only interesting, but surprising.”

French says the way influencer stressors co-occur with other stressors is similar to the way humans experience co-morbidities, such as when someone is diagnosed with heart disease. They are more likely to also have diabetes or high blood pressure or both, and each one impacts the other. “That’s similar to the way we examine bee colonies. We look at everything that’s going on in the colony and then compare or amalgamate all the colonies together to look at the broader patterns of what is happening and how everything is related. Two or multiple stressors can really synergize off each other leading to a much greater effect on bee health.”

From Québec to British Columbia, honey bee colonies were given the job of pollinating some of Canada’s most valuable crops — apples, canola oil and seed, highbush and lowbush blueberry, soybean, cranberry and corn. The study covered multiple time scales, providing numerous snapshots, rather than the usual single snapshot in time. The research team found that honey bees were exposed to an average of 23 stressors at once that combined to create 307 interactions.

Honey bees are a billion dollar industry. In 2021, honey bees contributed some $7 billion in economic value by pollinating orchards, vegetables, berries and oil seeds like canola, and produced 75 to 90 million pounds of honey. Figuring which stressors would provide the most benefit if managed would go a long way toward developing the right tools to tackle them, something beekeepers are often lacking.

The research is part of the BEECSI: ‘OMIC tools for assessing bee health project funded to the tune of $10 million by Genome Canada in 2018 to use genomic tools to develop a new health assessment and diagnosis platform powered by stressor-specific markers.

More research is needed to unravel how the stressors are interacting and impacting honey bee mortality and colony health going forward, says French. “It’s really teasing apart which of these compounds might have that relationship and how can we build off this to study those specific relationships.”

It can’t come soon enough, honey bees are currently facing poor health, colony loss, parasites, pathogens and heightened stressors worldwide. Some beekeepers in this country and the United States face a loss over winter of up to 60 per cent of their colonies.

“Our study suggests some combinations are occurring very frequently,” adds Zayed, “and that is relevant because we see them again and again, but we don’t know how these combinations affect bee health. It helps to prioritize which experiments we can now take back to the lab and establish how these interactions affect bees.”



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First evidence of human occupation in lava tube cave in Saudi Arabia

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‘Jumping genes’ repeatedly form new genes over evolution


Recent strides in interdisciplinary archaeological research in Arabia have unveiled new insights into the evolution and historical development of regional human populations, as well as the dynamic patterns of cultural change, migration, and adaptation to environmental fluctuations.

Despite the challenges posed by limited preservation of archaeological assemblages and organic remains in arid environments, these discoveries are reshaping our understanding of the region’s rich cultural heritage.

One such breakthrough led by Griffith University’s Australian Research Centre for Human Evolution (ARCHE), in collaboration with international partners, comes from the exploration of underground settings, including caves and lava tubes, which have remained largely untapped reservoirs of archaeological abundance in Arabia.

Through meticulous excavation and analysis, researchers have uncovered a wealth of evidence at Umm Jirsan, spanning from the Neolithic to the Chalcolithic/Bronze Age periods (~10,000-3,500 years ago).

“Our findings at Umm Jirsan provide a rare glimpse into the lives of ancient peoples in Arabia, revealing repeated phases of human occupation and shedding light on the pastoralist activities that once thrived in this landscape,” said Dr Mathew Stewart, the lead researcher and a Research Fellow at ARCHE.

“This site likely served as a crucial waypoint along pastoral routes, linking key oases and facilitating cultural exchange and trade.”

Rock art and faunal records attest to the pastoralist use of the lava tube and surrounding areas, painting a vivid picture of ancient lifeways.

Depictions of cattle, sheep, goat and dogs corroborate the prehistoric livestock practices and herd composition of the region.

Isotopic analysis of animal remains indicates that livestock primarily grazed on wild grasses and shrubs, while humans maintained a diet rich in protein, with a notable increase in the consumption of C3 plants over time, suggesting the emergence of oasis agriculture.

“While underground localities are globally significant in archaeology and Quaternary science, our research represents the first comprehensive study of its kind in Saudi Arabia,” added Professor Michael Petraglia, Director of ARCHE.

“These findings underscore the immense potential for interdisciplinary investigations in caves and lava tubes, offering a unique window into Arabia’s ancient past.”

The research at Umm Jirsan underscores the importance of collaborative, multidisciplinary approaches to archaeological inquiry and highlights the significance of Arabia’s archaeological heritage on the global stage.

Researchers involved in this study work in close partnership with the Heritage Commission, Saudi Ministry of Culture, and the Saudi Geological Survey. Additional partners include King Saud University and key institutions in the UK, the USA, and Germany.



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