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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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Warming of Antarctic deep-sea waters contribute to sea level rise in North Atlantic, study finds

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‘Jumping genes’ repeatedly form new genes over evolution


Analysis of mooring observations and hydrographic data suggest the Atlantic Meridional Overturning Circulation deep water limb in the North Atlantic has weakened. Two decades of continual observations provide a greater understanding of the Earth’s climate regulating system.

A new study published in the journal Nature Geoscience led by scientists at University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, and the National Oceanic and Atmospheric Administration’s Atlantic Oceanographic and Meteorological Laboratory, found that human-induced environmental changes around Antarctica are contributing to sea level rise in the North Atlantic.

The research team analyzed two decades of deep sea oceanographic data collected by observational mooring programs to show that a critical piece of Earth’s global system of ocean currents in the North Atlantic has weakened by about 12 percent over the past two decades.

“Although these regions are tens of thousands of miles away from each other and abyssal areas are a few miles below the ocean surface, our results reinforce the notion that even the most remote areas of the world’s oceans are not untouched by human activity,” said the study’s lead author Tiago Biló, an assistant scientist at the Rosenstiel School’s NOAA Cooperative Institute for Marine and Atmospheric Studies.

As part of the NOAA-funded project DeepT (Innovative analysis of deep and abyssal temperatures from bottom-moored instrument), the scientists analyzed data from several observational programs to study changes over time in a cold, dense, and deep water mass located at depths greater than 4,000 meters (2.5 miles) below the ocean surface that flow from the Southern Ocean northward and eventually upwells to shallower depths in other parts of the global ocean such as the North Atlantic.

This shrinking deep-ocean branch — that scientists call the abyssal limb — is part of the Atlantic Meridional Overturning Circulation (AMOC), a three-dimensional system of ocean currents that act as a “conveyer belt” to distribute heat, nutrients, and carbon dioxide across the world’s oceans.

This near-bottom branch is comprised of Antarctic bottom water, which forms from the cooling of seawater in the Southern Ocean around Antarctica during winter months. Among the different formation mechanisms of this bottom water, perhaps the most important is the so-called brine rejection, a process that occurs when salty water freezes. As sea ice forms, it releases salt into the surrounding water, increasing its density. This dense water sinks to the ocean floor, creating a cold, dense water layer that spreads northward to fill all three ocean basins — the Indian, Pacific, and Atlantic oceans. During the 21st century, the researchers observed that the flow of this Antarctic layer across 16°N latitude in the Atlantic had slowed down, reducing the inflow of cold waters to higher latitudes, and leading to warming of waters in the deep ocean.

“The areas affected by this warming spans thousands of miles in the north-south and east-west directions between 4,000- and 6,000-meters of depth,” said William Johns, a co-author and professor of ocean sciences at the Rosenstiel School. “As a result, there is a significant increase in the abyssal ocean heat content, contributing to local sea level rise due to the thermal expansion of the water.”

“Our observational analysis matches what the numerical models have predicted — human activity could potentially impose circulation changes on the entire ocean,” said Biló. “This analysis was only possible because of the decades of collective planning and efforts by multiple oceanographic institutions worldwide.”



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Octopus inspires new suction mechanism for robots

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‘Jumping genes’ repeatedly form new genes over evolution


A new robotic suction cup which can grasp rough, curved and heavy stone, has been developed by scientists at the University of Bristol.

The team, based at Bristol Robotics Laboratory, studied the structures of octopus biological suckers, which have superb adaptive suction abilities enabling them to anchor to rock.

In their findings, published in the journal PNAS today, the researchers show how they were able create a multi-layer soft structure and an artificial fluidic system to mimic the musculature and mucus structures of biological suckers.

Suction is a highly evolved biological adhesion strategy for soft-body organisms to achieve strong grasping on various objects. Biological suckers can adaptively attach to dry complex surfaces such as rocks and shells, which are extremely challenging for current artificial suction cups. Although the adaptive suction of biological suckers is believed to be the result of their soft body’s mechanical deformation, some studies imply that in-sucker mucus secretion may be another critical factor in helping attach to complex surfaces, thanks to its high viscosity.

Lead author Tianqi Yue explained: “The most important development is that we successfully demonstrated the effectiveness of the combination of mechanical conformation — the use of soft materials to conform to surface shape, and liquid seal — the spread of water onto the contacting surface for improving the suction adaptability on complex surfaces. This may also be the secret behind biological organisms ability to achieve adaptive suction.”

Their multi-scale suction mechanism is an organic combination of mechanical conformation and regulated water seal. Multi-layer soft materials first generate a rough mechanical conformation to the substrate, reducing leaking apertures to just micrometres. The remaining micron-sized apertures are then sealed by regulated water secretion from an artificial fluidic system based on the physical model, thereby the suction cup achieves long suction longevity on diverse surfaces but with minimal overflow.

Tianqi added: “We believe the presented multi-scale adaptive suction mechanism is a powerful new adaptive suction strategy which may be instrumental in the development of versatile soft adhesion.

“Current industrial solutions use always-on air pumps to actively generate the suction however, these are noisy and waste energy.

“With no need for a pump, it is well known that many natural organisms with suckers, including octopuses, some fishes such as suckerfish and remoras, leeches, gastropods and echinoderms, can maintain their superb adaptive suction on complex surfaces by exploiting their soft body structures.”

The findings have great potential for industrial applications, such as providing a next-generation robotic gripper for grasping a variety of irregular objects.

The team now plan to build a more intelligent suction cup, by embedding sensors into the suction cup to regulate suction cup’s behaviour.



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One third of China’s urban population at risk of city sinking, new satellite data shows

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‘Jumping genes’ repeatedly form new genes over evolution


Land subsidence is overlooked as a hazard in cities, according to scientists from the University of East Anglia (UEA) and Virginia Tech.

Writing in the journal Science, Prof Robert Nicholls of the Tyndall Centre for Climate Change Research at UEA and Prof Manoochehr Shirzaei of Virginia Tech and United Nations University for Water, Environment and Health, Ontario, highlight the importance of a new research paper analysing satellite data that accurately and consistently maps land movement across China.

While they say in their comment article that consistently measuring subsidence is a great achievement, they argue it is only the start of finding solutions. Predicting future subsidence requires models that consider all drivers, including human activities and climate change, and how they might change with time.

The research paper, published in the same issue, considers 82 cities with a collective population of nearly 700 million people. The results show that 45% of the urban areas that were analysed are sinking, with 16% falling at a rate of 10mm a year or more.

Nationally, roughly 270 million urban residents are estimated to be affected, with nearly 70 million experiencing rapid subsidence of 10mm a year or more. Hotspots include Beijing and Tianjin.

Coastal cities such as Tianjin are especially affected as sinking land reinforces climate change and sea-level rise. The sinking of sea defences is one reason why Hurricane Katrina’s flooding brought such devastation and death-toll to New Orleans in 2005.

Shanghai — China’s biggest city — has subsided up to 3m over the past century and continues to subside today. When subsidence is combined with sea-level rise, the urban area in China below sea level could triple in size by 2120, affecting 55 to 128 million residents. This could be catastrophic without a strong societal response.

“Subsidence jeopardises the structural integrity of buildings and critical infrastructure and exacerbates the impacts of climate change in terms of flooding, particularly in coastal cities where it reinforces sea-level rise,” said Prof Nicholls, who was not involved in the study, but whose research focusses on sea-level rise, coastal erosion and flooding, and how communities can adapt to these changes.

The subsidence is mainly caused by human action in the cities. Groundwater withdrawal, that lowers the water table is considered the most important driver of subsidence, combined with geology and weight of buildings.

In Osaka and Tokyo, groundwater withdrawal was stopped in the 1970s and city subsidence has ceased or greatly reduced showing this is an effective mitigation strategy. Traffic vibration and tunnelling is potentially also a local contributing factor — Beijing has sinking of 45mm a year near subways and highways. Natural upward or downward land movement also occurs but is generally much smaller than human induced changes.

While human-induced subsidence was known in China before this study, Profs Nicholls and Shirzaei say these new results reinforce the need for a national response. This problem happens in susceptible cities outside China and is a widespread problem across the world.

They call for the research community to move from measurement to understanding implications and supporting responses. The new satellite measurements are delivering new detailed subsidence data but the methods to use this information to work with city planners to address these problems needs much more development. Affected coastal cities in China and more widely need particular attention.

“Many cities and areas worldwide are developing strategies for managing the risks of climate change and sea-level rise,” said Prof Nicholls. “We need to learn from this experience to also address the threat of subsidence which is more common than currently recognised.”



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