https://www.sciencealert.com/swallowing-light-could-be-one-way-to-dissolve-ingestible-medical-devices-in-the-future

Swallowing a Pill Filled With Light Could Be The Key to Ingestible Medical Devices

DAVID NIELD
26 JAN 2020

The are an increasing number of medical devices that treat us by going in through the mouth (think bariatric balloon or esophageal stents) – but the process of getting them out again can be a lot more painful then putting them in.

main article imageNew research offers an alternative – devices that can break down in your stomach after you’ve swallowed a pill of light.

Yes, you read that right. The idea is that when medical devices inserted into the gastrointestinal tract reach the end of their life they could start to break down once they come into contact with certain kinds of light. They would then be processed through the body like any other kind of waste.

Thanks to newly developed light-sensitive hydrogel, devices could be easily removed if they weren’t working or after the course of treatment had finished – all patients would have to do is take a glowing LED pill that would trigger the dissolving process in the gut.

“We are developing a set of systems that can reside in the gastrointestinal tract, and as part of that, we’re looking to develop different ways in which we can trigger the disassembly of devices in the GI tract without the requirement for a major procedure,” says gastroenterologist Giovanni Traverso, from MIT.

The researchers tested their hydrogel in pig guts, finding that a bariatric balloon (often used to reduce appetite and treat obesity) based on the gel could be dissolved in as little as 30 minutes using an LED. These balloons are typically deflated via surgery and then removed via the mouth.

To make their device material, the researchers started with a light-sensitive polymer that includes a chemical bond that breaks when exposed to certain wavelengths of light. That was linked with stronger materials including polyacrylamide.

The end result is something that’s durable enough to last in the gut and yet still break down when exposed to light. By changing the mix of the hydrogel material, the researchers are able to vary the time it takes to break down.

light pill 2The bariatric balloon developed by the researchers. (Ritu Raman)

“You’re forming one polymer network and then forming another polymer network around it, so it’s really entangled,” says mechanical engineer Ritu Raman, from MIT. “That makes it very tough and stretchy.”

As well as being much more convenient, quicker and less painful than surgery, swallowing an LED is a very effective way of targeting ingestible devices – no light makes it down to the gastrointestinal tract naturally, so the LED doesn’t have to actually make contact with the device to start doing its work.

Different colours of light affect the degradation speed as well – ultraviolet light works faster than blue light, for example, but also carries a higher risk of causing damage to the cells in the body. All these factors will need to be tested in future research.

In the meantime, the technique shows a lot of future potential for a better way of removing devices from the body, from bariatric balloons to esophageal stents that can be used to help treat some types of cancer.

“We’re really looking at different triggers and how they perform, and whether we can apply them to different settings,” says Traverso.

“This study is a proof of concept that we can create this kind of material, and now we’re thinking about what are the best applications for it.”

The research has been published in Science Advances.

https://elemental.medium.com/you-have-no-idea-how-much-your-brain-is-ignoring-c587a1dc1fb5

You Have No Idea How Much Your Brain Is Ignoring

The eye-opening science behind ‘inattentional blindness’

Jeremy Sutton, PhD

Jan 24 · 3 min read

Photo: olasunkanmi ariyo/Getty Images

InInan iconic from 1999, Daniel Simons and Christopher Chabris, researchers at Harvard University, used a gorilla costume as a prop to explore visual perception.

Subjects were asked to watch a video and count the number of times players passed a basketball between a small, continually moving group of students. Partway through the video, a person dressed in a gorilla suit slowly walked into the frame, beat their chest, and walked off.

When Simons first tried the test with Harvard University students, he held his breath, but despite the gorilla being visible for nine seconds, only half of them noticed the unlikely walk-on. “Missing the gorilla is jarring. It’s natural to assume that you would see it, so it’s surprising and compelling when you realize what you’ve missed,” he says.

The was repeated in 2010, but this time it included subjects who were aware of the original video and its findings regarding unexpected objects. Though they identified the gorilla in the new film, they failed to notice other significant, including the backdrop’s color (shifting from red to gold) and a player walking off the court.

So, what is failing in us? Perhaps nothing.

For excellent evolutionary reasons, people have a remarkable ability to focus on what appears, in the moment, to be essential. A person tracking an antelope or avoiding a lion needs to be fully committed — distraction is not an option. Despite the apparent survival benefits of this hyper focus, people may be unaware of significant chunks of their surroundings.

“We remember vividly all the times we have noticed something unexpected or unusual, but have no idea how many times we have missed gorillas or unicycling clowns, unless a researcher explicitly brings it to our attention.”

This phenomenon, labeled “inattentional blindness” by cognitive scientists, occurs in response to a perceptual framework evolved by humans over thousands of years.

The brain attends to “sounds and other stimuli that it deems most important,” says George Slavich, a psychologist at the University of California, Los Angeles. Without this filtering mechanism, we would be overwhelmed by stimuli, our brains unable to process the excess of information.

 also shows that the human brain can be primed. Mentioning the word “doctor” before being shown a string of letters, and the subject is more likely to identify the word “nurse.” Priming works by stimulating an association in memory and provides further evidence of how easily attention can be influenced.

While such findings are interesting, they also raise serious concerns. A study in 2013 appearing in found that 83% of expert radiographers failed to notice a picture of — yes, you’ve guessed it — a gorilla in lung images. “Even expert searchers, operating in their domain of expertise, are vulnerable to inattentional blindness,” says Trafton Drew, an attention researcher at Harvard Medical School.

A published in November 2019 asked subjects to count how many times colored shapes bounced off the edge of a computer screen. While they kept track, a cross-shaped object passed in front of their field of vision for either 1.5 or 5 seconds. Surprisingly, the display time had only a small impact on whether subjects identified the rogue shapes.

“We remember vividly all the times we have noticed something unexpected or unusual, but have no idea how many times we have missed gorillas or unicycling clowns, unless a researcher explicitly brings it to our attention,” says Vanessa Beanland, member of the Australasian College of Road Safety, and reported in .

https://phys.org/news/2020-01-discovery-cells.html

Discovery sheds new light on how cells move

Discovery sheds new light on how cells move
Image of a layer of cells showing cell peripheries (green), nuclei (blue), and actin fibers that generate traction (magenta). Credit: Notbohm Research Group

When we cut our skin, groups of cells rush en masse to the site to heal the wound.

But the complicated mechanics of this collective cell movement—which are facilitated by rearrangements between each cell and its neighbors—have made it challenging for researchers to decipher what’s actually driving it.

“If we can understand the key factors causing , then we could perhaps develop new treatments to speed up wound healing,” says Jacob Notbohm, an assistant professor of engineering physics at the University of Wisconsin–Madison.

Notbohm and doctoral student Aashrith Saraswathibhatla recently made a surprising discovery that sheds new light on how this collective cell migration happens. They detailed their findings today in the journal Physical Review X.

Through experiments, they found that the force each cell applies to the surface beneath it—in other words, traction—is the dominant physical factor that controls  and motion as cells travel as a group.

Notbohm says this unexpected finding provides a new interpretation of recent theoretical models.

Researchers have known that cell shape plays an important role in how they rearrange and collectively migrate. For example, circular cells packed together within a single layer can’t easily exchange positions with neighboring cells; think of being stuck shoulder-to-shoulder in a large crowd where it’s impossible to move.

On the other hand, cells that have more elongated shapes can easily slide past their neighbors.

Credit: University of Wisconsin-Madison

“These long and skinny cells can be packed in infinite configurations, so it’s very easy for them to rearrange. That facilitates the motion of the collective,” Notbohm says.

Since elongated cells have greater perimeters, most computer models have predicted the forces at the periphery of each cell are the most important for dictating its shape.

Notbohm and Saraswathibhatla set out to test that theory in the lab.

Their experiments used fluorescent imaging to assess forces at the periphery of each cell in a single layer of epithelial cells, a type of cells that line surfaces in the body like skin and blood vessels. They also placed the cells on a soft gel surface and analyzed how the gel deformed as cells migrated across it. The gel test allowed them to quantify traction, or how strongly the  tugged on the surface.

In addition, they used chemicals to decrease or increase forces produced by each cell and studied the effects of those changes.

In the end, Notbohm says their experiments showed that, in fact, the force a cell applies to the surface beneath it primarily controls its shape.

“This was quite surprising because the key factors affecting a cell’s perimeter are underneath the cell. They are nowhere near the periphery of the cell,” he says.

And now, they can focus on what’s important. Looking at the cell-substrate interface, Notbohm hopes to enable further advances in this area.

“The good news is the general phenomena of the models is still correct. This discovery just changes our understanding about the theory,” he says. “That’s really important, because to eventually develop a new intervention to accelerate  you need to understand the key factors in the cell that are affecting its shape and motion.”


Explore further

Discovery reveals tractionless motion is possible


More information: Aashrith Saraswathibhatla et al. Tractions and Stress Fibers Control Cell Shape and Rearrangements in Collective Cell Migration, Physical Review X (2020). DOI: 10.1103/PhysRevX.10.011016

Journal information: Physical Review X

https://cleantechnica.com/2020/01/25/researchers-in-us-china-use-machine-learning-to-make-better-solar-panels/

Researchers In US & China Use Machine Learning To Make Better Solar Panels

January 25th, 2020 by 


Solar power and advanced computing are a key cleantech intersection point. From renewables return on investment optimization to optimal rooftop commercial solar deployment, machine learning is helping us get more efficient and effective in our global transformation.

But it’s deeper than that. Researchers in the US and China are using machine learning to discover new solar panel chemistries to increase the base efficiency and economic effectiveness of solar panels. They are trialing hundreds or thousands of combinations in virtual test beds before bringing them into the physical world, a key element of the machine-to-reality value proposition.

Bright light and rays illustration

Let’s start in the United States with Jinxin Li, Basudev Pradhan, Surya Gaur, and Jayan Thomas from the sun-drenched campus of the University of Central Florida. Their focus is on perovskite solar panels. This set of chemistries featuring inorganic and organic elements has achieved efficiencies of 28%, exceeding standard silicon maximum efficiencies, and is advancing quickly. However, the options for composition are very large, and the number of researchers limited. In their study, published under the title Predictions and Strategies Learned from Machine Learning to Develop High‐Performing Perovskite Solar Cells in Wiley, the team attempted to simplify this process. They used 333 data points from about 2,000 peer-reviewed studies on the subject to train a model to look for higher probability chemistries. They’ve not only identified the most likely candidates for physical research, but with reasonable accuracy predicted performance based on underlying chemical factors. Their work supports and suggests approaching the theoretical Shockley-Queisser limit for individual solar cell efficiency as well. While solar panels have diminished in price mostly due to massive economies of scale for manufacturing, distribution and construction, increased efficiency with cheap and plentiful minerals still has room to bear fruit.

Also in the US are Baskar Ganapathysubramanian and team at Iowa State University, supported by grants from the Department of Energy’s Advanced Research Projects Agency – Energy (ARPA-E). The extended team spans the United States with New York University, California’s Stanford University, and a member from NREL in Colorado. Their focus is on the application of machine learning to organic, thin-film solar panels. This subset of solar technology has been less efficient than conventional solar panels and the perovskite chemistries, but the benefit is highlighted in the name. Thinness equates to lightness, flexibility, and even transparency. They’ve been used in integrated photovoltaics in consumer devices, window-pane layers which generate electricity and conventional solar farms, but they’ve been in decline in recent years in favor of more efficient technologies. They too have room to improve, but run into the same problem of the vast number of compositional choices that can be made, something difficult to deal with through conventional research approaches. Enter Ganapathysubramanian’s team. Their intent is the same as the perovskite-focused researchers, to find chemistries which are higher efficiency and cheaper to manufacture. It’s early days for them, and their work is in aid of a larger goal of applying the approach to multiple domains.

The next team working on solar technology with machine learning approaches are Wenbo Sun, Yujie Zheng, et al., out of Chongqing University, the North China University of Science and Technology, and the Chinese Academy of Sciences. Their focus is on the emerging space of organic solar cells, which use organic polymers or molecules to capture the energy of the sun and convert it to useful electricity. Efficiency is lower still in this space so far, with maximum efficiencies under 20% to date. But the range of organic chemistries is vast, it’s a new field, and the upsides are large if they can be made more efficient and durable. Once again, this is a light, thin-film technology and inherently flexible and fast to manufacture. And once again, machine learning comes to the rescue. As the approach requires data and organic films are relatively new, the team first started by assembling a massive dataset of over 1,700 materials from literature. They then explored how to fingerprint the molecular structures most effectively for application of machine learning approaches, and finally verified it against a new set of materials to assess predictive quality. And predictive quality is good. Expect more advances from this team in this solar technology over the coming years, and a new breed of thin, light, and cheap solar panels to emerge from China because of it.

The world is vast, and the chemicals and organic compounds within it innumerable and dizzying in their combinations and permutations. Machine learning is helping researchers find the highest probability combinations for more efficient and cheaper solar technology, something which will benefit everyone in the world.

https://mobilesyrup.com/2020/01/26/tesla-update-hints-towards-future-changes-model-s-model-x/

New Tesla update hints towards future changes for Model S, Model X

A reverse-engineer has leaked that there may be a built-in wireless Qi charger in the future By Aisha Malik@AiishaMalik1JAN 26, 20201:03 PM

As the first new update of the year is starting to roll out to Teslas, a reverse engineer has examined the software and outlined what might be next. The researcher, who goes by Greentheonly on Twitter, notes that the Model S and Model X may potentially include a built-in wireless Qi charger in the future. He also notes that there may be a new suspension version, a new charge port and new seats. The last time the Model S got a major change for its interior was back in 2016, so it wouldn’t be surprising if the manufacturer is looking to make some updates. Last year, there were rumours that there might be a possible Model S refresh, and Elon Musk has hinted that a higher-performance Model S will be coming sometime this year. The higher-performance Model S is supposedly going to have bigger battery packs. The new software update is currently rolling out to vehicles in China, and is expected to roll out globally sometime soon.

https://www.theglobeandmail.com/opinion/article-older-longer-the-super-aging-of-canadians-has-taken-everyone-by/

Older, longer: The super-aging of Canadians has taken everyone by surprise

Every generation is having fewer children than the one before it, leaving fewer and fewer people to care for us in our increasingly long lives. It is a crisis we ignore at our own peril

John Ibbitson is a writer-at-large for The Globe and Mail. His latest book is Empty Planet: The Shock of Global Population Decline, co-authored with Darrell Bricker.

The oldest of the baby boomers will turn 75 next year. The generation that defined us all, that fought for peace and cheap drugs and no-fault divorce, that gave us the personal computer and the internet and the culture wars and the war on terror, that is responsible for the best and the worst of the human condition as we live it today, is getting old. And as always – always – they’re making it all about them.

The boomers are living inconveniently long lives. Over the course of the next three decades, the number of people aged 85 and older will more than triple.

“More and more people are living into their 80s and 90s than were ever expected to,” says Parminder Raina, Canada research chair in geroscience at McMaster University. “The rapidity of aging is the real issue for policy makers.”

And just as you’d expect, the boomers haven’t saved enough. Which means looking after them will cost younger generations a great deal of time and money.

Worst of all, because the boomers were also the first generation to stop having enough children to replace themselves, there are fewer young people available to look after the old.

Every generation is having fewer children than the generation before. Things are going to be even harder for Generation X. And harder still for the millennials.

“This is a fundamental, paradigmatic shift in society, and for too long we’ve buried our heads,” says Michael Nicin, executive director of Ryerson University’s National Institute on Ageing.

This isn’t some abstract policy challenge. This is about us, caring for our parents or our spouse. This is us, worried about our children’s future. This is about everyone getting older every day, with not enough money to pay for it.

Unless governments, families and individuals act now to bend the curve on the cost of aging, many of us will not enjoy our later years.

When the pensions and public health-care systems that Canadians rely on today were first put in place in the 1960s, the life expectancy of a man was 69 years, just four years after he was likely to retire. But a man who turns 65 today will live, on average, another 19 years, and a woman will live another 22 years, according to Statistics Canada.

And longevity continues to increase. The fastest-growing age group in Canada is centenarians. There are more than 10,000 of them today, three times the number in 2001, and there should be about 40,000 by mid-century.

Over the same decades in which longevity has increased, the fertility rate has decreased. Today it sits at 1.5, half a baby short of the 2.1 children per woman, on average, needed to keep a population stable. If it weren’t for this country’s high immigration intake, Canada’s population would eventually start to decline, just as it is declining or about to decline in dozens of countries around the world, from China to Japan to Italy to Russia.

As a result of increasing longevity and decreasing fertility, Canadian society is aging rapidly. In 1982, the median age in Canada was 30. Today it is 41. There are now more people 65 and older than people 14 and younger in Canada, and that will widen in the years ahead.
“Lower fertility rates are going to mean that services that have traditionally been provided by the family – namely women – will need to be paid for,” says Bonnie-Jeanne MacDonald, who researches family security issues at the National Institute on Ageing. “It won’t be cheap.”

That’s an understatement.

The costs of caring for the elderly will be staggering. By the time someone who is around 40 today retires, long-term-care costs will be eating up about 20 per cent of all government revenue generated by personal income taxes.

And even as those costs go up, Canada’s tax base will erode further because fewer people are entering the work force every year.

“The role of population aging on economic growth might have been underappreciated,” says Colin Busby, a research director at the Institute for Research on Public Policy, a Montreal-based think tank. “It might be an even stronger driver of the decline in economic growth and government revenues going forward.”

Individually, Canadians are ill-prepared for leaving work. Half of all Canadians approaching retirement do not have a workplace pension. The median level of retirement savings for these people is $3,000. No, there isn’t a missing zero.

Three. Thousand. Dollars.

“Canadians without pension plans are not saving adequately on their own using the retirement saving tax-incentive tools given to them,” Ms. MacDonald says.

The cost to governments of caring for older Canadians is set to skyrocket. By 2050, there will be more than twice as many people needing long-term care – care provided outside a hospital. By then, the cost to all levels of government will have tripled, from $22-billion to $71-billion.

Many of those needing care will have dementia. Eight in 10 people in long-term care today have some form of the condition, according to Carole Estabrooks, director of the TREC (Translating Research in Elder Care) program at the University of Alberta. The number of Canadians with dementia is expected to grow from 564,000 in 2016 to 920,000 in 2031, an increase of 63 per cent.

“It’s a huge issue,” she says.

And sloughing off the burden of care onto families will not be an option for any future hardhearted government, because 75 per cent of the cost of long-term care in Canada is already provided, for free, by family members, usually women. And that burden will increase with every passing year.

Almost all of the overworked, underpaid personal support workers in nursing homes are also women. Their work is greatly undervalued. “It’s personal support, it’s companionship,” Ms. Estabrooks says. “It’s helping the people they care for have a good day, have a good moment, trying to ensure they get some small enjoyment, some pleasure out of life. And that’s the kind of stuff that tends to get shorted.” But as labour shortages increase, wages are bound to rise. In any case, whether paid or unpaid, with every year there will be more people needing care and fewer people available to provide it.

A registered nurse and caregiver walk down the narrow hallways of a now-closed retirement residence in Duncan, B.C.Are you retirement-ready?

Try The Globe and Mail’s calculator to find out how much of your working income you’ll need in retirement.

At this stage, most Canadians aren’t prepared to accept realistic measures to rein in the increasing costs of an aging society. One measure would be to raise the age of retirement. With most Canadians healthy into their 80s, pensioning someone off at 65 is like giving them a paid vacation.

But when Stephen Harper’s Conservatives raised the age for receiving Old Age Security from 65 to 67, the howls prompted Justin Trudeau’s Liberal government to drop the age back to 65. In any case, whether through financial need, poor planing or both, many Canadians start taking Canada Pension Plan benefits when they turn 60, even though the long-term benefit is lower than it would be if they waited till 65 or, even better, 70.

Another approach might be to forcibly unlock the wealth accumulated by older Canadians. In the United States, according to a report in Forbes magazine, the silent generation (people over 75) held about 1.3 times the amount of wealth of boomers, more than twice that of Gen Xers and 23 times that of millennials. Equity built up in real estate accounted for much of the discrepancy.

Instead of giving seniors discounts and tax breaks, perhaps it’s time to ask them to pay the full costs of the health and long-term care they receive. Such a proposal would be political suicide, however, since there are so many seniors, who historically have been more likely to vote than their millennial counterparts.

One way to help smooth the aging curve might lie in recruiting skilled young immigrants to replace the missing workers from the dearth of births. And Canada is doing exactly that. There were more than 570,000 people in Canada on student visas at the end of 2018, almost 75 per cent more than in 2014. Many of these students can apply for permanent-resident status after graduation.

But immigration can have only a limited impact on societal aging, in part because immigrants often apply to bring their parents over as well. And opening the immigration floodgate beyond the 341,000 that Canada is expected to take in this year could provoke strong opposition from the native born. The populist Coalition Avenir Québec government in Quebec, for example, is cutting back on immigrants and requiring new arrivals to take a Quebec values test.

Another approach to coping with the costs of aging has barely registered with most people: long-term-care insurance. As with other forms of workplace insurance, workers and employers would make contributions toward a fund that would cover the costs of home care, assisted living, nursing home and palliative care when they need it later in life.

There are plenty of questions: How much would it cost? Would older people today be eligible to receive the funds, or would only those who had contributed for decades qualify? Several countries, including Germany, already have such a program in place, which could serve as a template.

At McMaster University, Prof. Raina would like to see long-term-care insurance or other forms of government support for people who must work less in order to care for someone who has dementia or other intensive needs. He is also a strong proponent of care centres for the elderly, where caregivers can drop off their charges for part of the day while they work or just take a break.

“I think some kind of respite care that is based in the community is really, really important,” he says.

Ms. Estabrooks at TREC emphasizes the need to help seniors “age in place.”

“We’ve got to enhance community supports, and home care is probably the biggest one,” she says. But what matters most is moving from this study and that pilot program to full-scale initiatives. “We can do this by tackling each problem one solution at a time.“

Inge Csongradi, 89, sits in the North York apartment where she has lived by herself for two decades.Housing anxiety for seniors

In the Toronto area’s heated housing market, three women over 80 face hard choices about whether to stay or go. Photographer Emma Kreiner tells their stories.

Without long-term solutions to the fiscal challenges of an aging society, intergenerational tensions are likely to rise. In some countries, those tensions are already severe.

In December’s British elections, English attitudes toward Brexit – with supporters of leaving the European Union inclined toward the Conservatives and opponents toward most other parties – were defined by age more than by geography or class. The youngest voters most fiercely opposed Brexit, and the oldest most fervently supported it, no matter where they lived or what their income.

“Age is now one of the key dividing lines in British politics,” said Gideon Skinner, public affairs research director for Ipsos MORI. In the election, according to the British polling firm, Labour had a 26-point lead among 18-to-34-year-olds, while the Conservatives had a 37-point lead among people 65 and older.

Some believe younger voters are more socially tolerant than older voters. But that isn’t entirely true. “Younger generations are generally far more accepting of diversity of gender, race, religion as compared with an older generation,” observes Lorraine Mercer, a professor of gerontology at Huntington University, which is part of Sudbury’s Laurentian University. “And yet, I don’t think they’re as accepting of older people. All the stereotypes of older people they still buy into.” Ageism – discriminating against a person because they are older – may be the last barrier to full diversity.

Although, as Prof. Raina says, ageism spans the generations. “Older people can be ageist toward other older people.”

There is, however, one massively important, although impossible to quantify, counterbalance to the prospect of growing intergenerational tension: love.

As Mr. Nicin points out, children want their parents to live long and healthy lives. And parents are anxious not to be a burden to their children. Whatever the official age of retirement, many people are working past 65 of their own volition. Pension experts are exploring new options to encourage retirement savings.

“We are all worried about each other,” Mr. Nicin says. “We all care for each other.” He expects to see an increase in intergenerational housing over the years, as children, parents and grandparents lean on one another for support. “The more we depend on each other, and not on the state, the better off we are,” he believes.

For as long as we can foresee, there will be more older and fewer younger people among us every year. If we are to live well, we must care for one another, however old we are and whatever we may need.

 

https://phys.org/news/2020-01-genes-stabilize-dna-patterns.html

‘Jumping genes’ help stabilize DNA folding patterns

dna
Credit: CC0 Public Domain

“Jumping genes”—bits of DNA that can move from one spot in the genome to another—are well-known for increasing genetic diversity over the long course of evolution. Now, new research at Washington University School of Medicine in St. Louis indicates that such genes, also called transposable elements, play another, more surprising role: stabilizing the 3-D folding patterns of the DNA molecule inside the cell’s nucleus.

The study appears Jan. 24 in the journal Genome Biology.

The DNA molecule inside the nucleus of any human cell is more than six feet long. To fit into such a small space, it must fold into precise loops that also govern how  are turned on or off. It might seem counterintuitive that bits of DNA that randomly move about the  can provide stability to these folding patterns. Indeed, the discovery contradicts a long-held assumption that the precise order of letters in the DNA sequence always dictates the broader structure of the DNA molecule.

“In places where the larger 3-D folding of the genome is the same between mice and humans, you expect the sequence of the letters of the DNA anchoring that shape to be conserved there as well,” said senior author Ting Wang, Ph.D., the Sanford C. and Karen P. Loewentheil Distinguished Professor of Medicine. “But that’s not what we found, at least not in the portions of the genome that in the past have been called ‘junk DNA.'”

Studying DNA folding in mouse and human blood cells, the researchers found that in many regions where the folding patterns of DNA are conserved through evolution, the genetic sequence of the DNA letters establishing these folds is not. It is ever so slightly displaced. But this changing sequence, a genetic turnover, doesn’t cause problems. Because the structure largely stays the same, the function presumably does, too, so nothing of importance changes.

“We were surprised to find that some young  serve to maintain old structures,” said first author Mayank N.K. Choudhary, a doctoral student in Wang’s lab. “The specific sequence may be different, but the function stays the same. And we see that this has happened multiple times over the past 80 million years, when the common ancestors of mice and humans first diverged from one another.”

The fact that a new transposable element can insert itself and serve the same role as an existing anchor creates a redundancy in the regulatory portions of the genome—regions of the DNA molecule that determine how and when genes are turned on or off.

According to the researchers, this redundancy makes the genome more resilient. In providing both novelty and stability, jumping genes may help the mammalian genome strike a vital balance—allowing animals the flexibility to adapt to a changing climate, for example, while preserving biological functions required for life, protecting against the DNA damage that is wrought by living and reproducing on Earth over the span of deep time, measured in tens to hundreds of millions of years.

Even so, the researchers were careful to distinguish between portions of the genome that hold genes responsible for producing proteins and the rest of the genome. In genes that code for proteins, the genetic sequence and the structure are both conserved, and this study does not contradict that. However, the new research suggests that jumping genes in the non-protein coding areas of the genome follow different rules of conservation than the protein-coding genes.

“Our study changes how we interpret genetic variation in the noncoding regions of the DNA,” Wang said. “For example, large surveys of genomes from many people have identified a lot of variations in noncoding regions that don’t seem to have any effect on gene regulation, which has been puzzling. But it makes more sense in light of our new understanding of transposable elements—while the local sequence can change, but the function stays the same.

“We may need to revisit these types of studies in light of the new understanding we now have of transposable elements,” he added. “We have uncovered another layer of complexity in the genome sequence that was not known before.”


Explore further

Taming the genome’s ‘jumping’ sequences


More information: Mayank NK Choudhary et al, Co-opted transposons help perpetuate conserved higher-order chromosomal structures, Genome Biology (2020). DOI: 10.1186/s13059-019-1916-8

Journal information: Genome Biology