Health24.com | ‘Hidden’ gene discovered in Covid-19 virus could give more insight into its ability to spread

  • Scientists have discovered a ‘hidden’ gene in the genetic code of SARS-CoV-2
  • This overlapping gene, the team said, is unlikely to be detected by the human body’s T-cells
  • Earlier findings have also found mysterious genes, all helpful in the search for treatments and vaccines 

Researchers from the American Museum of Natural History have identified a new “hidden” gene in SARS-CoV-2, the virus that causes Covid-19, and say this may explain why it is so highly infectious.

The discovery of the “overlapping gene”, named ORF3d, could have a significant impact on how we combat the virus, the research team wrote. Overlapping genes (OLGs) are a type of ‘gene within a gene’, effectively concealed in a string of nucleotides, ScienceAlert explains.

“Overlapping genes may be one of an arsenal of ways in which coronaviruses have evolved to replicate efficiently, thwart host immunity, or get themselves transmitted,” said lead author Chase Nelson, a postdoctoral researcher at Academia Sinica in Taiwan and a visiting scientist at the American Museum of Natural History.

“Knowing that overlapping genes exist and how they function may reveal new avenues for coronavirus control, for example through antiviral drugs.”

Their findings were published in the journal eLife.

ORF3d unlikely to be detected by T-cells

According to the team’s findings, the newly discovered gene is present in a previously discovered pangolin coronavirus. This, they say, possibly reveals repeated loss or gain of this gene during the evolution of the new coronavirus, as well as related viruses.

The gene has also shown to elicit a strong antibody response in Covid-19 patients, the researchers said, demonstrating that its protein is manufactured during human infection.

“We don’t yet know its function or if there’s clinical significance,” Nelson said. “But we predict this gene is relatively unlikely to be detected by a T-cell response, in contrast to the antibody response.

“And maybe that has something to do with how the gene was able to arise.”

T-cells are “natural killers”, whose job is to find infected cells in the human body and destroy them, Professor Thomas Scriba, deputy director of immunology and laboratory director at the South African Tuberculosis Vaccine Initiative, University of Cape Town, previously told Health24. 

Mysterious genes explained

Overlapping genes are hard to spot, the researchers explained, as they are virtually hidden from view in the virus’s genome, and therefore easily overlooked.

Most scientific computer programmes are not designed to find them, they said, although OLGs are relatively common in DNA and RNA viruses – partly because RNA viruses (such as SARS-CoV-2) have a high mutation rate.

“Missing overlapping genes puts us in peril of overlooking important aspects of viral biology,” Nelson said.

“In terms of genome size, SARS-CoV-2 and its relatives are among the longest RNA viruses that exist. They are thus perhaps more prone to ‘genomic trickery’ than other RNA viruses.”

Previous discoveries on hidden mutations

Earlier this year, scientists from a separate study also suggested that SARS-CoV-2 exploits a rare, ‘silent’ (hidden) gene mutation in certain people, and said it may provide clarity on why two young and healthy individuals can be so differently affected by the virus, Health24 reported. 

In another breakthrough study, researchers uncovered a second receptor, called neuropilin-1, which may explain why the virus is so highly infectious.

This receptor is widespread in human tissues, they said, and explained that the new coronavirus has a convenient advantage when infecting human cells. These discoveries are all critical in the race to develop a vaccine and treatment for Covid-19.

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Image: Getty/Andriy Onufriyenko

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COVID-delayed Arctic research cruise yields late-season data

Researchers studying the Bering and Chukchi seas for three weeks in October found no ice and a surprisingly active ecosystem as they added another year’s data to a key climate change record.

The research vessel Norseman II carried scientists from the University of Alaska Fairbanks, the University of Maryland Center for Environmental Science and Clark University.

Maintaining the continuity of long-term observations is crucial as the region is affected by climate change. For example, the researchers collected sediments and small bottom-dwelling animals to help document harmful algal blooms that are becoming more common as Arctic waters warm. The blooms pose a threat to the humans and marine mammals that eat them.

Because of pandemic-related delays, the cruise began on Oct. 2 — a much later start than originally planned. Historically, the Bering and Chukchi sea ecosystem transitioned to lower-level activity as sea ice formed in October.

This year, unseasonably warm ocean temperatures delayed sea ice formation by several weeks. The lack of ice likely allowed the greater biological activity observed by the researchers.

“The recovered data are already showing the effects of oceanic heat that extends further into the fall and early winter,” said Seth Danielson of UAF’s College of Fisheries and Ocean Sciences.

The scientists collected data for several marine science programs monitoring the Pacific Arctic ecosystem.

The Distributed Biological Observatory, led by Jacqueline Grebmeier of UMCES, has been sampling productive hot spots since the late 1980s in U.S. Arctic waters.

The Arctic Marine Biodiversity Observing Network, led by Katrin Iken at UAF’s College of Fisheries and Ocean Sciences, is part of a national network studying how biodiversity and species distributions are changing as a result of climate change in the U.S. Arctic.

The researchers also visited the Chukchi Ecosystem Observatory, a set of highly instrumented oceanographic moorings that monitor the ecosystem year-round. “We only get one chance each year to deploy fresh sensors with new batteries, so this cruise was important to avoid interruptions to the observations,” said Danielson, who leads the project.

“This was a really worthwhile effort that paid off in making biological data available from a part of the year where there have been historically few observations,” said Grebmeier, the cruise’s chief scientist.

To protect communities in the Bering Strait from potential exposure to the COVID-19 virus, the team completed quarantines and multiple tests in Anchorage before the cruise. They traveled by chartered aircraft to Nome and were taken directly to the research vessel, bypassing the passenger terminal.

Everyone aboard also adhered to COVID-19 health and safety mandates from their institutions and followed an isolation and travel plan in accordance with the Port of Nome and the State of Alaska.

Funding for the cruise was provided by the National Oceanic and Atmospheric Administration, the North Pacific Research Board and the National Oceanic Partnership Program, which also includes funding by the Bureau of Ocean Energy Management.

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Materials provided by University of Alaska Fairbanks. Note: Content may be edited for style and length.

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Sensor for smart textiles survives washing machine, cars and hammers

Think about your favorite t-shirt, the one you’ve worn a hundred times, and all the abuse you’ve put it through. You’ve washed it more times than you can remember, spilled on it, stretched it, crumbled it up, maybe even singed it leaning over the stove once.

We put our clothes through a lot and if the smart textiles of the future are going to survive all that we throw at them, their components are going to need to be resilient.

Now, researchers from the Harvard John A. Paulson School of Engineering and Applied Sciences and the Wyss Institute for Biologically Inspired Engineering have developed an ultra-sensitive, seriously resilient strain sensor that can be embedded in textiles and soft robotic systems.

The research is published in Nature.

“Current soft strain gauges are really sensitive but also really fragile,” said Oluwaseun Araromi, a Research Associate in Materials Science and Mechanical Engineering at SEAS and the Wyss Institute and first author of the paper. “The problem is that we’re working in an oxymoronic paradigm — highly sensitivity sensors are usually very fragile and very strong sensors aren’t usually very sensitive. So, we needed to find mechanisms that could give us enough of each property.”

In the end, the researchers created a design that looks and behaves very much like a Slinky.

“A Slinky is a solid cylinder of rigid metal but if you pattern it into this spiral shape, it becomes stretchable,” said Araromi. “That is essentially what we did here. We started with a rigid bulk material, in this case carbon fiber, and patterned it in such a way that the material becomes stretchable.”

The pattern is known as a serpentine meander, because its sharp ups and downs resemble the slithering of a snake. The patterned conductive carbon fibers are then sandwiched between two prestrained elastic substrates.

The overall electrical conductivity of the sensor changes as the edges of the patterned carbon fiber come out of contact with each other, similar to the way the individual spirals of a slinky come out of contact with each other when you pull both ends. This process happens even with small amounts of strain, which is the key to the sensor’s high sensitivity.

Unlike current highly sensitive stretchable sensors, which rely on exotic materials such as silicon or gold nanowires, this sensor doesn’t require special manufacturing techniques or even a clean room. It could be made using any conductive material.

The researchers tested the resiliency of the sensor by stabbing it with a scalpel, hitting it with a hammer, running it over with a car, and throwing it in a washing machine ten times. The sensor emerged from each test unscathed.

To demonstrate its sensitivity, the researchers embedded the sensor in a fabric arm sleeve and asked a participant to make different gestures with their hand, including a fist, open palm, and pinching motion. The sensors detected the small changes in the subject’s forearm muscle through the fabric and a machine learning algorithm was able to successfully classify these gestures.

“These features of resilience and the mechanical robustness put this sensor in a whole new camp,” said Araromi.

Such a sleeve could be used in everything from virtual reality simulations and sportswear to clinical diagnostics for neurodegenerative diseases like Parkinson’s Disease.

Harvard’s Office of Technology Development has filed to protect the intellectual property associated with this project.

“The combination of high sensitivity and resilience are clear benefits of this type of sensor,” said Robert Wood, the Charles River Professor of Engineering and Applied Sciences at SEAS and senior author of the study. “But another aspect that differentiates this technology is the low cost of the constituent materials and assembly methods. This will hopefully reduce the barriers to get this technology widespread in smart textiles and beyond.”

“We are currently exploring how this sensor can be integrated into apparel due to the intimate interface to the human body it provides,” says Conor Walsh, the Paul A. Maeder Professor of Engineering and Applied Sciences at SEAS and co-author of the study. “This will enable exciting new applications by being able to make biomechanical and physiological measurements throughout a person’s day, not possible with current approaches.”

The research was co-authored by Moritz A. Graule, Kristen L. Dorsey, Sam Castellanos, Jonathan R. Foster, Wen-Hao Hsu, Arthur E. Passy, James C. Weaver, Senior Staff Scientist at SEAS and Joost J. Vlassak, the Abbott and James Lawrence Professor of Materials Engineering at SEAS.

It was funded through the university’s strategic research alliance with Tata. The 6-year, $8.4M alliance was established in 2016 to advance Harvard innovation in fields including robotics, wearable technologies, and the internet of things (IoT).

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Novel population of neurons identified that control binocular eye movements in 3D space

University of Alabama at Birmingham researchers have discovered a previously undescribed population of neurons that help control our eyes as they view in three-dimensional space.

During normal viewing, we direct our eyes between objects in the three-dimensional space many times a minute. With each change, the left and right eyes will rotate, generally in the same direction, but mostly by different degrees of rotation. These unequal movements are known as disjunctive saccades.

Disjunctive saccades differ from two other eye movements: one, called conjugate saccades, where the eyes rotate in unison, and one called symmetrical vergence eye movements, where the eyes rotate in equal but opposite directions. The underlying mechanism for disjunctive saccades is not known.

Several models of eye movement predicted the existence of a population of neurons called saccade-vergence burst neurons, or SVBNs, that would produce a burst of activity solely during disjunctive saccades, while not firing during the other two types of eye movements.

The UAB researchers, led by Julie Quinet, Ph.D., hunted for these putative neurons in a region of the midbrain located near to the oculomotor nucleus called the central mesencephalic reticular formation, or cMRF. Recent anatomical studies had suggested that the cMRF might contain premotor neurons involved in the neural control of disjunctive saccades.

Using brain recordings from trained rhesus monkeys, Quinet and colleagues found and recorded 18 SVBNs in the cMRF. “To our knowledge,” said Quinet, a researcher V in the UAB Department of Ophthalmology and Visual Sciences, “no such class of cells has been reported in prior recording studies.”

This novel population of SVBNs displayed three unique characteristics that were predicted by models: 1) The neurons discharged when animals performed a disjunctive saccade; 2) The neurons remained silent during the unison eye movement called conjugate saccades and also during the eye movement when the eyes rotate in equal but opposite directions, called symmetric vergence eye movement, and; 3) The neurons burst without regard to the direction — rightward or leftward — of the disjunctive saccade. Furthermore, the bursts of spikes during disjunctive saccades were highly correlated with vergence velocity — the speed at which the eyes move toward or away from each other.

Intriguingly, half of the recorded cells increased their firing rate for convergence disjunctive saccades, while half increased their firing rate for divergence disjunctive saccades.

Quinet and colleagues say that further studies of disjunctive saccades in brain areas that may supply input to SVBNs can help explain and advance solutions to treat strabismus, a condition in which eyes do not properly align with each other while looking at an object.

The results of this study and previous studies elsewhere and at UAB, Quinet says, suggest that SVBNs could play a role in all the components of the near triad responses — lens accommodation, pupillary constriction and vergence.

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Materials provided by University of Alabama at Birmingham. Original written by Jeff Hansen. Note: Content may be edited for style and length.

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Will AI Make You an Addict?

The novel I’m writing is set in the future, tentatively in the year 2047, so it’s roughly one human generation ahead of us. For technology, however, that’s many generations ahead.

Consider that the first iPhone shipped in 2007 (13 years ago). If you got an iPhone 4S when it first came out, that was 9 years ago, and the 5S was 7 years ago.

The iPad is 10.5 years old. The Apple Watch is 5.5 years old.

Look back 27 years to 1993. Back then I was using a 486DX 50mhz computer with a 250MB hard drive. I think it was about $2500 when I bought it. I did some contract programming for a local game developer that year, and I remember using a 486DX 33mhz machine at their office each day. I wrote games for Windows 3.1, and I also heavily used DOS apps (with MS-DOS 6.0), mainly because Windows apps were still pretty slow.

Technically there was an Internet. I think we were using 14.4k modems back then since 28.8K ones didn’t come out till the following year… and 56K a couple years after that.

Web browsing, like with Netscape Navigator, didn’t really start becoming a thing till 1994-95. I build my first website in 1995 for my computer game business. Before the Web started taking off, people often thought of the Internet as geeky college stuff, or it was some kind of paid service like AOL, CompuServe, or Prodigy.

So that was 27 years ago, which seems like ages ago. Now I’m trying to write a novel projected 27 years into the future. That’s difficult, and I’ll surely guess wrong about a lot of things. But it’s a fun thought experiment nonetheless, especially if you love tech as I do.

My current approach is to just journal about the world and let my brain start making connections. As I see some ideas flowing onto the screen, I begin thinking about how they’ll combine. I think about the benefits and drawbacks of these combos. This helps me assemble the world in which my story can take place.

I also have to consider that the pace of change in the next 27 years will be way faster than what happened over the last 27 years. So it might be more like comparing today with 1950s tech.

One trend in particular that seems interesting to explore is AI and personalization.

For instance, I imagine that sometime within the next 27 years, you’ll be able to say most or all of these things to one of your devices, and you’ll be able to expect a good result:

  • Create and play an original episode of Star Trek: The Next Generation with the original cast, just for me. Cast my wife as a guest character.
  • Generate a new sci-fi series that you think I’ll like. Give it 5 seasons, 10-12 episodes per season, and 40-45 minutes per episode. Have it star Brad Pitt, Sandra Bullock, and Tom Hanks at their ages from the year 2000. And include a robot character with Jim Carrey’s voice.
  • Generate and add 10 attractive photos of me to that new dating app I installed.
  • Generate a new open-world fantasy video game similar to Zelda: Breath of the Wild 5. Name the lead character Schmoopie. Include the Three Stooges as quest companions that I meet as I play. Make it take about 200 hours to finish if I do all of the side quests. Make all the food and characters in the game world vegan. Save it to be played on my XBox One XS version X One. Monitor my responses as I play to make sure I’m having fun.
  • Plan a vacation trip for my wife and me to Italy in the spring. Include Rome and Venice. Make it two weeks in duration. Include the major stops you think we’d appreciate, but also give us plenty of time to wander and explore. Keep it under $7K total cost for the trip, but not too much under. Book it and add it to my calendar. Book-end the trip with a self-driving car pickup and drop off at my house. Create a 5-minute preview video of us enjoying the trip, and send it to my wife and me. After the trip, generate a 30-minute highlight video of us on the trip, and add it to our family camera roll.
  • Generate a new 12-song Depeche Mode album in the style of Violator but with shades of Songs of Faith and Devotion – with Alan Wilder as a band member please. Play it during my run tomorrow.

I think we’ll see a big explosion of AI and personalization, especially when it comes to media. I think it’s just a matter of time before AI is smart enough to generate custom experiences. AI can already generate original photos, artwork, and music now. And it can generate movies too with some major limitations. It’s also being used to upscale older videos to 4K resolution or better. It will take time, but I think that AI-generated content will eventually become the primary source of entertainment for most people. I think human-created content will still be around, but AI will improve more rapidly in this area, and the costs are much, much lower. It’s probably just a matter of time before AI surpasses humans at creating TV shows, movies, video games, VR worlds, and more.

I think we’ll see some intermediate steps between now and then, like TV shows or movies where you can change the actors. There may be legal hurdles to that though.

Fortunately the goal of creating a story world isn’t accuracy. I think the goal is to identify interesting sources of conflict. How will the world of the future challenge people?

One big issue I see is the rise of addiction. We’re already seeing AI being used in this way by Facebook. Now imagine if you were able to use AI for your own pleasure, and you give it access to data that it can use for that purpose. Suppose that while you’re watching a movie or playing a game, the AI can monitor your pulse, analyze your face in real-time, and use that data to sense how your biology is responding in each moment. Then it can generate more personalized content for you. It’s an echo chamber for one.

This creates interesting opportunities to though, especially in a capitalist society. We’re also likely to see more AI thrown at the problem of fighting addiction.

I appreciate fictional stories that highlight future problems. They help us map out the possibility space, including dangers to be avoided. A few good examples are 1984, The Terminator, and Gattaca. While fictional and exaggerated, they also point to genuine risks.

Writing a novel that helps to serve as a potential warning appeals to me. The story I’m writing (now past 17K words) is actually pretty dark. Here are some questions I’m currently exploring through the story arc:

  • How might the relationship between AI and addiction unfold?
  • What if people are empowered to use AI in ways that could lead to addictive behaviors?
  • How far will corporations go in using AI to addict their customers to their products and services?
  • Which commands that people might give AI are likely to lead to addictions?
  • What can humans do about AIs that are actively trying to condition addictive patterns?
  • How might AI be used to fight or prevent addictions?
  • Could humanity actually trap itself in an inescapable cage of AI-fueled addiction? If so, what would that cage look like?

While we could get lost in projecting many different technologies forward, for this purpose I favor keeping the world relatively simple and easy to grasp, so readers can be more immersed in the characters, the plot, and the themes rather than having to read endless description about the world.

As I work on this project, I note that the risks I’m identifying are also real. I think people will become increasingly vulnerable to tech-related addictions in the years ahead. Writing this book helps me think about how that may play out and what the potential solutions might be. So there’s an interesting relationship between exploring ahead with a fiction project and helping people prepare for upcoming personal challenges.

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Weighing space dust with radar

It is thought that over 1,000 kilograms of so-called interplanetary dust falls to Earth every day. This dust is essentially an untold number of small faint meteors, discarded remnants of asteroids and comets that pass by the Earth. Two ways to study faint meteors are radar and optical observations, each with advantages and limitations. Astronomers have combined specific observations with both methods, and can now use radar to make the kinds of observations that previously only optical telescopes could make.

Our solar system is a busy place — in addition to the large bodies we are all familiar with exist an uncountably large number of rocky asteroids and icy comets. These mostly stay put in their orbits far from Earth but many also roam around the solar system. As they do, they shed some material due to collisions, deformations or heating. Due to this, the Earth is surrounded by small particles we call interplanetary dust. By investigating the size and composition of the interplanetary dust, astronomers can indirectly investigate the activity and makeup of the parent bodies.

“When in space, interplanetary dust is practically invisible. However, around 1,000 kilograms falls to Earth every day in the form of tiny meteors which appear as bright streaks in the night sky,” said astronomer Ryou Ohsawa from the Institute of Astronomy at the University of Tokyo. “We can observe these with ground-based radar and optical instruments. Radar is useful as it can cover wide areas and gather vast readings, but optical telescopes can give more detailed information useful for our studies. So we set out to bridge this gap to boost our observational capacity.”

Ground-based radar is very good at detecting the motion of meteors, but it does not reveal much information about the mass or composition of the meteors. Optical telescopes and sensors can infer those details based on the light given off by falling meteors due to interaction with the atmosphere. However, telescopes have a limited field of view and until recently lacked the sensitivity to see faint meteors at all. Ohsawa and his team wished to imbue radar observatories with the powers of optical ones. After a few years, they have finally succeeded.

“We thought that if you could observe enough meteors simultaneously with both radar and optical facilities, details of the meteors in the optical data may correspond to previously unseen patterns in the radar data too,” said Ohsawa. “I am pleased to report this is in fact the case. We recorded hundreds of events over several years and have now gained the ability to read information about meteor mass from subtle signals in radar data.”

In 2009, 2010 and 2018, the team used the Middle and Upper Atmosphere (MU) Radar facility, operated by Kyoto University and located in Shigaraki, Shiga Prefecture, and the Kiso Observatory, operated by the University of Tokyo, on the Nagano Prefecture side of Mount Ontake. They are 173 kilometers apart, which is important: the closer the facilities, the more accurately the data from them can be correlated. MU points directly upwards, but Kiso can be angled, so it was pointed 100 km above the site of MU. The team saw 228 meteors with both facilities and this was plenty to derive a statistically reliable relationship to connect radar and optical observations.

“Data analysis was laborious,” said Ohsawa. “A sensitive instrument called the Tomo-e Gozen wide-field camera mounted to the Kiso telescope captured over a million images a night. This is too much for us to analyze manually so we developed software to automatically recognize faint meteors. From what we’ve learned here we hope to extend this project and begin using radar to investigate the composition of meteors. This could help astronomers explore comets and aspects of solar system evolution like never before.”

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Materials provided by University of Tokyo. Note: Content may be edited for style and length.

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