Scientists Discover First Nitrogen-Fixing Organelle

In two recent papers, an international team of scientists describes the first known nitrogen-fixing organelle within a eukaryotic cell, which the researchers are calling a nitroplast. Phys.Org reports: The discovery of the organelle involved a bit of luck and decades of work. In 1998, Jonathan Zehr, a UC Santa Cruz distinguished professor of marine sciences, found a short DNA sequence of what appeared to be from an unknown nitrogen-fixing cyanobacterium in Pacific Ocean seawater. Zehr and colleagues spent years studying the mystery organism, which they called UCYN-A. At the same time, Kyoko Hagino, a paleontologist at Kochi University in Japan, was painstakingly trying to culture a marine alga. It turned out to be the host organism for UCYN-A. It took her over 300 sampling expeditions and more than a decade, but Hagino eventually successfully grew the alga in culture, allowing other researchers to begin studying UCYN-A and its marine alga host together in the lab. For years, the scientists considered UCYN-A an endosymbiont that was closely associated with an alga. But the two recent papers suggest that UCYN-A has co-evolved with its host past symbiosis and now fits criteria for an organelle.

In a paper published in Cell in March 2024, Zehr and colleagues from the Massachusetts Institute of Technology, Institut de Ciencies del Mar in Barcelona and the University of Rhode Island show that the size ratio between UCYN-A and their algal hosts is similar across different species of the marine haptophyte algae Braarudosphaera bigelowii. The researchers use a model to demonstrate that the growth of the host cell and UCYN-A are controlled by the exchange of nutrients. Their metabolisms are linked. This synchronization in growth rates led the researchers to call UCYN-A “organelle-like.” “That’s exactly what happens with organelles,” said Zehr. “If you look at the mitochondria and the chloroplast, it’s the same thing: they scale with the cell.”

But the scientists did not confidently call UCYN-A an organelle until confirming other lines of evidence. In the cover article of the journal Science, published today, Zehr, Coale, Kendra Turk-Kubo and Wing Kwan Esther Mak from UC Santa Cruz, and collaborators from the University of California, San Francisco, the Lawrence Berkeley National Laboratory, National Taiwan Ocean University, and Kochi University in Japan show that UCYN-A imports proteins from its host cells. “That’s one of the hallmarks of something moving from an endosymbiont to an organelle,” said Zehr. “They start throwing away pieces of DNA, and their genomes get smaller and smaller, and they start depending on the mother cell for those gene products — or the protein itself — to be transported into the cell.”

Coale worked on the proteomics for the study. He compared the proteins found within isolated UCYN-A with those found in the entire algal host cell. He found that the host cell makes proteins and labels them with a specific amino acid sequence, which tells the cell to send them to the nitroplast. The nitroplast then imports the proteins and uses them. Coale identified the function of some of the proteins, and they fill gaps in certain pathways within UCYN-A. “It’s kind of like this magical jigsaw puzzle that actually fits together and works,” said Zehr. In the same paper, researchers from UCSF show that UCYN-A replicates in synchrony with the alga cell and is inherited like other organelles.

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Company That Plans To Bring Back the Mammoth Takes a Key Step

John Timmer reports via Ars Technica: A company called Colossal plans to pioneer the de-extinction business, taking species that have died within the past few thousand years and restoring them through the use of DNA editing and stem cells. It’s grabbed headlines recently by announcing some compelling targets: the thylacine, an extinct marsupial predator, and an icon of human carelessness, the dodo. But the company was formed to tackle an even more audacious target: the mammoth, which hasn’t roamed the Northern Hemisphere for thousands of years. Obviously, there are a host of ethical and conservation issues that would need to be worked out before Colossal’s plans go forward. But there are some major practical hurdles as well, most of them the product of the distinct and extremely slow reproductive biology of the mammoth’s closest living relatives, the elephants. At least one of those has now been cleared, as the company is announcing the production of the first elephant stem cells. The process turned out to be extremely difficult, suggesting that the company still has a long road ahead of it. […] Overall, it’s a project that has a high probability of failure and may ultimately require generations of scientists. If we do successfully de-extinct a species, the first example will probably be a different species, even though the projects launched later.

But Colossal is forging ahead and cleared one of the many hurdles it faces: It created the first induced stem cells from elephants and will be placing a draft manuscript describing the process on a public repository on Wednesday. (Colossal provided Ars with an advanced version of the draft that, outside of a few editing errors, appears largely complete.) Beyond providing the technical details of how the process works, the manuscript describes a long, failure-ridden route to eventual success. Several methods have been developed to allow us to induce stem cells from the cells of an adult organism. The original Nobel-winning process developed by Shinya Yamanaka involved inserting the genes that encode four key embryonic regulatory genes into adult cells and allowing them to reprogram the adult cell into an embryonic state. That has proven effective in a variety of species but has a couple of drawbacks due to the fact that the four genes can potentially stick around, interfering with later development steps. Although there are ways around that, others have developed a cocktail of chemicals that perform a similar function by activating signaling pathways that, collectively, can also reprogram adult cells. When it works, this simplifies matters, as you only have to remove the chemicals to allow the stem cells to adopt other fates. Colossal tried both of these. Neither worked with elephant cells: “Multiple attempts with current standard reprogramming methods were tried, and failed, and resulted in no, or incomplete, reprogramming.” Apparently, lots of additional trial and error ensued. The eventual solution ended up being based in part on combining the two primary options: Cells were first exposed to a chemical reprogramming cocktail and then given the four genes used in the alternative reprogramming method. On its own, however, that wasn’t enough. The researchers also had to address a quirk of elephant biology.

Obviously, for Colossal, this is a means to an end: the mammoth. But that’s remarkably underplayed in the manuscript. Instead, its emphasis is on the technology’s use in the conservation of existing species. [T]he researchers note that studying things like elephant development and metabolism in actual elephants is not especially realistic. But we can potentially induce the stem cells developed here into any cell we’d want to study — nerve, liver, heart, and so on. So, the stem cells described here could be a useful tool for research. So, these cells are being presented as a valuable tool for the research community. Still, you can expect the people behind the de-extinction project to be getting to work on some of the easier things: showing that the genome in the cells can be edited and that they can be induced to start the process of embryogenesis. Separately, some unfortunate individuals will need to be working on the hard problems we mentioned earlier.

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A Shape-Shifting Plastic With a Flexible Future

New submitter Smonster shares a report from the New York Times: With restrictions on space and weight, what would you bring if you were going to Mars? An ideal option might be a single material that can shift shapes into any object you imagine. In the morning, you could mold that material into utensils for eating. When breakfast is done, you could transform your fork and knife into a spade to tend to your Martian garden. And then when it’s happy hour on the red planet, that spade could become a cup for your Martian beer. What sounds like science fiction is, perhaps, one step closer to reality.

Researchers at the University of Chicago Pritzker School of Molecular Engineering have created a new type of plastic with properties that can be set with heat and then locked in with rapid cooling, a process known as tempering. Unlike classic plastics, the material retains this stiffness when returned to room temperature. The findings, published in the journal Science on Thursday, could someday change how astronauts pack for space.

“Rather than taking all the different plastics with you, you take this one plastic with you and then just give it the properties you need as you require,” said Stuart Rowan, a chemist at the University of Chicago and an author of the new study. But space isn’t the only place the material could be useful. Dr. Rowan’s team also sees its potential in other environments where resources are scare — like at sea or on the battlefield. It could also be used to make soft robots and to improve plastics recycling.

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Scientists Create Eco-Friendly Paint That Keeps the Surface Beneath Cool

A team of researchers in Florida have created a way to mimic nature’s ability to reflect light and create beautifully vivid color without absorbing any heat like traditional pigments do. Debashis Chanda, a nanoscience researcher with the University of Central Florida, and his team published their findings in the journal Science Advances. NPR reports: Beyond just the beautiful arrays of color that structure can create, Chanda also found that unlike pigments, structural paint does not absorb any infrared light. Infrared light is the reason black cars get hot on sunny days and asphalt is hot to the touch in summer. Infrared light is absorbed as heat energy into these surfaces — the darker the color, the more the surface colored with it can absorb. That’s why people are advised to wear lighter colors in hotter climates and why many buildings are painted bright whites and beiges. Chanda found that structural color paint does not absorb any heat. It reflects all infrared light back out. This means that in a rapidly warming climate, this paint could help communities keep cool.

Chanda and his team tested the impact this paint had on the temperature of buildings covered in structural paint versus commercial paints and they found that structural paint kept surfaces 20 to 30 degrees cooler. This, Chanda said, is a massive new tool that could be used to fight rising temperatures caused by global warming while still allowing us to have a bright and colorful world. Unlike white and black cars, structural paint’s ability to reflect heat isn’t determined by how dark the color is. Blue, black or purple structural paints reflect just as much heat as bright whites or beige. This opens the door for more colorful, cooler architecture and design without having to worry about the heat.

It’s not just cleaner, Chanda said. Structural paint weighs much less than pigmented paint and doesn’t fade over time like traditional pigments. “A raisin’s worth of structural paint is enough to cover the front and back of a door,” he said. Unlike pigments which rely on layers of pigment to achieve depth of color, structural paint only requires one thin layer of particles to fully cover a surface in color. This means that structural paint could be a boon for aerospace engineers who rely on the lowest weight possible to achieve higher fuel efficiency. The possibilities for structural paint are endless and Chanda hopes that cans of structural paint will soon be available in hardware stores.

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False Memories Can Form Within Seconds, Study Finds

In a new study, scientists found that it’s possible for people to form false memories of an event within seconds of it occurring. This almost-immediate misremembering seems to be shaped by our expectations of what should happen, the team says. Gizmodo reports: “This study is unique in two ways, in our opinion. First, it explores memory for events that basically just happened, between 0.3 and 3 seconds ago. Intuitively, we would think that these memories are pretty reliable,” lead author Marte Otten, a neuroscientist at the University of Amsterdam, told Gizmodo in an email. “As a second unique feature, we explicitly asked people whether they thought their memories are reliable — so how confident are they about their response?” To do this, they recruited hundreds of volunteers over a series of four experiments to complete a task: They would look at certain letters and then be asked to recall one highlighted letter right after. However, the scientists used letters that were sometimes reversed in orientation, so the volunteers had to remember whether their selection was mirrored or not. They also focused on the volunteers who were highly confident about their choices during the task.

Overall, the participants regularly misremembered the letters, but in a specific way. People were generally good at remembering when a typical letter was shown, with their inaccuracy rates hovering around 10%. But they were substantially worse at remembering a mirrored letter, with inaccuracy rates up to 40% in some experiments. And, interestingly enough, their memory got worse the longer they had to wait before recalling it. When they were asked to recall what they saw a half second later, for instance, they were wrong less than 20% of the time, but when they were asked three seconds later, the rate rose as high as 30%.

According to Otten, the findings — published Wednesday in PLOS One — indicate that our memory starts being shaped almost immediately by our preconceptions. People expect to see a regular letter, and don’t get easily fooled into misremembering a mirrored letter. But when the unexpected happens, we might often still default to our missed prediction. This bias doesn’t seem to kick in instantaneously, though, since people’s short-term memory was better when they had to be especially quick on their feet. “It is only when memory becomes less reliable through the passage of a tiny bit of time, or the addition of extra visual information, that internal expectations about the world start playing a role,” Otten said.

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Gene-edited Hens May End Cull of Billions of Chicks

Israeli researchers say they have developed gene-edited hens that lay eggs from which only female chicks hatch. From a report: The breakthrough could prevent the slaughter of billions of male chickens each year, which are culled because they don’t lay eggs. The female chicks, and the eggs they lay when they mature, have no trace of the original genetic alteration Animal welfare group, Compassion in World Farming, has backed the research. Dr Yuval Cinnamon from the Volcani institute near Tel Aviv, who is the project’s chief scientist, told BBC News that the development of what he calls the ”Golda hen” will have a huge impact on animal welfare in the poultry industry.

“I am very happy that we have developed a system that I think can truly revolutionise the industry, first of all for the benefit of the chickens but also for all of us, because this is an issue that affects every person on the planet,” he said. The scientists have gene edited DNA into the Golda hens that can stop the development of any male embryos in eggs that they lay. The DNA is activated when the eggs are exposed to blue light for several hours. Female chick embryos are unaffected by the blue light and develop normally. The chicks have no additional genetic material inside them nor do the eggs they lay, according to Dr Cinnamon. “Farmers will get the same chicks they get today and consumers will get exactly the same eggs they get today,” he said. “The only minor difference in the production process is that the eggs will be exposed to blue light.”

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Why the Laws of Physics Don’t Actually Exist

Theoretical physicist Sankar Das Sarma wrote a thought-provoking essay for New Scientist magazine’s Lost in Space-Time newsletter:
I was recently reading an old article by string theorist Robbert Dijkgraaf in Quanta Magazine entitled “There are no laws of physics”. You might think it a bit odd for a physicist to argue that there are no laws of physics but I agree with him. In fact, not only do I agree with him, I think that my field is all the better for it. And I hope to convince you of this too.

First things first. What we often call laws of physics are really just consistent mathematical theories that seem to match some parts of nature. This is as true for Newton’s laws of motion as it is for Einstein’s theories of relativity, Schrödinger’s and Dirac’s equations in quantum physics or even string theory. So these aren’t really laws as such, but instead precise and consistent ways of describing the reality we see. This should be obvious from the fact that these laws are not static; they evolve as our empirical knowledge of the universe improves.

Here’s the thing. Despite many scientists viewing their role as uncovering these ultimate laws, I just don’t believe they exist…. I know from my 40 years of experience in working on real-life physical phenomena that the whole idea of an ultimate law based on an equation using just the building blocks and fundamental forces is unworkable and essentially a fantasy. We never know precisely which equation describes a particular laboratory situation. Instead, we always have to build models and approximations to describe each phenomenon even when we know that the equation controlling it is ultimately some form of the Schrödinger equation!
Even with quantum mechanics, space and time are variables that have to be “put in by hand,” the article argues, “when space and time should come out naturally from any ultimate law of physics. This has remained perhaps the greatest mystery in fundamental physics with no solution in sight….”

“It is difficult to imagine that a thousand years from now physicists will still use quantum mechanics as the fundamental description of nature…. I see no particular reason that our description of how the physical universe seems to work should reach the pinnacle suddenly in the beginning of the 21st century and become stuck forever at quantum mechanics. That would be a truly depressing thought…!”

“Our understanding of the physical world must continue indefinitely, unimpeded by the search for ultimate laws. Laws of physics continuously evolve — they will never be ultimate.”
Thanks to long-time Slashdot reader InfiniteZero for sharing the article!

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Physicists Use Google’s Quantum Computer to Create Holographic Wormhole Between Black Holes

“In an experiment that ticks most of the mystery boxes in modern physics, a group of researchers announced Wednesday that they had simulated a pair of black holes in a quantum computer,” reports the New York Times [alternate URL here. But in addition, the researchers also sent a message between their two black holes, the Times reports, “through a shortcut in space-time called a wormhole.

“Physicists described the achievement as another small step in the effort to understand the relation between gravity, which shapes the universe, and quantum mechanics, which governs the subatomic realm of particles….

Quanta magazine reports:
The wormhole emerged like a hologram out of quantum bits of information, or “qubits,” stored in tiny superconducting circuits. By manipulating the qubits, the physicists then sent information through the wormhole, they reported Wednesday in the journal Nature. The team, led by Maria Spiropulu of the California Institute of Technology, implemented the novel “wormhole teleportation protocol” using Google’s quantum computer, a device called Sycamore housed at Google Quantum AI in Santa Barbara, California. With this first-of-its-kind “quantum gravity experiment on a chip,” as Spiropulu described it, she and her team beat a competing group of physicists who aim to do wormhole teleportation with IBM and Quantinuum’s quantum computers.

When Spiropulu saw the key signature indicating that qubits were passing through the wormhole, she said, “I was shaken.”

The experiment can be seen as evidence for the holographic principle, a sweeping hypothesis about how the two pillars of fundamental physics, quantum mechanics and general relativity, fit together…. The holographic principle, ascendant since the 1990s, posits a mathematical equivalence or “duality” between the two frameworks. It says the bendy space-time continuum described by general relativity is really a quantum system of particles in disguise. Space-time and gravity emerge from quantum effects much as a 3D hologram projects out of a 2D pattern. Indeed, the new experiment confirms that quantum effects, of the type that we can control in a quantum computer, can give rise to a phenomenon that we expect to see in relativity — a wormhole….

To be clear, unlike an ordinary hologram, the wormhole isn’t something we can see. While it can be considered “a filament of real space-time,” according to co-author Daniel Jafferis of Harvard University, lead developer of the wormhole teleportation protocol, it’s not part of the same reality that we and the Sycamore computer inhabit. The holographic principle says that the two realities — the one with the wormhole and the one with the qubits — are alternate versions of the same physics, but how to conceptualize this kind of duality remains mysterious. Opinions will differ about the fundamental implications of the result. Crucially, the holographic wormhole in the experiment consists of a different kind of space-time than the space-time of our own universe. It’s debatable whether the experiment furthers the hypothesis that the space-time we inhabit is also holographic, patterned by quantum bits.
“I think it is true that gravity in our universe is emergent from some quantum [bits] in the same way that this little baby one-dimensional wormhole is emergent” from the Sycamore chip, Jafferis said. “Of course we don’t know that for sure. We’re trying to understand it.”
Here’s how principal investigator Spiropulu summarizes their experiment. “We found a quantum system that exhibits key properties of a gravitational wormhole yet is sufficiently small to implement on today’s quantum hardware.”

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Scientists Have Discovered a New Set of Blood Groups

Chris Baraniuk, reporting for Wired: The unborn baby was in trouble. Its mother’s doctors, at a UK hospital, knew there was something wrong with the fetus’s blood, so they decided to perform an emergency C-section many weeks before the baby was due. But despite this, and subsequent blood transfusions, the baby suffered a brain hemorrhage with devastating consequences. It sadly passed away. It wasn’t clear why the bleeding had happened. But there was a clue in the mother’s blood, where doctors had noticed some strange antibodies. Some time later, as the medics tried to find out more about them, a sample of the mother’s blood arrived at a lab in Bristol run by researchers who study blood groups. They made a startling discovery: The woman’s blood was of an ultrarare type, which may have made her baby’s blood incompatible with her own.

It’s possible that this prompted her immune system to produce antibodies against her baby’s blood — antibodies that then crossed the placenta and harmed her child, ultimately leading to its loss. It may seem implausible that such a thing could happen, but many decades ago, before doctors had a better understanding of blood groups, it was much more common. Through studying the mother’s blood sample, along with a number of others, scientists were able to unpick exactly what made her blood different, and in the process confirmed a new set of blood grouping — the “Er” system, the 44th to be described. You’re probably familiar with the four main blood types — A, B, O, and AB. But this isn’t the only blood classification system. There are many ways of grouping red blood cells based on differences in the sugars or proteins that coat their surface, known as antigens.

The grouping systems run concurrently, so your blood can be classified in each — it might, for instance, be type O in the ABO system, positive (rather than negative) under the Rhesus system, and so on. Thanks to differences in antigens, if someone receives incompatible blood from a donor, for example, the recipient’s immune system may detect those antigens as foreign and react against them. This can be highly dangerous, and is why donated blood needs to be a suitable match if someone is having a transfusion. On average, one new blood classification system has been described by researchers each year during the past decade. These newer systems tend to involve blood types that are mind-bogglingly rare but, for those touched by them, just knowing that they have such blood could be lifesaving. This is the story of how scientists unraveled the mystery of the latest blood system — and why it matters.

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Scientists Break the Direction of Time Down To the Cellular Level In Mind-Bending Study

A new study looks at interactions between microscopic neurons in salamanders to understand how the “arrow of time” is biologically generated. Motherboard reports: The second law of thermodynamics says that everything tends to move from order to disorder, a process known as entropy that defines the arrow of time. A stronger arrow of time means it would be harder for a system to go back to a more ordered state. “Everything that we perceive as a difference between the past and the future stems fundamentally from that one principle about the universe,” said Christopher Lynn, the lead author of the study. Lynn said that his motivation for the study was “to understand how the arrows of time we see in life” fit into this larger idea of entropy on the scale of the entire universe.

Using previously done research on salamanders, Lynne and colleagues at City University of New York and Princeton examined how the arrow of time is represented in interactions between the amphibians’ neurons in response to watching a movie. Their research is soon to be published in the journal Physical Review Letters. On one hand, it’s somewhat obvious that an arrow of time would be biologically produced. “To be alive, almost, you have to have an arrow of time because you develop from a baby to an adult, and you’re constantly moving and taking in stimuli,” Lynne said. Indeed, entropy here is irreversible — you cannot go back. What the team found was anything but intuitive, however.

Lynne and colleagues looked at a separate 2015 study where researchers had salamanders watch two different movies. One depicted a scene of fish swimming around, similar to what a salamander might experience in everyday life. As in the real world, the video had a clear arrow of time — that is, if you watched it in reverse, it would look different than if you played it forwards. The other video contained only a gray screen with a black, horizontal bar in the middle of the screen, which moved quickly up and down in a random, jittery way. This video didn’t have an obvious arrow of time. A major question for the researchers was if they could pick out signs of “local irreversibility” in interactions between small groups of retinal neurons in response to this stimulus. Would interactions with irreversibility — they would look different if played in reverse, having an “arrow of time” — present in simpler or more complex interactions between neurons? “You can go look at a system and you can ask: are the more complicated interactions strongly producing the arrow of time, or is it the simpler dynamics?” said Lynn.

The researchers found that the interactions between simple pairs of neurons primarily determined the arrow of time, no matter which movie the salamanders watched. In fact, the authors found a stronger arrow of time for the neurons when salamanders watched the video with the gray screen and black bar — in other words, the video without an arrow of time in its content elicited a greater arrow of time in the neurons. “We naively thought that if the stimulus has a stronger arrow of time, that would show up on your retina,” said Lynn. “But it was the opposite. So that’s why it was surprising to us.” While the researchers can’t say for sure why this is, Lynn said that it might be because salamanders are more used to seeing something like the fish movie, and processing the more artificial movie took greater energy. In a more disordered system, which would have a greater arrow of time, more energy is consumed. “Being alive will still define an arrow of time,” Lynne said, no matter the stimulus.

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