America’s Department of Energy has three R&D labs, according to Wikipedia, one of which is Sandia National Labs. And that New Mexico-based lab has just announced that “A milestone in quantum sensing is drawing closer, promising exquisitely accurate, GPS-free navigation.” with research into “a motion sensor so precise it could minimize the nation’s reliance on global positioning satellites.”

Until recently, such a sensor — a thousand times more sensitive than today’s navigation-grade devices — would have filled a moving truck. But advancements are dramatically shrinking the size and cost of this technology. For the first time, researchers from Sandia National Laboratories have used silicon photonic microchip components to perform a quantum sensing technique called atom interferometry, an ultra-precise way of measuring acceleration. It is the latest milestone toward developing a kind of quantum compass for navigation when GPS signals are unavailable. The team published its findings and introduced a new high-performance silicon photonic modulator — a device that controls light on a microchip — as the cover story in the journal Science Advances… The new modulator is the centerpiece of a laser system on a microchip. Rugged enough to handle heavy vibrations, it would replace a conventional laser system typically the size of a refrigerator…

Besides size, cost has been a major obstacle to deploying quantum navigation devices. Every atom interferometer needs a laser system, and laser systems need modulators. “Just one full-size single-sideband modulator, a commercially available one, is more than $10,000,” said Sandia scientist Jongmin Lee. Miniaturizing bulky, expensive components into silicon photonic chips helps drive down these costs. “We can make hundreds of modulators on a single 8-inch wafer and even more on a 12-inch wafer,” Kodigala said. And since they can be manufactured using the same process as virtually all computer chips, “This sophisticated four-channel component, including additional custom features, can be mass-produced at a much lower cost compared to today’s commercial alternatives, enabling the production of quantum inertial measurement units at a reduced cost,” Lee said.

As the technology gets closer to field deployment, the team is exploring other uses beyond navigation. Researchers are investigating whether it could help locate underground cavities and resources by detecting the tiny changes these make to Earth’s gravitational force. They also see potential for the optical components they invented, including the modulator, in LIDAR, quantum computing, and optical communications.

Thanks to Slashdot reader schwit1 for sharing the news.

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sciencehabit shares a report from Science Magazine: A species of lungfish found in South America has claimed the title of the animal with the biggest genome sequenced so far. The DNA of Lepidosiren paradoxa comprises a staggering 91 billion chemical letters or “bases,” 30 times as many as the human genome, researchers report today in Nature. However, those 91 billion bases of DNA only contain about the same number of genes that humans have — roughly 20,000 — with the rest consisting of noncoding, perhaps even “junk” DNA. By comparing this genome with those of other lungfishes, the researchers determined that L. paradoxa adds the equivalent of a human genome to its DNA every 10 million years.

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RockDoctor (Slashdot reader #15,477) writes: The BBC are reporting sharks have tested positive for cocaine.
Thirteen sharpnose sharks which were captured off the coast near Rio de Janeiro. They were tested for the drug in liver and muscle tissue samples — and returned positive results at concentrations as much as 100 times higher than previously reported for other aquatic creatures.

The research was published in Science of the Total Environment. The little-known “sharpnose” sharks were examined because they spend their entire lives in coastal waters. This makes them more likely to be exposed to drugs from human activities than the more cinematic species starring in “Cocaine Shark” or “Cocaine Sharks”, two recent productions on the subject featuring hammerheads and tiger sharks (the “trash cans of the sea”).

The likeliest source is effluent from drug processing labs inland, though the snorting population of Rio may have added their contribution into the sewers too…

Whether cocaine is changing the behaviour of the sharks is not known. Perhaps it would affect their aim with their head-mount lasers, bringing closer their conquest of the land with it’s tasty, tasty humans. Hollywood, hopefully, as the answers.

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Long-time Slashdot reader jrronimo says JILA physicist Jun Ye’s group “has made a breakthrough towards the next stage of precision timekeeping.”

From their paper recently published to arXiv:

Optical atomic clocks use electronic energy levels to precisely keep track of time. A clock based on nuclear energy levels promises a next-generation platform for precision metrology and fundamental physics studies…. These results mark the start of nuclear-based solid-state optical clocks and demonstrate the first comparison of nuclear and atomic clocks for fundamental physics studies. This work represents a confluence of precision metrology, ultrafast strong field physics, nuclear physics, and fundamental physics.

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Borrowing the idea of “bug bounties” from the technology industry could provide a systematic way to detect and correct the errors that litter the scientific literature. Malte Elson, writing at Nature: Just as many industries devote hefty funding to incentivizing people to find and report bugs and glitches, so the science community should reward the detection and correction of errors in the scientific literature. In our industry, too, the costs of undetected errors are staggering. That’s why I have joined with meta-scientist Ian Hussey at the University of Bern and psychologist Ruben Arslan at Leipzig University in Germany to pilot a bug-bounty programme for science, funded by the University of Bern. Our project, Estimating the Reliability and Robustness of Research (ERROR), pays specialists to check highly cited published papers, starting with the social and behavioural sciences (see go.nature.com/4bmlvkj). Our reviewers are paid a base rate of up to 1,000 Swiss francs (around US$1,100) for each paper they check, and a bonus for any errors they find. The bigger the error, the greater the reward — up to a maximum of 2,500 francs.

Authors who let us scrutinize their papers are compensated, too: 250 francs to cover the work needed to prepare files or answer reviewer queries, and a bonus 250 francs if no errors (or only minor ones) are found in their work. ERROR launched in February and will run for at least four years. So far, we have sent out almost 60 invitations, and 13 sets of authors have agreed to have their papers assessed. One review has been completed, revealing minor errors. I hope that the project will demonstrate the value of systematic processes to detect errors in published research. I am convinced that such systems are needed, because current checks are insufficient. Unpaid peer reviewers are overburdened, and have little incentive to painstakingly examine survey responses, comb through lists of DNA sequences or cell lines, or go through computer code line by line. Mistakes frequently slip through. And researchers have little to gain personally from sifting through published papers looking for errors. There is no financial compensation for highlighting errors, and doing so can see people marked out as troublemakers.

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Science Alert reports that a team of researchers found “that changes in glucose metabolism could help cancer grow by temporarily disabling a gene that protects us from tumors called BRCA2.”

The team first examined people who inherited one faulty copy of BRCA2. They found that cells from these people were more sensitive to methylglyoxal (MGO), which is produced when cells break down glucose for energy in the process of glycolysis. Glycolysis generates over 90 percent of the MGO in cells, which a pair of enzymes typically keep to minimal levels. In the event they can’t keep up, high MGO levels can lead to the formation of harmful compounds that damage DNA and proteins. In conditions like diabetes, where MGO levels are elevated due to high blood sugar, these harmful compounds contribute to disease complications.

The researchers discovered that MGO can temporarily disable the tumor-suppressing functions of the BRCA2 protein, resulting in mutations linked to cancer development…

As the BRCA2 allele isn’t permanently inactivated, functional forms of the protein it produces can later return to normal levels. But cells repeatedly exposed to MGO may continue to accumulate cancer-causing mutations whenever existing BRCA2 protein production fails. Overall, this suggests that changes in glucose metabolism can disrupt BRCA2 function via MGO, contributing to the development and progression of cancer…

This new information may lead to strategies for cancer prevention or early detection. “Methylglyoxal can be easily detected by a blood test for HbA1C, which could potentially be used as a marker,” Venkitaraman says. “Furthermore, high methylglyoxal levels can usually be controlled with medicines and a good diet, creating avenues for proactive measures against the initiation of cancer.”

Their research has been published in Cell.

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Nicola Davis reports via The Guardian: If every day appears to go in a blur, try seeking out new and interesting experiences, researchers have suggested, after finding memorable images appear to dilate time. Researchers have previously found louder experiences seem to last longer, while focusing on the clock also makes time dilate, or drag. Now researchers have discovered the more memorable an image, the more likely a person is to think they have been looking at it for longer than they actually have. Such images were also easier for participants to recall the next day. Prof Martin Wiener, co-author of the study who is based at George Mason University in the U.S., said the findings could help develop improve artificial intelligence that interacts with humans, while they also offer opportunities to tweak our perceptions, given research has previously shown non-invasive brain stimulation can be used to lengthen a perceived interval.

The results from two groups, totaling about 100 people, revealed participants were more likely to think they had been looking at small, highly cluttered scenes — such a crammed pantry — for a shorter duration than was the case, whereas the reverse occurred when people viewed large scenes with little clutter, such as the interior of an aircraft hangar. The team also carried out experiments involving 69 participants that found images known from previous work to be more memorable were more likely to be judged as having been shown for longer than was the case. Crucially, the effect seemed to go both ways.

“We also found that the longer the perceived subjective duration of an image, the more likely you were to remember it the next day,” said Wiener. When the team carried out an analysis using deep learning models of the visual system, they discovered more memorable images were processed faster. What’s more, the processing speed for an image was correlated with how long participants thought they had been looking at it. “Images may be more memorable because they are processed faster and more efficiently in the visual system, and that drives the perception of time,” said Wiener. The team suggest time dilation might serve a purpose, enabling us to gather information about the world around us. The findings have been published in the journal Nature Human Behavior.

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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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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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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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