Category: 7. Science

Researchers at Tsinghua University have released a novel Python toolkit, scLT-kit, which automates the processing and analysis of single-cell lineage tracing data, delivering clear insights into how individual cells develop, differentiate, and respond to treatments. Think of scLT-kit as a “GPS for cell genealogies”—it takes messy, high-dimensional data and plots each cell’s journey, making complex lineage relationships easy to follow. This tool addresses the growing need for flexible, user-friendly software to handle complex single-cell datasets.

Novel Model to Decode Cell Dynamics Energises Regenerative Medicine and Cancer Research

Understanding how cells change over time is crucial for fields ranging from regenerative medicine to cancer therapy. By making lineage tracing analyses more accessible, scLT-kit can accelerate research into tissue development, drug resistance, and disease progression. Its streamlined workflows could help biologists, pharmaceutical developers, and policymakers better evaluate how cells respond to treatments, ultimately informing new strategies for diagnosis and therapy.

“With scLT-kit, we’ve improved a previously labor-intensive, bespoke analysis into a seamless, reproducible workflow,” says Prof. Jin Gu. “Our goal was to empower every lab—whether focused on development, drug resistance, or disease progression—to extract lineage insights from single-cell data in minutes, not months.”

Automated Barcode Analysis Uncovers Predictable Developmental Clones—and Unruly Drug-Resistant Tumor Cells

Through a series of analyses, the researchers uncovered the following insights:

• scLT-kit reliably processes time-series single-cell RNA-seq data tagged with heritable barcodes, providing rapid quality checks and summary statistics of barcoding efficiency and clone sizes.
• In developmental datasets (e.g., blood progenitors and C. elegans embryos), cells sharing the same barcode showed higher similarity in gene expression than unrelated cells.
• In tumor cell lines treated with EGFR inhibitors (osimertinib or erlotinib), this within-clone similarity was less pronounced, reflecting the high heterogeneity of cancer persisters.
• The toolkit computes measures of cell fate diversity, showing that normal development features more predictable outcomes, whereas drug-treated cancer cells exhibit greater randomness in fate decisions.
• scLT-kit identifies subpopulations with distinct fate trajectories and uncovers genes linked to these fates through differential expression analysis.

All-in-One Python Package Delivers Barcode QC, Lineage Networks and Interactive Sankey Plots

scLT-kit combines standard single-cell RNA-seq processing with two specialized modules for lineage data. The scLT-statistics module calculates barcoding fractions and clone sizes at each time point. The scLT-analysis module builds lineage-based networks to infer how clusters of cells transition over time, visualizing dynamics with Sankey plots. Four quantitative indicators assess cell fate randomness and neighbor similarity. Finally, the package uses established statistical tests to link gene expression changes to specific fate outcomes, all within an easy-to-install Python package available on PyPI and GitHub.

Streamlined Workflows Lower the Barrier to Single-Cell Lineage Tracing in Development and Disease

scLT-kit brings robust, automated workflows to single-cell lineage tracing studies, lowering the barrier for labs to explore cell dynamics in development and disease. By integrating data quality checks, dynamic analysis, and gene-level insights, this toolkit promises to advance our understanding of how cells make fate decisions under both normal and perturbed conditions. The full study was published in Frontiers of Computer Science in April 2025 (https://doi.org/10.1007/s11704-025-41249-9).

Frontiers of Computer Science (FCS) is a leading peer-reviewed international journal co-published by HEP and Springer Nature. FCS publishes papers in all major branches of computer science including (not limited to): Architecture, Software, Artificial intelligence, Theoretical computer science, Networks and communication, Information systems, Image and graphics, Information security, Interdisciplinary. Papers published in FCS include research articles, review articles, letters. FCS is indexed by SCI(E), EI, Scopus, et al. The Latest IF will be 4.8, Q1. It is also class B journal in the CCF recommended journals directory.

 

Newswise — Just like any living organism, the soil has its own metabolism. Plants, worms, insects, and most importantly, microorganisms in the soil, break down organic matter, consume and generate nutrients, and process other materials to give the soil a life of its own. Soil microbiomes, which drive much of the metabolism in these ecosystems, are immensely complex – comprised of thousands of species with untold interactions and dynamics.

Given the complexity of the soil, however, it can be nearly impossible to understand how the communities of microbes living there respond to changes in the environment, such as temperature, moisture, acidity, and nutrient availability. Solving this problem is critical if we want to understand how soil microbiomes adapt to ever-changing environmental conditions and climate change.

New research from the University of Chicago shows that a deceptively simple mathematical model can describe how the soil responds to environmental change. Using just two variables, the model shows that changes in pH levels consistently result in three distinct metabolic states of the community.

The study, published this week in Nature, highlights how describing the collective behavior of complex systems mathematically can cut through the complexity, enabling predictions of how the soil and its metabolism will respond to change.  Ultimately, this will help scientists design interventions for improving agriculture or restoring ecosystems.

“When people think about these ecosystems, they assume you have to write down a mathematical description of the entire system, which involves thousands of variables, interacting species, and the resources they’re consuming,” said Seppe Kuehn, PhD, Associate Professor of Ecology and Evolution at the University of Chicago, and the senior author of the paper. “So, the fact that we were able to describe this in a simple way was extremely intellectually satisfying.”

A herculean effort to analyze the soil

The study is the result of a herculean effort by Kiseok Lee, PhD, a recently graduated student from Kuehn’s lab. He sampled 20 natural soils across the pH gradient from Cook Agronomy Farm in Pullman, Washington, that have large natural variations in pH but few differences in other environmental factors. Then, he manipulated each native soil’s pH by small increments in the lab, resulting in 1,500 microcosm experiments.

The pH level is a measure of the concentration of hydrogen ions in a solution. Lower pH means more acidic (more hydrogen ions), and higher pH means more basic or alkaline (fewer hydrogen ions).

Levels of pH in the soil are important because they affect the types of microorganisms living there, their metabolic activity, and the soil’s chemistry. The researchers wanted to test the effects of changing pH on anaerobic nitrate respiration, which is the process by which anaerobic microbes (i.e. ones that don’t require oxygen) use nitrate to generate energy. Nitrate respiration is a key metabolic process in agriculture and soil health.

Lee painstakingly placed samples onto plates, each with 48 wells for holding the soil, along with some water, nitrates, and acid or base solution to change the pH. Preparing and incubating the samples took months. After that, Lee took time-series measurements of nitrate in each microcosm—a total of 15,000 measurements, all by hand. “I was the machine,” Lee said, when asked if he was able to automate any of the sampling and testing.

Deceptively simple modeling

Lee and Kuehn worked with Siqi Liu, PhD, co-first author and a former graduate student in the lab of study co-corresponding author Madhav Mani, PhD, Associate Professor of Engineering Sciences and Applied Mathematics at Northwestern University, along with co-corresponding author Mikhail Tikhonov, PhD, Associate Professor of Physics at Washington University in St. Louis.

The team created a model to describe the dynamics in each of the 1,500 samples as they metabolized the nitrate. They found that a simple model predicted the activity with just two parameters: indigenous biomass activity and the amount of growth-limiting nutrient available. Depending on how the pH was changed, they saw three consistent results:

• Regime I, or the “acidic death regime”:  Large changes toward acidity caused the death of functional biomass
• Regime II, “nutrient-limiting regime”: During moderate changes, acidic or basic, the nitrate metabolism was limited by the availability of a limiting nutrient (carbon), resulting in linear nitrate dynamics
• Regime III, “resurgent growth regime”: Large changes toward basic conditions caused dominant groups of microbes to become less active, while rare groups rapidly grew and metabolized nitrate exponentially

“No matter how you perturb the pH, there’s just these three dynamic classes of behavior that the whole ecosystem can exhibit. Outside of that, it doesn’t look like anything else is allowed,” Kuehn said. “That’s really quite striking, because you have all this complexity at the lower level giving rise to this relative simplicity at the higher level.”

“This connects to an important theoretical question: when is it OK to summarize dozens of diverse species with a single coarse model?” Tikhonov said. “Here, Kiseok and Siqi managed to show that a coarsened description is not only an excellent approximation of the data but captures something general about community response to perturbations.”

Putting the new model to use

Understanding how the soil microbiome responds to these changes is useful for designing interventions. For example, if nitrogen fertilizer runoff from farms contaminates nearby waterways, officials could take measures to increase pH and remove excess nitrate to prevent algae blooms.

“If you want to understand how these systems are going to respond to future perturbations, then delimiting the set of possible responses is obviously very useful,” Kuehn said.

The researchers also think the same modeling approach can be applied to other environmental factors.

“Focusing on the resilience of the community, which is expressed by biomass activity and the limiting nutrient, shows us that different amounts of perturbations will elicit different effects,” Lee said. “I think this means that we can apply it to elucidating functional responses in other microbial systems against different environmental changes, whether it be from temperature, pH, salinity, or something else.”

The study, “Functional regimes define soil microbiome response to environmental change,” was supported by the National Science Foundation, the National Institute for General Medical Sciences, the Center for Living Systems at UChicago, the National Institute for Mathematics and Theory in Biology, the Simons Foundation, and the Chan-Zuckerberg Initiative. Additional authors include Kyle Crocker and Jocelyn Wang from UChicago and David Huggins from the United States Department of Agriculture.

An illustration of Mars surface operations with the Single-Person Spacecraft. Credit: Genesis Engineering Solutions

The idea of humans in spacesuits trying to walk on the tiny, potato-shaped Martian moon Phobos is not in the least bit practical.

With surface gravity roughly 2,000 times lower than that of Earth, “walking would be a real problem due to the low gravity. Even extremely slow steps would cause you to take huge leaps,” said Stephan Ulamec of the German Aerospace Center, DLR, who faced similar problems when his team landed the Philae spacecraft on a comet in 2014. Philae bounced, big time — but still took great pictures.

Happily, as delegates at AIAA’s ASCEND conference in Las Vegas learned on Thursday, a Boeing-led team has worked out one possible way that astronauts could explore the surface of Phobos without the gravitational hassle of effectively weighing around a mere 50 grams: inside the Single Person Spacecraft, a cylindrical extravehicular activity pod that’s being developed by Genesis Engineering of Maryland. The company has been developing the technology for the last decade, and it was optioned in 2021 for solo spacewalking excursions from Blue Origin’s Orbital Reef space station.

Defying Phobos’ low gravity by vectoring with its 16 nitrogen thrusters and equipped with arrays of dexterous robotic graspers and manipulators, the SPS could assist with any surface exploration and sampling operations, said Ben Donahue, principal investigator with Boeing’s Space Launch System applications research team in Huntsville, Alabama.

Donahue is interested in making spacewalks possible on Phobos because, as he said during his paper presentation, he is proposing that by 2035, NASA could launch a crewed, nuclear-powered mission to the moon involving at least four launches of its Space Launch System rockets. The idea is that the mission would establish an off-Mars “staging post” 6,000 km above Mars. There, the technologies for Mars surface exploration and communication for human missions on Mars itself could be more cost-effectively validated outside the planet’s gravity well and atmosphere.

“It’d be a base station for the future on Mars. One of its main purposes would be to validate the transportation and habitation components, so you don’t have to deal with all that on later missions to Mars’ surface,” Donahue told me by phone in a break between ASCEND sessions.

Multiple launches would be needed because Donahue and his co-authors want to mate together four separate components for a large Mars Transfer vehicle at the Earth-Moon Lagrange-2 point: two identical hydrogen and uranium-fueled nuclear-thermal propulsion stages; a long-duration crew habitat; a crewed Orion spacecraft and a small Earth reentry capsule.

Once mated, the Orion would be jettisoned, and the MTV sets off from the Lagrange point toward Mars.

After the nine-month outbound trip, the MTV would closely orbit Phobos, perhaps being anchored to it, and crews would have 600 days to complete their mission before embarking on the nine-month journey back to Earth, Donahue said. Astronauts would also embark on explorations of the Mars surface in SPS vehicles, gathering samples and teleoperating robots such as rovers’ helicopters and balloons. They would also establish Phobos as a telecommunications relay for future Mars missions.

Inside the SPS, an astronaut would breathe a normal oxygen and nitrogen mixture at regular air pressure and wouldn’t require a spacesuit — eliminating the time-consuming need to pre-breathe oxygen for many hours before any surface excursions.

This is the design’s chief advantage, said Donahue: “You can stay out longer, you can fly around and cover greater distances. It’s just an appropriate solution to this mission.”

Still, challenges remain, according to Ulamec of DLR. His team is readying its own Phobos mission: the IDEFIX rover that is to ride along on the Japan Aerospace Exploration Agency’s MMX sample return mission that’s set to launch in 2026.

“If you want to anchor a big spacecraft to Phobos, doing so is not trivial. How would it be done?” he asked.

(CNN) — The asteroid known as 2024 YR4 is out of sight yet still very much on scientists’ minds.

The building-sized object, which initially appeared to be on a potential collision course with Earth, is currently zooming beyond the reach of telescopes on its orbit around the sun. But as scientists wait for it to reappear, its revised trajectory is now drawing attention to another possible target: the moon.

Discovered at the end of 2024, the space rock looked at first as if it might hit our planet by December 22, 2032. The chance of that impact changed with every new observation, peaking at 3.1% in February — odds that made it the riskiest asteroid ever observed.

Ground- and space-based telescope observations were crucial in helping astronomers narrow in on 2024 YR4’s size and orbit. With more precise measurements, researchers were ultimately able to rule out an Earth impact.

The latest observations of the asteroid in early June, before YR4 disappeared from view, have improved astronomers’ knowledge of where it will be in seven years by almost 20%, according to NASA.

That data shows that even with Earth avoiding direct impact, YR4 could still pose a threat in late 2032 by slamming into the moon. The impact would be a once-in-a-lifetime event for humanity to witness — but it could also send fine-grained lunar material hurtling toward our planet.

While Earth wouldn’t face any significant physical danger should the asteroid strike the moon, there is a chance that any astronauts or infrastructure on the lunar surface at that time could be at risk — as could satellites orbiting our planet that we depend on to keep vital aspects of life, including navigation and communications, running smoothly.

Any missions in low-Earth orbit could also be in the pathway of the debris, though the International Space Station is scheduled to be deorbited before any potential impact.

Initially, YR4 was seen as a case study in why scientists do the crucial work of planetary defense, discovering and tracking asteroids to determine which ones have a chance of colliding with Earth. Now, astronomers say this one asteroid could redefine the range of risks the field addresses, expanding the purview of the work to include monitoring asteroids that might be headed for the moon as well.

“We’re starting to realize that maybe we need to extend that shield a little bit further,” said Dr. Paul Wiegert, a professor of astronomy and physics at the University of Western Ontario. “We now have things worth protecting that are a bit further away from Earth, so our vision is hopefully expanding a little bit to encompass that.”

In the meantime, researchers are assessing just how much chaos a potential YR4 lunar impact could create — and whether anything can be done to mitigate it.

‘City killer’ on the moon

The threatening hunk of rock appears as just a speck of light through even the strongest astronomical tools. In reality, YR4 is likely about 60 meters (about 200 feet) in diameter, according to observations in March by the James Webb Space Telescope, the most powerful space-based observatory in operation.

“Size equals energy,” said Julien de Wit, associate professor of planetary sciences at the Massachusetts Institute of Technology, who observed YR4 with Webb. “Knowing YR4’s size helped us understand how big of an explosion it could be.”

Astronomers believe they have found most of the near-Earth asteroids the field would classify as “planet killers” — space rocks that are 1 kilometer (0.6 mile) across or larger and could be civilization-ending, said Dr. Andy Rivkin, planetary astronomer from the Johns Hopkins University’s Applied Physics Laboratory in Maryland. The planet killer that slammed into Earth 66 million years ago and led to the extinction of dinosaurs was estimated to be roughly 6 miles (about 10 kilometers) in diameter.

Smaller asteroids such as YR4, which was colloquially dubbed a “city killer” after its discovery, could cause regional devastation if they collide with our planet. About 40% of near-Earth space rocks larger than 140 meters (460 feet) but smaller than a kilometer — capable of more widespread destruction — have been identified, according to NASA.

But astronomers have never really had a chance to watch a collision of that size occur on the moon in real time, Wiegert said. The latest glimpses of YR4 on June 3 before it passed out of view revealed a 4.3% chance of a YR4 lunar impact — small but decent enough odds for scientists to consider how such a scenario might play out.

A striking meteor shower — and a risk

Initial calculations suggest the impact has the largest chance of occurring on the near side of the moon — the side we can see from Earth.

“YR4 is so faint and small we were able to measure its position with JWST longer than we were able to do it from the ground,” said Rivkin, who has been leading the Webb study of YR4. “And that lets us calculate a much more precise orbit for it, so we now have a much better idea of where it will be and won’t be.”

The collision could create a bright flash that would be visible with the naked eye for several seconds, according to Wiegert, lead author of a recent paper submitted to the American Astronomical Society journals analyzing the potential lunar impact.

The collision could create an impact crater on the moon estimated at 1 kilometer wide (0.6 miles wide), Wiegert said — about the size of Meteor Crater in Arizona, Rivkin added. It would be the largest impact on the moon in 5,000 years and could release up to 108 kilograms (238 pounds) of lunar rocks and dust, according to the modeling in Wiegert’s study.

Even pieces of debris that are just tens of centimeters in size could present a hazard for any astronauts who may be present on the moon, or any structures they have built for research and habitation, Wiegert said. The moon has no atmosphere, so the debris from the event could be widespread on the lunar surface, he added.

On average, the moon is 238,855 miles (384,400 kilometers) away from Earth, according to NASA.

Particles the size of large sand grains, ranging from 0.1 to 10 millimeters in size, of lunar material could reach Earth between a few days and a few months after the asteroid strike because they’ll be traveling incredibly fast, creating an intense, eye-catching meteor shower, Wiegert said.

“There’s absolutely no danger to anyone on the surface,” Wiegert said. “We’re not expecting large boulders or anything larger than maybe a sugar cube, and our atmosphere will protect us very nicely from that. But they’re traveling faster than a speeding bullet, so if they were to hit a satellite, that could cause some damage.”

Not all lunar debris that reaches the Earth is so small, and it depends on the angle and type of impact to the moon, according to Washington University in St. Louis. Space rocks slamming into the lunar surface over millions of years have resulted in various sizes of lunar meteorites found on Earth.

Preparing for impact

Hundreds to thousands of impacts from millimeter-size debris could affect Earth’s satellite fleet, meaning satellites could experience up to 10 years’ equivalent of meteor debris exposure in a few days, Wiegert said.

Humankind depends on vital space infrastructure, said Dan Oltrogge, chief scientist at COMSPOC, a space situational awareness software company that develops solutions for handling hazards such as space debris.

“Space touches almost every aspect of our lives today, ranging from commerce, communications, travel, industry, education, and social media, so a loss of access to and effective use of space presents a serious risk to humanity,” Oltrogge said.

The event is unlikely to trigger a Kessler Syndrome scenario in which debris from broken satellites would collide with others to create a domino effect or fall to Earth. Instead, it might be more akin to when a piece of gravel strikes a car windshield at high speed, meaning solar panels or other delicate satellite parts might be damaged, but the satellite will remain in one piece, Wiegert said.

While a temporary loss of communication and navigation from satellites would create widespread difficulties on Earth, Wiegert said he believes the potential impact is something for satellite operators, rather than the public, to worry about.

Protecting Earth and the moon

Scientists and astronomers around the world are thinking about the possible scenarios since they could not rule out a lunar impact before YR4 disappeared from view, Wiegert said.

“We realize that an impact to the moon could be consequential, so what would we do?” de Wit said.

A potential planetary defense plan might be clearer if the asteroid were headed straight for Earth. Rivkin helped test one approach in September 2022 as the principal investigator of NASA’s Double Asteroid Redirection Test, or DART, which intentionally slammed a spacecraft into the asteroid Dimorphos in September 2022.

Dimorphos is a moonlet asteroid that orbits a larger parent asteroid known as Didymos. Neither poses a threat to Earth, but the double-asteroid system was a perfect target to test deflection technology because Dimorphos’ size is comparable to asteroids that could harm our planet in the event of an impact.

The DART mission crashed a spacecraft into the asteroid at 13,645 miles per hour (6 kilometers per second) to find out whether such a kinetic impact would be enough to change the motion of a celestial object in space.

It worked. Since the day of the collision, data from ground-based telescopes has revealed that the DART spacecraft did alter Dimorphos’ orbital period — or how long it takes to make a single revolution around Didymos — by about 32 or 33 minutes. And scientists have continued to observe additional changes to the pair, including how the direct hit likely deformed Dimorphos due to the asteroid’s composition.

Similarly, if YR4 strikes the moon and doesn’t result in damaging effects for satellites, it could create a tremendous opportunity for researchers to learn how the lunar surface responds to impacts, Wiegert said.

But whether it would make sense to send a DART-like mission to knock YR4 off a collision course with the moon remains to be seen. It will depend on future risk assessments by planetary defense groups when the asteroid comes back into view around 2028, de Wit said.

Though defense plans for a potential moon impact still aren’t clear, YR4’s journey underscores the importance — and the challenges — of tracking objects that are often impossible to see.

Hidden threats

YR4 was detected by the Asteroid Terrestrial-impact Last Alert System, or ATLAS telescope, in Río Hurtado, Chile, two days after the asteroid had already made its closest pass by Earth, hidden by the bright glare of the sun as it approached our planet.

The same thing occurred when an asteroid measuring roughly 20 meters (about 65 feet) across hit the atmosphere and exploded above Chelyabinsk, Russia, on February 15, 2013, damaging thousands of buildings, according to the European Space Agency. While no one died, about 1,500 people were injured when the windows in homes and businesses blew out due to the shock wave.

Trying to observe asteroids is challenging for many reasons, Rivkin said. Asteroids are incredibly faint and hard to see because rather than emitting their own light, they only reflect sunlight. And because of their relatively tiny size, interpreting observations is not a clear-cut process like looking through a telescope at a planet such as Mars or Jupiter.

“For asteroids, we only see them as a point of light, and so by measuring how bright they are and measuring their temperature, basically we can get a size based on how big do they have to be in order to be this bright,” Rivkin said.

For decades, astronomers have had to search for faint asteroids by night, which means missing any that may be on a path coming from the direction of the sun — creating the world’s biggest blind spot for ground-based telescopes that can’t block out our star’s luminosity.

But upcoming telescopes — including NASA’s NEO Surveyor expected to launch by the end of 2027 and the European Space Agency’s Near-Earth Object Mission in the InfraRed, or NEOMIR satellite, set for liftoff in the early 2030s — could shrink that blind spot, helping researchers detect asteroids much closer to the sun.

“NEOMIR would have detected asteroid 2024 YR4 about a month earlier than ground-based telescopes did,” said Richard Moissl, head of ESA’s Planetary Defence Office, in a statement. “This would have given astronomers more time to study the asteroid’s trajectory and allowed them to much sooner rule out any chance of Earth impact in 2032.”

NASA and other space agencies are constantly on the lookout for potentially hazardous asteroids, defined as such based on their distance from Earth and ability to cause significant damage should an impact occur. Asteroids that can’t get any closer to our planet than one-twentieth of Earth’s distance from the sun are not considered to be potentially hazardous asteroids, according to NASA.

When the new Vera C. Rubin Observatory, located in the Andes in Chile, released its first stunning images of the cosmos in June, researchers revealed the discovery of more than 2,100 previously unknown asteroids after seven nights of observations.
Of those newly detected space rocks, seven were near-Earth objects.

A near-Earth object is an asteroid or comet on an orbit that brings it within 120 million miles (about 190 million kilometers) of the sun, which means it has the potential to pass near Earth, according to NASA. None of the new ones detected by Rubin were determined to pose a threat to our planet.

Rubin will act as a great asteroid hunter, de Wit said, while telescopes such as Webb and NEO Surveyor could be trackers that follow up on Rubin’s discoveries. A proposal by Rivkin and de Wit to use Webb to observe YR4 in the spring of 2026 has just been approved. Webb is the only telescope with a chance of glimpsing the asteroid before 2028.

“This newly approved program will buy decision makers two extra years to prepare — though most likely to relax, as there is an 80% chance of ruling out impact — while providing key experience-based lessons for handling future potential impactors to be discovered by Vera Rubin,” de Wit said.

And because of the twists and turns of YR4’s tale thus far, asteroids that have potential to affect the moon could become objects of even more intense study in the future.

“If this really is a thing that we only have to worry about every 5,000 years or something, then maybe that’s less pressing,” Rivkin said. “But even just asking what would we do if we did see something that was going to hit the moon is at least something that we can now start thinking about.”

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