Tag Archives: biology

Biologist Resurrects 3.2 Billion-Year-Old Enzyme: Discoveries in Ancient Biology | Science News

Posted on by
Reply

A groundbreaking research team from the University of Wisconsin-Madison has successfully reverse-engineered a primitive nitrogen-fixing enzyme. This discovery sheds light on how life thrived before the Earth was transformed by oxygen and establishes reliable chemical markers for detecting extraterrestrial life.

Resurrection and characterization of an ancestral nitrogenase. Image credit: Rucker et al., doi: 10.1038/s41467-025-67423-y.

Led by Professor Betül Kaçar, the research focuses on an essential enzyme known as nitrogenase, which plays a pivotal role in converting atmospheric nitrogen into bioavailable forms.

“We selected an enzyme that significantly influences life on Earth and investigated its evolutionary history,” Professor Kaçar stated.

“Without nitrogenase, the existence of modern life as we know it would be impossible.”

Traditionally, scientists have depended on geological evidence to reconstruct Earth’s historical life.

However, significant fossils and rock samples are scarce and often require fortuitous discovery.

Professor Kaçar and his team view synthetic biology as a valuable tool to bridge these gaps, allowing them to construct specific ancient enzyme reconstructions, insert these into microorganisms, and study them in contemporary lab settings.

“The Earth of 3 billion years ago was vastly different from the world we recognize today,” remarked Dr. Holly Rucker.

“Before the Great Oxidation Event, the atmosphere was rich in carbon dioxide and methane, and life predominantly consisted of anaerobic microorganisms.”

“Understanding how these microorganisms accessed vital nutrients like nitrogen enhances our comprehension of how life persisted and evolved before oxygen-dependent organisms began to alter the planet.”

“Though fossilized enzymes are unavailable for study, these enzymes can leave discernible isotopic traces, measurable in rock samples.”

“Much of the prior research assumed ancient enzymes produced isotopic signatures akin to modern enzymes,” added Dr. Rucker.

“This holds true for nitrogenase; the isotopic traces we observe from ancient times correspond with modern signatures, providing deeper insights into the enzyme itself.”

The researchers discovered that ancient nitrogenase enzymes, despite having different DNA sequences, maintain the same mechanisms for isotopic signatures observed in the rock record.

“As astrobiologists, our understanding of Earth helps us comprehend the potential for life elsewhere in the universe,” Professor Kaçar emphasized.

“The quest for life begins right here on our 4-billion-year-old planet.”

“To grasp future possibilities and life beyond our planet, we must first understand our own history.”

The results were published today in the online journal Nature Communications, accessible here.

_____

Rucker et al. 2026. The revived nitrogenase reproduces the standard N isotope biosignature spanning two billion years. Nat Commun 17,616; doi: 10.1038/s41467-025-67423-y

Source: www.sci.news

Biotechnology Firms Seek to Develop the “ChatGPT of Biology”: Does It Deliver?

Posted on by
Reply

Basecamp researchers gather genetic data in Malta

Greg Funnell

A British biotech firm, Basecamp Research, has spent recent years gathering extensive genetic data from microorganisms inhabiting extreme environments worldwide, uncovering 10 billion new species among over a million scientifically recognized entities. This vast database of planetary biodiversity aims to assist in training “biology chats” to address inquiries regarding life on Earth, although its effectiveness remains uncertain.

Jorg Overmann from the Leibniz Institute DSMZ, which houses one of the world’s most extensive collections of microbial cultures, asserts that while an increase in known genetic sequences is beneficial, it likely won’t lead to significant discoveries in drug development or chemistry without deeper insights into the organisms from which they originated. “In the end, I’m skeptical that a better understanding of unique features will be achieved merely through brute force in the sequencing domain,” he remarks.

Recent years have seen a surge in machine learning models aimed at identifying patterns and predicting relationships within vast biological datasets. The most well-known of these is Alphafold, which can predict the 3D structure of proteins using only genetic data, and was awarded the 2024 Nobel Prize in Chemistry at Google DeepMind.

This “genometric biology” approach has grown significantly, but according to Francis Din at the University of California, Berkeley, progress has been limited. One reason for this is the underrepresentation of biodiversity data. “Current biological models are primarily trained with datasets that favor well-studied species (e.g., E. coli, mice, humans), leading to poor prediction capabilities for traits associated with sequences from other branches of the Tree of Life,” she explains.

Basecamp researchers aim to bridge this biodiversity gap. Their expanding database now includes samples from over 120 locations across 26 countries, as detailed in a report by the company. Jonathan Finn, the company’s Chief Science Officer, notes that their sampling efforts target extreme environments that have yet to be thoroughly examined, spanning from the icy depths of the Arctic Ocean to the warm jungle hot springs. “Most of the samples we’re prioritizing are prokaryotic: bacteria, microorganisms, and their viruses,” Finn states. “We are also aware that some fungi are present.”

Genetic analyses of these samples have illuminated gene variations that are broadly shared across the Tree of Life. Based on this research, the company estimates that their data encompasses over a million species of genetic information not found in public genomic databases utilized for training AI models. This includes around 9.8 billion newly identified genes, increasing the overall known gene count tenfold, each potentially encoding useful proteins, according to the researchers.

“By providing these models with richer data, we enhance our understanding of biological mechanisms,” Finn explains. “We aim to create a ChatGPT for Biology.”

It’s estimated that Earth hosts trillions of microorganism species, many of which remain poorly characterized. Thus, it’s not unexpected that the company has identified such a wealth of novel life forms. “As we explore more, discovering diverse gene variants becomes almost inevitable,” notes Leopold Parts at the Wellcome Sanger Institute in the UK.

Nevertheless, Basecamp promotes the notion that all newly discovered materials might hold value. It’s not alone in this sentiment. “This is among the most thrilling advances I’ve encountered in quite some time,” remarks Nathan Frey, a machine learning researcher at Genentech, a US biotech firm. He emphasizes that most AI biology projects focus on algorithm improvement or generating additional lab data rather than venturing out to collect samples directly from nature.

However, skepticism arises regarding whether this database will yield the meaningful advancements the company aspires to achieve. For starters, it remains uncertain how much this newfound diversity in proteins reflects valuable new functions like enzymes and proteins that can degrade plastic useful for gene editing. “They must demonstrate that this novelty has practical utility,” cautions Parts.

Moreover, if the new genes significantly differ from known genes, Overmann expresses doubts about how easily existing tools can predict functionality or how such data can be utilized for training new models. “I can’t discern the functions of most of my genes,” he states. The company may have created a valuable new repository of biological data, but in traditional lab settings, even the most advanced AI may still face challenges in interpretation.

topic:

Source: www.newscientist.com

Opponent of Biology Discovers Authentic Collagen in Edmontosaurus Fossil Bones

Posted on by
Reply

The detection of soft tissues (such as proteins) in fossil bones is a growing research field, and new research, led by Liverpool University, has contributed to such discoveries. The authors use three independent analytical combinations to indicate that some dinosaur bones of collagen bones are the original fossils.

Tuinstra et al。 In order to replenish the two mass-specific (MS) technologies used, the total attenuation (ATR) -ftir and intersection polarized microscopes (Xpol), which replenish two mass spectrometics (MS) technologies. Edmont Saurus SP. Fossil bones. Image credit: Tuinstra et al。 , Doi: 10.1021/ACS.ANALCHEM.4C03115.

In their research, Professor Steve Taylor and his colleagues of Liverpool University examined the 22 kg hip bone of herbivorous dinosaurs that bred ducks. Edmont Saurus。

The specimen was excavated from the late Cretaceous band of the Helkleak layer in Harding County, South Dakota, USA.

Using advanced mass spectrometry and other technologies, old -life scholars have identified collagen remnants with fossil bones.

“This study shows that organic body molecules, such as collagen -like proteins, seem to be present in some fossils,” said Taylor.

“Our results have a wide range of meanings. First, the hypothesis that organic matters contained in fossils need to be caused from contamination.”

“Second, it suggests to reconsider the cross -polarized microscopes of fossil bones collected over the first century.”

“These images may clarify the intact patches of bone collagen, and may provide candidates for ready -made fossil candidates for further protein analysis.”

“This may release a new insight about dinosaurs. For example, we will clarify the connection between dinosaur species as it is.”

“Finally, the result of this survey tells you an interesting mystery about how these proteins have long lasted in fossils.”

“This study not only solves the scientific discussion for many years, but also has a further path to study ancient life, and can be seen on the biochemical preservation of the fossils of extinct creatures.”

Team result Published in the journal on January 17th Analytical chemistry。

______

Lucien Tuinstra et al。 Evidence of endogenous collagen Edmont Saurus Fossil bones. anus. ChemistryReleased online on January 17, 2025. Doi: 10.1021/ACS.ANALCHEM.4C03115

Source: www.sci.news

Understanding Traitors: Exploring the Intersection of Forensic Psychology and Evolutionary Biology

Posted on by
Reply

Claudia Winkleman, The Traitors host

BBC /Studio Rambert

Food -up, torch light, knife Sharp: Viewers in the UK are ready for different delicious finale Traitor Tonight, at a video game show, a TV game show is trying to drive away the ruthless (strictly non -realistic) murderers walking between them.

For psychologists -Experts and armrests- Traitor This is the gold mine of the unauthorized human behavior, which is disassembled and analyzed. And it's not just psychology. Game theory, human evolution, and criminal science are only a few of the scientific fields that provide clues to Makabeli's dynamics.

I found something that I really needed to win to investigate a betrayal (academically speaking …) Traitor。 Warning: If there is no latest information on the show, there is a spoiler first.

Please be careful about compatible bias

“Having a strong feature seems to be that others are influential and potentially intimidating,” says a forensic psychologist. Kuala LightHost A Podcast About Traitor With a colleague at the British Chester University. She selects contestants such as shadows (too intelligent), Ellen (too emotional), and Armani (too much confidence).

Their falls are likely to be linked Compatible biasThe characteristics of human beings that most of us comply with social norms. Individuals who do not fit may be hated or distrustful.

This is not a place of altruism

Emily EmotThe London University College's evolution anthropologist says that players should not be able to “do not actually exist in evolutionary literature.”

“Remember, it's not a cooperative game,” she says. “It's a deceptive game, a survival game. You need to be there to win, so it's a mistake to commit some players because they trust the nearby people. “

Emot says that we have evolved to go ahead of others. Therefore, altruistic behaviors found in the show are said to have selfish benefits behind them. And such obvious altruism is not a bad tactic, whether you are faithful or traitor.

“In the context of the game, cooperative is functioning as a signal for reliability. A good example may not be open to the shield. [which protects you from the next murder] During the show task. “

However, here is Makabeli's intelligence. Because everyone knows the rules of the game, excellent players do not take altruistic actions at face value. “In this game, you may have an impure motivation for you, so it’s not a honest signal,” says Emot.

So be careful of wonderful people. an Thousands of messages analysis Between players DiplomacyGames that share similarities TraitorExcessive polite players have discovered that they are more likely to betray others.

Be careful of bias in the group

“We know from social psychology that they have what they are called when they form a social group. Bias in the groupAnd this can really accelerate TraitorLight says. “”[Contestants] Display priority actions to those in the group with them. This is why everything did not work for Mina after recruiting Charlotte as a traitor.

Charlotte is recruited as a traitor by Mina

BBC /Studio Rambert

For Mina, who was always looking for a female traitor, her group was a so -called sister relationship she created. “She identified it as a sister relationship. She used this word well,” says Light. “The problem is that Charlotte had already had a faithful person and a strong group's identity, and when she was hired by her will, she did not have the loyalty to the new group. did.”

And what happened? Charlotte immediately crossed Mina, and Mina was voted the next night.

Light says that the same group's bias can lead to a flock thinking when the player is voting, which can lead to an unrogical trust in people in the game.

What is a good liar?

A nervous or inconsistent answer to the question is generally considered doubtful, even if someone tells the truth. That's because these actions are tied to a stereotype about what a liar is doing. The better gifts are always those who say the same thing. Emma BarrettPsychologist and criminal scholar at the University of Manchester University.

“One of the most notable things is the same story in the exact same way, and they don't really explain it in detail when they re -speak it,” she says. The story may sound plausible, but repeatedly adds details as you remember. “People sometimes make a mistake in consistency, but that's not a way to work with real memories.”

Think like a scientist

Hunting for the traitor -Introduction to the 3rd season of the traitor

BBC /Studio Rambert

Faithful people are not very good at it TraitorBut another tactic that they can use is to encourage suspicious traitor to speak more than they want. Barrett says.

“If you are faithful, the good strategy to detect a traitor is to subtly encourage them as they speak.” “For example, if you want to know if you are a police officer and someone gave you a false address, one of the questions you might ask is,” Oh, how do you get there? What is your nearest station?

If you are suspicious, try a game theory?

The majority of information is always lost to the minority based on sufficient information. Based on this, it was created by Russian psychologist Dimitry Davidoff mafia -Which parlor game Traitor Based on the 1980s. since then, mafia It is used as the basis of many game theory experiments and models.

The good news is that Davidoff is not correct at all. He believed that the probability of a faithful person to keep the bad guys away is better than a coincidence. But many the study The model discovered that the possibility of victory was almost equal, and was leaned in support of people who were faithful to live games for the weight of the lie that the traitor had to talk about.

In other words, forget cold mathematics. If you really want to win TraitorYou must be just injustice than anyone else.

topic:

Source: www.newscientist.com

Health and Biology Experiments Conducted by ISS Crew during Dragon’s Countdown

Posted on by
Reply

Loral O’Hara, NASA astronaut and Expedition 70 aeronautical engineer, proudly displays the research hardware that supports the UMAMI (Understanding Microgravity for Animal-Microbial Interactions) astrobiology experiment. Dr. O’Hara has in her possession an Advanced Space Experiment Processor (ADSEP) fluid processing cassette (FPC) that facilitates observations of the effects of spaceflight on the molecular and chemical interactions between beneficial microorganisms and their animal hosts. Credit goes to NASA for this image.

The top research goals for the Expedition 70 crew earlier in the week included crew health and astrobiology. The crew members of the International Space Station (ISS) were occupied with various standard laboratory maintenance tasks. In the meantime, SpaceX’s Dragon cargo spacecraft is scheduled to depart as early as Wednesday.

Studying the effects of weightlessness is a priority for doctors and scientists, as they observe how various life forms, including humans, adapt and survive in the harsh environment of microgravity. NASA and its international partners are planning further long-term missions into space in order to learn more about the biology of aging and its impact on disease mechanisms. NASA astronaut and Expedition 70 flight engineer Jasmine Moghbeli was seen wearing a BioMonitor vest and headband to test her ability to comfortably monitor the health of astronauts throughout the day. She also spent time processing cell samples in the Kibo experimental module’s life science glovebox.

Today, a pair of CubeSats were deployed outside the orbital outpost for exploration. Flight engineer Satoshi Furukawa of the Japan Aerospace Exploration Agency (JAXA) photographed the deployment of two small satellites and then maintained and supported optical hardware regenerative medicine experiment. In the end, Furukawa prepared: Sapphire-VI Fire safety experiments conducted remotely on board a ship Cygnus space cargo ship After leaving the space station.

Astronauts Loral O’Hara and Andreas Mogensen were stowing their spacewalk gear in Quest’s airlock. ESA (European Space Agency) astronaut and Expedition 70 Commander Andreas Mogensen used the Advanced Space Experiment Processor 2 (ADSEP-2) to store and process samples for a variety of biological and physical science experiments.

Cosmonauts Oleg Kononenko and Konstantin Borisov inspected and photographed eggs packed inside a centrifuge in the Nauka scientific module. Flight engineer Nikolai Chubut spent the day developing the life support systems inside the Zarya and Zvezda modules.

The Dragon supply mission’s departure was targeted for 5:05 p.m. EST Wednesday, Dec. 20, with coverage beginning at 4:45 p.m. on the NASA+ streaming service and NASA Television. As the departure was being organized, joint teams continued to work to assess optimal autonomous ports of entry and return weather conditions.

Source: scitechdaily.com

The merger of quantum biology and AI fueled genome editing advancements

Posted on by
Reply

Scientists at Oak Ridge National Laboratory have utilized quantum biology and explainable artificial intelligence to advance CRISPR Cas9 technology for genome editing in microorganisms. This breakthrough has enabled more precise genetic modification of microorganisms, opening up possibilities for the production of renewable fuels and chemicals. The research at Oak Ridge National Laboratory has significantly improved the efficiency of CRISPR Cas9 genome editing in microorganisms and contributed to renewable energy development.

CRISPR is a powerful tool for bioengineering, used to modify the genetic code to improve the performance of organisms or correct mutations. ORNL scientists developed a method to improve the accuracy of the CRISPR Cas9 gene editing tool used to modify microorganisms for the production of renewable fuels and chemicals. They have leveraged their expertise in quantum biology, artificial intelligence, and synthetic biology to achieve this.

To improve the modeling and design of guide RNAs, ORNL scientists sought to better understand what is happening at the most fundamental level in the cell nucleus, where genetic material is stored. They turned to quantum biology to study how electronic structure affects the chemical properties and interactions of nucleotides, such as DNA and RNA.

Furthermore, scientists at ORNL have built an explainable artificial intelligence model called iterated random forest, which has been used to train the model on a dataset of about 50,000 guide RNAs targeting the genome of Escherichia coli. This model has provided important features regarding the nucleotides that allow for better selection of guide RNAs.

Improving the CRISPR Cas9 model provides scientists with a high-throughput pipeline for linking genotype to phenotype in functional genomics. This research will impact efforts at the ORNL-led Center for Bioenergy Innovation (CBI), such as improving bioenergy feedstock plants and bacterial fermentation of biomass.

The results of this research significantly improve the prediction of guide RNAs. This represents an exciting advance toward understanding how avoid ‘mistakes’ and improving the ability to use CRISPR tools to predictively modify the DNA of more organisms. The study was funded by SEED SFA and CBI, part of the DOE Office of Science’s Biological and Environmental Research Program, ORNL’s Laboratory-Directed Research and Development Program, and OLCF and Compute’s High Performance Computing Resources and Data Environment for Science, both supported by the Office of Science.

Source: scitechdaily.com