Why are water bears so tenacious? New research reveals their "secrets" | Science and Technology Weekly

Compiled by Zhou Shuyi and Wang Xiang

Why are water bears so tenacious? New research reveals their mechanism of radiation tolerance

From outer space to deep-sea hydrothermal vents, tardigrades have demonstrated amazing survival abilities in extreme environments. In a study published in Science on October 25, Chinese scientists revealed the multi-omics characteristics of tardigrades' tolerance to ultra-strong radiation and the complex molecular mechanisms behind it. This discovery not only enriches our understanding of extreme environment biology, but also provides a new perspective for future biotechnology and medical development.

Tardigrades are a type of aquatic invertebrate with a very small body, most of which are no longer than 1 mm. They are found all over the world, including the Arctic, tropical regions, deep seas, and hot springs, and can withstand extreme conditions such as strong radiation, high temperature, high pressure, low temperature, dryness, and even the vacuum environment of outer space.

The new study reported a new species of Hypsibius henanensis, which can withstand up to 5000 Gy of gamma-ray radiation (the lethal dose of radiation for humans is about 5 Gy). The researchers established a laboratory culture system for it and mapped a high-quality genome map (112.6M, with 14,701 protein-coding genes annotated and evenly distributed on 6 chromosomes). They integrated the dynamic changes of transcriptome and proteome in response to ultra-strong radiation for the first time in the world, combined with molecular evolution and functional characteristic analysis, and revealed the molecular mechanism of the tolerance of the Henan Hypsibius to ultra-strong radiation.

According to reports, based on the 2,801 differentially expressed genes obtained through omics analysis, researchers classified radiation tolerance mechanisms into three categories: First, foreign genes horizontally transferred from bacteria, fungi, and plants to tardigrades give them special stress resistance, such as the production of betaine pigments with strong antioxidant activity, thereby reducing radiation damage; a total of 75 highly credible related genes were identified in this study, of which 13 were significantly upregulated after irradiation. Second, about 30% of the genes in the tardigrade genome are tardigrade-specific, and tardigrade-specific proteins tend to be highly disordered and participate in processes such as DNA damage repair through phase separation. Third, ancient proteins shared with other phyla (such as mitochondrial respiratory chain assembly proteins) have special radiation response patterns in tardigrades.

It is worth noting that the study found that these molecules that play an anti-radiation role in water bears can significantly enhance the latter's anti-radiation ability after being transferred into human cells. This suggests that they have important potential application value and has found a theoretical basis for the development of a "golden bell cover" to resist damage from ultra-strong radiation.

Radiation damage in space is one of the key medical issues that restricts human deep space exploration and long-term on-orbit residence. In addition, a variety of nuclear-related operating environments are seriously threatened by ultra-strong radiation. He Fuchu, an academician of the Chinese Academy of Sciences and director of the National Key Laboratory of Medical Proteomics, said that the study of the stress resistance mechanism of tardigrades, an extreme life form, may update human understanding of the basic composition principles and operating mechanisms of life systems and open the door to a comprehensive understanding of radiation tolerance mechanisms.

Using epigenetics to store photos in DNA

In the era of big data, the flood of data has posed a severe challenge to storage technology. DNA molecules have ultra-high data storage density and ultra-long life, and have become a highly anticipated disruptive storage medium. However, traditional DNA storage relies on the "de novo synthesis" information writing route, which has obvious defects in cost and speed. A study published in Nature on October 23 proposed a DNA storage strategy that does not require de novo synthesis, achieving efficient and low-cost large-scale DNA storage, and providing a new idea for the development of practical DNA storage technology in the future.

The "epi-bit" DNA storage developed by the researchers uses prefabricated DNA templates and molecular movable type blocks to typeset molecular information through DNA self-assembly-mediated molecular information typesetting and selective enzymatic methyl modification transfer, thus achieving molecular-level "movable type printing" information printing. They successfully wrote high-definition images of the "White Tiger" tile end of the Han Dynasty in China and the giant panda "Feiyun" into DNA molecules, with a data volume of more than 275,000 bits, which is more than 300 times larger than other non-traditional DNA storage technologies previously published. The information reading uses a portable nanopore sequencer to achieve high-throughput reading of complex epi-bit information on DNA templates, and through parallel analysis of more than 240 different modification patterns at a time, the original data is restored losslessly. The experimental results verified the feasibility and accuracy of this innovative molecular storage technology, and also demonstrated the stability of epi-bits.

Large-scale epigenomic DNA storage and readout analysis. | PKUCQB

It is worth noting that the new research also demonstrates the potential for distributed storage applications of this technology. The team invited 60 young volunteers from different backgrounds to write their private data into DNA in a non-professional environment (ordinary classroom). The relevant data cannot be interpreted until sequencing. This distributed DNA storage method can not only greatly reduce the threshold for using DNA storage, but also ensure data privacy, and is expected to promote personal applications of DNA storage.

"Batch printing information on the blank sheet of DNA represents an important technological breakthrough in DNA storage, compared to the traditional 'de novo synthesis' route of adding molecular bits of information one by one," said Qian Long, an author of the paper and a researcher at Peking University. "In the future, anyone and anywhere will be able to achieve simple, accurate and efficient DNA data storage without relying on large experimental instruments. At the same time, combined with more diverse base modifications, base analogs and more accurate sequencing technologies, the scale and reliability of epi-bit DNA storage will be further improved."

They invented the first wheel 6,000 years ago

No one knows who invented the wheel, or when the first one was invented. Many historians suspect that the wheel was invented independently over and over again in different parts of the world and at different times in history. Previous research suggests that the wheel was in widespread use around the world as early as 3000 BC.

A study published in Royal Society Open Science on October 23 suggests that the invention and use of the wheel may have originated in a copper mine in Eastern Europe. About 6,000 years ago, miners in the Carpathian Mountains used the earliest wheels to move ore from deep in the mines.

Archaeologists have discovered more than 150 four-wheeled chariot-shaped pottery vessels at sites in the Carpathian Mountains in Eastern Europe. It is speculated that these vessels were drinking cups for ceremonial purposes. Carbon-14 dating shows that they were made no later than 3600 BC. Researchers believe that they were inspired by small wheeled carts used to transport ore in mine tunnels. Based on structural mechanics calculation analysis and topological optimization, researchers simulated and reconstructed the possible evolution of wheels. They proposed four possible evolutionary stages of wheels: the first stage is a free-rolling cylindrical roller (research calls it "free rollers"), such as a tree trunk with branches cut off. People have found that rolling rollers can reduce friction dissipation and help save effort. However, this method requires constantly replenishing used rollers to the front, which is difficult to achieve in narrow mines. So the miners improved it, and the wheel came to the second stage: adding grooves to the rollers so that the rollers move forward with the goods to form a "cart".

The evolution of the wheel and axle system. | Royal Society Open Science

In the third stage, the middle section of the drum becomes thinner and becomes the prototype of the axle. Researchers speculate that this may be to enhance passability and better overcome obstacles. At this stage, the axle and the wheel are relatively fixed and are a whole. In the fourth stage, the wheel can rotate independently of the axle, which allows the outer wheel to rotate faster than the inner wheel when turning, improving steering performance. Computational simulations show that the wheel-axle connection of the fixed wheelset will be subject to greater stress and more susceptible to damage. Research suggests that mine passages can be artificially straightened and do not require high steering performance. The movable wheelset was invented about 500 years after the invention of the fixed wheelset.

Can't quit carbs? It may be due to inherited genes

If you find it hard to resist the temptation of pasta and rice, it may be ancient DNA at work. A study published in Science on October 17 showed that the initial duplication of the salivary amylase gene (AMY1) in humans may have occurred more than 800,000 years ago, long before the emergence of agriculture. This allowed early humans to break down starch in food more efficiently, providing an advantage for humans to adapt to starch-rich foods.

Scientists have long known that most modern humans carry multiple copies of AMY1, which helps us break down starch initially when we chew. The more copies of AMY1 a person has, the stronger their ability to secrete amylase, and the more calories they can get from starchy foods. But scientists have been unable to determine when and how the number of copies of this gene was amplified in the human body.

To track the early duplication of AMY1, the researchers used optical genomic mapping and long-read sequencing (LRS) technology to analyze 68 ancient human genomes, including a 45,000-year-old sample from Siberia. The study found that as early as the hunting and gathering period before the agricultural era, each normal human cell (diploid cell) already had 4 to 8 copies of AMY1, indicating that humans carried multiple copies of AMY1 and were active in Eurasia long before they domesticated plants and ate a lot of starch.

The study also found that Neanderthals and Denisovans had multiple copies of AMY1, suggesting that AMY1 may have first replicated more than 800,000 years ago, before modern humans diverged from Neanderthals and much earlier than previously thought. The study suggests that the initial replication of AMY1 was like the "first ripple" in a pond, creating an evolutionary opportunity for humans that shaped our species. As humans migrated to different places and adapted to different lifestyles, variations in the number of AMY1 copies provided an advantage for humans to adapt to new diets, especially starch-rich foods. In addition, over the past 4,000 years, the average number of AMY1 copies carried by European farmers has increased significantly, which may be related to the fact that a starch-rich diet gives individuals with more AMY1 copies an evolutionary advantage.

The researchers said that individuals with more AMY1 copies digest starch more efficiently and tend to have more offspring. The study of AMY1 copy number variation will help explore its impact on metabolic health and deepen the understanding of the mechanisms of starch digestion and glucose metabolism.

Boeing-built satellite disintegrates in space

The Intelsat 33e (IS-33e) satellite of the International Communications Satellite Corporation (Intelsat) recently disintegrated in space, generating a large amount of debris. The company said it is coordinating with the satellite manufacturer Boeing and related agencies to analyze the cause of the satellite disintegration.

According to reports, the satellite was designed and manufactured by Boeing, launched in August 2016 and put into use in January 2017, mainly providing communication services to users in Europe, Africa and parts of the Asia-Pacific region. The original estimated service life of the satellite was 15 years.

Intelsat's website posted an announcement on October 19 that an abnormal condition occurred on the IS-33e satellite, resulting in the interruption of satellite services. An update on the 21st said the satellite was "completely lost". The company is coordinating with Boeing and relevant US government agencies to analyze relevant data and observations. The company said that since the abnormal condition of the satellite occurred, it has been communicating with affected customers and partners, and the interrupted services have been transferred to other satellites operated by the company or satellites operated by third parties.

According to media reports, the satellite is valuable and Intelsat had demanded $78 million in insurance compensation due to a technical failure of the satellite. However, it was reported that the satellite was not within the insurance period when it disintegrated.

The U.S. Space Force said it has confirmed that the IS-33e satellite disintegrated in geostationary orbit at 04:30 UTC on the 19th (12:30 Beijing time on the 19th). The Space Force is tracking about 20 fragments associated with the satellite, and no fragments that pose a direct threat have been found.

The Russian State Space Corporation Press Office announced that Russian professionals recorded more than 80 fragments of the satellite, which could threaten satellites in geostationary orbit; analysis of the trajectory of the fragments showed that the satellite disintegrated instantly. In addition, some media reported the incident using the term "satellite explosion."

Previously, the IS-29e satellite, also manufactured by Boeing and in the same series as the IS-33e satellite, was scrapped in geostationary orbit in 2019, having only been in orbit for three years. (CCTV News)

Papers "riding on the hype"? Mentioning AI will increase citation rates

As artificial intelligence (AI) becomes more popular, more and more researchers are beginning to use AI tools. A study recently published in Nature Human Behaviour found that scientific research papers that mention AI have a higher citation rate than those that do not mention AI.

The researchers analyzed about 75 million papers published from 1960 to 2019, covering 19 disciplines. The results showed that papers with AI terms such as "machine learning" and "deep neural networks" in the title or abstract are more likely to be among the top 5% of the most cited papers in their field, and tend to receive more citations in other fields.

The study also found that over the past 20 years, all 19 disciplines involved in the study have increased their use of AI tools, but the growth rates vary. Computer science, mathematics, and engineering have the highest usage rates, while history, art, and political science have the lowest usage rates. Geology, physics, chemistry, and biology are in between. By detecting and analyzing the usage trends of certain AI-related verb-object phrases (such as "analyzing data" or "generating images") in the literature, the researchers evaluated the benefits of using AI tools in different fields and found similar trends: computer science, mathematics, and engineering have the highest potential benefits from using AI, while history, art, and political science have the lowest potential benefits.

In the research field, the term AI in computer science is the most used. | Nature News

The new study quantified how AI has changed scientific research, but it also has limitations. The authors of the paper admit that given that the research time window ends in 2019, the study does not cover the latest developments in AI, such as the rise of ChatGPT, a type of tool based on large language models that has changed the way some researchers conduct research. Marinka Zitnik, an expert in biomedical informatics at Harvard Medical School, said that the new study did not delve into why a particular verb or noun appears in a paper. Just because they appear at the same time does not mean that AI is necessarily useful in this field.

The results of the study have also raised concerns among some scholars. Lisa Messeri, an associate professor of anthropology at Yale University, said she is worried that some researchers will abuse AI tools and ignore the quality of their research simply to increase the citation rate of their papers.

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