Latest news with #bioRxiv
Scientific American
4 days ago
- Health
- Scientific American
Bird Flu on Dairy Farms May Be Airborne After All
The H5N1 avian influenza virus can now be found not only in milk and on milking equipment but also in farm wastewater and in the air, say researchers who have been trying to figure out how the virus spreads on dairy farms. The researchers identified the virus in both large and small aerosol particles in the air on farms affected by bird flu in California, according to a new preprint paper posted on the biology server bioRxiv. 'There is a lot of H5N1 virus on these farms,' says Seema Lakdawala, an associate professor of microbiology and immunology at the Emory University School of Medicine and senior author of the new study, which has yet to go through scientific peer review. 'It is everywhere. We need to be expanding biosafety measures, biosecurity measures and trying to control where the virus is.' On supporting science journalism If you're enjoying this article, consider supporting our award-winning journalism by subscribing. By purchasing a subscription you are helping to ensure the future of impactful stories about the discoveries and ideas shaping our world today. The finding—that the virus is 'everywhere'—fits with what has been seen in previously published work, says Richard Webby, who studies host-microbe interactions at St. Jude Children's Research Hospital. 'It's a ridiculously contaminated environment,' Webby says. The high concentrations of H5N1 in the environment may explain why the virus transmits so readily among cattle on dairy farms, as well as why a study from last fall found that 7 percent of tested dairy farm workers had antibody evidence of a previous bird flu infection. H5N1-infected cattle were first reported in March 2024. Since then the Centers for Disease Control and Prevention has found 41 human cases directly stemming from contact with milking cows. And the disease has spread readily within herds. But exactly how it's spreading has been oddly difficult to pin down. Another recent preprint study by the Ohio State University veterinary medicine professor Andrew Bowman and his colleagues found that, when liquid containing the virus was put into cows' teats, only a very low dose was necessary to cause an infection. But strangely, when the researchers milked the well cows with contaminated equipment—the way the virus was assumed to be spreading on farms—the healthy cows did not fall ill. 'It seems like it shouldn't be that hard to make transmission happen, given the way we see it spread through dairy farms in the field,' said Bowman in an interview with Scientific American in June. Lakdawala and her team wanted to figure out how the virus moves between cows in hopes of finding a way to slow or stop the spread. They began testing affected dairy farms in California in the winter of 2024 and ended up assessing a total of 14 farms by early 2025, a period representing the peak of the dairy cattle outbreak. The researchers used aerosol sampling devices to test both cow exhalations and the ambient air in milking parlors and barns. They also tested milk and the entire wastewater system, from the drains in milking parlors to the manure lagoons outdoors. The team found plenty of opportunities for the virus to transmit, given that viral particles were found all over. 'It's not a single event or a single thing that drives transmission,' Lakdawala says. 'The likelihood is: overbombardment of viruses in the environment is leading to efficient transmission. They're inhaling it; they're probably also finding it on their bodies; they're licking it; they're finding it on the milking equipment—all of it together.' The researchers found one sample with mutations in an area on the H5N1 genome that's known to change when avian viruses become more adept at spreading between humans. It's not clear whether that particular mutation would have helped the virus infect humans more effectively. Luckily, that version of the pathogen did not go on to reproduce: it seems to have emerged and, just as quickly, to have died out. Another recent paper, published by Webby and his team in the journal Nature Communications in July, found that, so far, the virus circulating in cattle still looks very much like the virus circulating in birds. That research also found that the bovine virus couldn't spread through the air between ferrets, which are used because they transmit flu viruses much like humans do. 'We've dodged a little bit of a bullet so far with cows and this virus,' Webby says. But with so much virus on affected farms, there's a chance that future human-oriented mutations could arise, Lakdawala warns. She suspects the virus becomes aerosolized during both milking and cleaning. Also, workers often spray down floors and other farm surfaces with wastewater that they now know can contain infected milk. Face shields that can block large droplets and large aerosols without the discomfort of masks might be one way to reduce cow-to-human infections among workers. Rapid 'at-barn' H5N1 tests, not unlike the at-home flu or COVID tests people can purchase at drug stores, would help farmers identify and isolate sick cows before they could infect others, she says. And treating infectious milk before it's dumped—perhaps with a weak acid such as vinegar or lemon juice to inactivate the virus, Lakdawala says—could keep H5N1 out of wastewater. 'This is highlighting to me that we really need to work harder to get this entire outbreak under control,' she says.
Time of India
5 days ago
- Science
- Time of India
Computer science research papers show fastest uptake of AI use in writing, analysis finds
Academy Empower your mind, elevate your skills Researchers analysed the use of large language models in over a million pre-print and published scientific papers between 2020 and 2024, and found the largest, fastest growth in use of the AI systems in computer science papers -- of up to 22 %.Powered by artificial intelligence (AI), large language models are trained on vast amounts of text and can therefore respond to human requests in the natural from Stanford University and other institutes in the US looked at 1,121,912 pre-print papers in the archives 'arXiv' and 'bioRxiv', and published papers across Nature journals from January 2020 to September on how often words commonly used by AI systems appeared in the papers, the team estimated the involvement of a large language model -- ChatGPT in this study -- in modifying content in a research published in the journal Nature Human Behaviour "suggest a steady increase in LLM (large language model) usage, with the largest and fastest growth estimated for computer science papers (up to 22%)."The researchers also estimated a greater reliance on AI systems among pre-print papers in the archive 'bioRxiv' written by authors from regions known to have a lower number of English-language speakers, such as China and continental papers related to mathematics and those published across Nature journals showed a lower evidence of use of AI in modifying content, according to the study team said that shorter papers and authors posting pre-prints more often showed a higher rate of AI use in writing papers, suggesting that researchers trying to produce a higher quantity of writing are more likely to rely on LLMs."These results may be an indicator of the competitive nature of certain research areas and the pressure to publish quickly," the team researchers also looked at a smaller number of papers to understand how scholars disclose use of AI in their inspection of randomly selected 200 computer science papers that were uploaded to the pre-print archive 'arXiv' in February 2024 revealed that "only two out of the 200 papers explicitly disclosed the use of LLMs during paper writing".Future studies looking at disclosure statements might help to understand researchers' motivation for using AI in writing example, policies around disclosing LLM usage in academic writing may still be unclear, or scholars may have other motivations for intentionally avoiding to disclose use of AI, the authors said.A recent study, published in the journal Science, estimated that at least 13% of research abstracts published in 2024 could have taken help from a large language model, as they included more of 'style' words seen to be favoured by these AI from the University of Tubingen, Germany, who analysed more than 15 million biomedical papers published from 2010 to 2024, said that AI models have caused a drastic shift in the vocabulary used in academic writing.
The Hindu
29-07-2025
- Health
- The Hindu
SB43154 drug used in cancer research shows promise against COVID-19 in preclinical studies: Scientists
After a long battle and research, Indian scientists have found out that a drug used in cancer studies has the potential to provide substantial protection against the coronavirus infection in preclinical studies. Remarkably, even after more than 50 consecutive generations exposed to the drug, the virus was unable to develop resistance. Scientists from the Indian Council of Medical Research (ICMR) and Indian Council of Agricultural Research (ICAR) have jointly found that the drug -- SB431542, an ALK5 inhibitor -- is highly effective against the coronavirus. Study findings This discovery was a collaborative effort between the National Centre for Veterinary Type Culture in Hisar and National Institute of Virology (NIV) under the ICMR in Pune, said NIV Director Dr Naveen Kumar. The study was first released as a preprint on bioRxiv and has since been accepted for publication in the Journal of Virology. If future human trials confirm its effectiveness, the drug could become a groundbreaking tool in the fight against COVID-19. Since December 2019, when the coronavirus emerged from China's Wuhan, it has spread to nearly every country in the world. Since 2020, more than 30 anti-Covid vaccines have received the World Health Organization's (WHO) approval for global use. "However, health experts believe vaccines alone are not enough. The virus continues to mutate, and many existing treatments like Remdesivir and monoclonal antibodies will quickly lose effectiveness," Kumar said. In this context, Indian scientists have been screening small molecule inhibitors that mainly target cellular kinases and phosphatases. One such compound, SB431542 -- originally developed to block TGF-β (Transforming Growth Factor-beta) signalling and commonly used in preclinical cancer, inflammation and fibrosis research -- has now been found by Indian researchers to also inhibit the coronavirus effectively. Kumar explained that SB431542 fights the virus in three fronts. It first blocks the virus from entering human cells by targeting the TGF-β/Smad pathway. Secondly, it disrupts the ability of the virus to assemble inside cells by interfering with ORF3a-related lysosomal dysfunction. Finally, it prevents the virus from killing the infected cell (a process called apoptosis), which helps stop the virus from escaping and spreading to other cells. This three-pronged approach has not been observed in any existing antiviral drug. Interestingly, the drug acted through both direct and indirect mechanisms -- it directly targets the viral ORF3a protein and indirectly hinders the virus by blocking the host cell's TGF-β signaling pathway. SB431542 was also tested against the chicken coronavirus (Infectious Bronchitis Virus or IBV) in specific pathogen-free chicken embryos. Embryos treated with the drug developed normally and showed no mortality, while those in the untreated control group failed to develop properly and did not survive. Kumar emphasised that even after exposing the virus to the drug over 50 successive generations (passage), it failed to develop resistance. This suggests that the chances of the virus evolving a drug-resistant variant against this compound are extremely low. This is a major advancement over existing antivirals like Remdesivir, against which the virus builds resistance quickly.
The Print
28-07-2025
- Health
- The Print
SB43154 drug used in cancer research shows promise against COVID-19 in preclinical studies: Scientists
This discovery was a collaborative effort between the National Centre for Veterinary Type Culture in Hisar and National Institute of Virology (NIV) under the ICMR in Pune, said NIV Director Dr Naveen Kumar. Remarkably, even after more than 50 consecutive generations exposed to the drug, the virus was unable to develop resistance. Scientists from the Indian Council of Medical Research (ICMR) and Indian Council of Agricultural Research (ICAR) have jointly found that the drug — SB431542, an ALK5 inhibitor — is highly effective against the coronavirus. New Delhi, Jul 28 (PTI) After a long battle and research, Indian scientists have found out that a drug used in cancer studies has the potential to provide substantial protection against the coronavirus infection in preclinical studies. The study was first released as a preprint on bioRxiv and has since been accepted for publication in the Journal of Virology. If future human trials confirm its effectiveness, the drug could become a groundbreaking tool in the fight against COVID-19. Since December 2019, when the coronavirus emerged from China's Wuhan, it has spread to nearly every country in the world. Since 2020, more than 30 anti-Covid vaccines have received the World Health Organization's (WHO) approval for global use. 'However, health experts believe vaccines alone are not enough. The virus continues to mutate, and many existing treatments like Remdesivir and monoclonal antibodies will quickly lose effectiveness,' Kumar said. In this context, Indian scientists have been screening small molecule inhibitors that mainly target cellular kinases and phosphatases. One such compound, SB431542 — originally developed to block TGF-β (Transforming Growth Factor-beta) signalling and commonly used in preclinical cancer, inflammation and fibrosis research — has now been found by Indian researchers to also inhibit the coronavirus effectively. Kumar explained that SB431542 fights the virus in three fronts. It first blocks the virus from entering human cells by targeting the TGF-β/Smad pathway. Secondly, it disrupts the ability of the virus to assemble inside cells by interfering with ORF3a-related lysosomal dysfunction. Finally, it prevents the virus from killing the infected cell (a process called apoptosis), which helps stop the virus from escaping and spreading to other cells. This three-pronged approach has not been observed in any existing antiviral drug. Interestingly, the drug acted through both direct and indirect mechanisms — it directly targets the viral ORF3a protein and indirectly hinders the virus by blocking the host cell's TGF-β signaling pathway. SB431542 was also tested against the chicken coronavirus (Infectious Bronchitis Virus or IBV) in specific pathogen-free chicken embryos. Embryos treated with the drug developed normally and showed no mortality, while those in the untreated control group failed to develop properly and did not survive. Kumar emphasised that even after exposing the virus to the drug over 50 successive generations (passage), it failed to develop resistance. This suggests that the chances of the virus evolving a drug-resistant variant against this compound are extremely low. This is a major advancement over existing antivirals like Remdesivir, against which the virus builds resistance quickly. PTI PLB RC This report is auto-generated from PTI news service. ThePrint holds no responsibility for its content.
Yahoo
06-07-2025
- Science
- Yahoo
What is life? A little microbe raises big questions.
It's tiny and needy, but is it alive? That's a question prompted by recent research that highlights a surprisingly complex part of biology. The organism in question is a microbe called Sukunaarchaeum mirabile, discovered by researchers in Canada and Japan who were looking at the DNA of a species of marine plankton, according to a new paper published on bioRxiv. They've found it's unusually reliant on an alive host to survive, which could further blur the lines between cellular life and viruses — which generally considered to not be alive. The National Human Genome Research Institute describes viruses as existing "near the boundary between the living and the nonliving." Viruses can't function without interacting with a living cell. On their own, they're also essentially inert – unable to move – as a 2017 study notes. Enter Sukunaarchaeum mirabile, which could complicate things further. "This organism represents a totally new branch in the archaeal tree of life," lead researcher Takuro Nakayama of the University of Tsukuba told USA TODAY. (Archaea are microorganisms that define the limits of life on Earth.) "Sukunaarchaeum is not a virus, but a highly streamlined cellular organism," Nakayama said. According to the new study, which has yet to be peer-reviewed, "the discovery of Sukunaarchaeum pushes the conventional boundaries of cellular life and highlights the vast unexplored biological novelty within microbial interactions." Named for a Japanese deity known for its tiny size, Sukunaarchaeum has one of the smallest genomes ever recorded: "Its genome is drastically reduced – less than half the size of the previously smallest known archaeal genome," Nakayama said. The authors in the study write that "its genome is profoundly stripped-down, lacking virtually all recognizable metabolic pathways, and primarily encoding the machinery for its replicative core: DNA replication, transcription, and translation." "This suggests an unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses,' the study says. "Sukunaarchaeum could be just the tip of the iceberg, pointing to a hidden diversity of life forms with ultra-reduced genomes within the so-called 'microbial dark matter,'" Nakayama told USA TODAY. Indeed, the discovery of Sukunaarchaeum's bizarrely viruslike way of living 'challenges the boundaries between cellular life and viruses,' Kate Adamala, a synthetic biologist at the University of Minnesota Twin Cities who was not involved in the work, told Science magazine. 'This organism might be a fascinating living fossil – an evolutionary waypoint that managed to hang on.' The study concludes that "further exploration of symbiotic systems may reveal even more extraordinary life forms, reshaping our understanding of cellular evolution." "I am not an expert on the philosophical definition of 'life," Nakayama said, adding that the definition is not uniform among scientists and is a subject of continuous debate. "Many scientists would agree that cellular structure, the ability to replicate, and the ability to metabolize are key features of life. Viruses typically lack these features," he said. "The discovery of Sukunaarchaeum is interesting in this context because it lacks one of those key features: metabolism. The existence of a cellular organism that seemingly lacks its own metabolism provides a new and important perspective to the ongoing discussion about the definition and minimal requirements of life." Contributing: Joel Shannon, USA TODAY This article originally appeared on USA TODAY: A mysterious microbe raises questions about life
