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A colour enhanced transmission electron micrograph showing a section of an E. coli B cell swarmed in T2 phages.

AI-designed bacteriophages were capable of infecting and killing host bacteria. Credit: Lee D. Simon/Science Photo Library

AI helps to design E. coli-killing viruses

Using artificial intelligence (AI), researchers have designed novel viruses capable of killing strains of Escherichia coli. The team used the DNA of a simple bacteriophage called ΦX174 to guide AI models to generate viral genomes with the specific function of infecting antibiotic-resistant strains of E. coli. Researchers used the model’s suggested sequences to select 302 viable phages. When put to the test, 16 of these phages could infect E. coli, and combinations of them could kill three strains of the bacterium, a feat the original ΦX174 couldn’t pull off.

Nature | 5 min read

Reference: bioRxiv preprint (not peer reviewed)

US vaccine meeting ends with confusion

An influential panel of US vaccine advisers that became controversial after it was abruptly reconstituted by US health secretary and long-time anti-vaccine activist Robert F. Kennedy Jr has come together, with vague results. The panel stopped short of recommending COVID-19 vaccines, but left room for government programmes and private health insurers to continue covering the shots. The group indefinitely delayed its guidance on hepatitis B vaccination for newborn babies. And it overturned its decision, made just the day before, about free measles, mumps, rubella and varicella (MMRV) vaccines for under-4s. MMRV doses were to have been made available free to some children, but now they won’t.

Nature | 6 min read

Grant money trickles back into Harvard

Harvard University scored a victory in court two weeks ago, when a US judge ruled that its research grants should be reinstated and its funding unfrozen. Millions from the US National Science Foundation and National Institutes of Health are flowing back to the university, but researchers report that the restoration has been patchy and much damage has been done. On Friday, in a joint status update before a judge, both Harvard and the US government asked for more time to “work through implementation issues” of complying fully with the court order.

Nature | 6 min read

Atomic conveyor could boost quantum tech

A ‘conveyor belt’ of atoms arranged in orderly rows could resolve a major stumbling block towards developing a large-scale quantum computer. The new approach uses an array of rubidium atoms inside a high-vacuum vessel, with a gas of more rubidium atoms suspended just below it. Using laser beams called ‘optical tweezers’, researchers scooped up atoms from the gas to prepare a second array as a back-up. When the first array loses atoms — an inevitability during quantum calculations — the back-up array can be moved up to interact with and replenish it, which keeps the computer in action.

Nature | 4 min read

Reference: Nature paper

Animation depicting the atom motions in the iterative assembly and continuous maintenance of a large-scale atomic array.

A micrograph showing the operation of a ‘conveyor belt’ of atom arrays. At each step, a fresh array is created at the bottom, then brought up to interact with an existing array, which might have lost some atoms while performing quantum computation. The old array is then moved up and discarded.Credit: Neng-Chun Chiu et al/Nature

Features & opinion

How warfare drove the rise of civilizations

In The Great Holocene Transformation, complexity scientist Peter Turchin sets out to explain how, over the past 10,000 years, small collectives of farmers and foragers grew into powerhouse societies. His answer, “depressingly and paradoxically, is war”, says science writer Laura Spinney in her review. Turchin has addressed the same question in a previous book, she writes, but “this time, he shows his workings, and he has more data and better tools”. Ironically, this data-driven approach is likely to further repel some of the conventional historians that Turchin has previously failed to win over, Spinney says.

Nature | 7 min read

Recording tools write daily diary for cells

By outfitting cells with the molecular equivalent of flight recorders, scientists can now log, in real time, the signals that cells receive, the paths they travel and the developmental decisions they make — all inscribed indelibly in genomic ink. It is early days, but researchers have used these tools to trace the growth of mouse embryos and capture gene activity in animal brains. Scientists are also exploring how to harness these tools for real-time disease monitoring — by engineering cells that patrol the body and log signs of trouble in molecular memory.

Nature | 11 min read

Cell recording devices. An explainer graphic showing three different approaches to logging events within cells. The first is recombinase enzymes, below that CRISPR-Cas9 gene editing and protein assembly.

Where I work

A white man with glasses, ochre trousers and purple shirt operates a big white and green machine.

Johannes Huber is a wood scientist and engineer at Luleå University of Technology in Skellefteå, Sweden.Credit: Elin Berge for Nature

Wood scientist Johannes Huber uses computed tomography (CT) scanning to test the properties of wood samples without breaking them. “Wood has character; no two logs are alike,” he says. Using industrial CT scanners, Huber can create detailed models of the wood’s internal structure. “If we can evaluate it non-destructively, we can optimize how we use this material,” he says. (Nature | 3 min read)

Quote of the day

“Sometimes they are the end of tubes in the digestive system, sometimes the end of feet and hands, i.e., digits. Therefore, both mark the end of something.”

To develop their fingers and toes, tetrapods recycled an ancient region of the genome that was once active in the formation of the rear orifice of fish, says geneticist Aurélie Hintermann, who co-authored a study on the topic. (Science Alert | 4 min read)

Reference: Nature paper