Biology

nitrogen-using-bacteria-can-cut-farms’-greenhouse-gas-emissions 

Nitrogen-using bacteria can cut farms’ greenhouse gas emissions 

agriculture, bacteria, Biology, climate change, fertilizer, nitrogen, Science / /

Keeping crops from the greenhouse —

Nitrogen fertilizers get converted to nitrous oxide, a potent greenhouse gas.

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A tractor amidst many rows of small plants, with brown hills in the background.

Fritz Haber: good guy or bad guy? He won the Nobel Prize in Chemistry in 1918 for his part in developing the Haber-Bosch process, a method for generating ammonia using the nitrogen gas in air. The technique freed agriculture from the constraint of needing to source guano or manure for nitrogen fertilizer and is widely credited for saving millions from starvation. About half of the world’s current food supply relies on fertilizers made using it, and about half of the nitrogen atoms in our bodies can be traced back to it.

But it also allowed farmers to use this newly abundant synthetic nitrogen fertilizer with abandon. This has accentuated agriculture’s role as a significant contributor to global warming because the emissions that result from these fertilizers is a greenhouse gas—one that has a warming potential almost 300 times greater than that of carbon dioxide and remains in the atmosphere for 100 years. Microbes in soil convert nitrogen fertilizer into nitrous oxide, and the more nitrogen fertilizer they have to work with, the more nitrous oxide they make.

Agriculture also leaks plenty of the excess nitrogen into waterways in the form of nitrate, generating algal blooms that create low-oxygen ‘dead zones’ where no marine life can live.

One way to reduce nitrogen emissions from farms would be to simply use fertilizer more efficiently. But—as we’ve seen with fossil fuels (and antibiotics and plastics)—when humans have a miraculous substance on our hands, we just can’t seem to use it at levels that minimize its impact. We instead seem compelled to throw around as much of the stuff as we can. But even if we were to start using less fertilizer now, we are past time to choose a single technique to curb greenhouse gas emissions; we need to put them all into action.

Denitrifying bacteria reduces levels of nitrous oxide in soil by converting it to the molecular form of nitrogen found in air. They use it as an oxidizer for respiration under conditions with low or no oxygen. So adding these nitrogen-respiring bacteria to soil could help decrease nitrous oxide emissions.

Modifying the microbiome of soil is just as hard as modifying the microbiome in our bodies. So instead of trying to promote the growth of any denitrifying bacteria that might happen to already be in soil, researchers decided to grow them externally and then add them in. Their source was partially treated sewage, called digestate, that was destined as organic fertilizer anyway. Keeping the digestate in oxygen-free conditions enriched their levels of one strain of nitrogen-respiring bacteria.

The researchers homed in on this particular strain because it has the enzyme needed to break down nitrous oxide, but not the enzymes used to make it from other nitrogen compounds. And although it is not the fastest, most efficient strain at nitrogen respiration, it won because it is the most tenacious: It grows to high concentrations even when oxygen is present, and it works well in soil.

When this digestate was mixed into soil, fertilizer-induced emissions were reduced by 50–95 percent, depending on the pH and organic carbon content of the soils. The effect lasted over the entire growing season. The presence of the added nitrogen-respiring bacteria did not seem to affect the indigenous microbiota already present in the soil, and the added bacteria did not carry genes for antibiotic resistance or pathogenicity, which is obviously essential if they are to be used in farming. What hasn’t been tested yet, however, is whether the presence of these bacteria influence the growth of crops.

Using mathematical modeling of future emissions, the researchers concluded that adding these bacteria to soil could reduce nitrous oxide emissions by 60 percent, and if they are added to all liquid manure systems in Europe, Europe could reduce its anthropogenic nitrous oxide emissions by 3 to 4 percent.

Nature, 2024.  DOI: 10.1038/s41586-024-07464-3

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mutations-in-a-non-coding-gene-associated-with-intellectual-disability

Mutations in a non-coding gene associated with intellectual disability

Biology, developmental disorders, Genetics, neurobiology, neurodevelopment, RNA, Science, spacing / /

Splice of life —

A gene that only makes an RNA is linked to neurodevelopmental problems.

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Colored ribbons that represent the molecular structure of a large collection of proteins and RNAs.

Enlarge / The spliceosome is a large complex of proteins and RNAs.

Almost 1,500 genes have been implicated in intellectual disabilities; yet for most people with such disabilities, genetic causes remain unknown. Perhaps this is in part because geneticists have been focusing on the wrong stretches of DNA when they go searching. To rectify this, Ernest Turro—a biostatistician who focuses on genetics, genomics, and molecular diagnostics—used whole genome sequencing data from the 100,000 Genomes Project to search for areas associated with intellectual disabilities.

His lab found a genetic association that is the most common one yet to be associated with neurodevelopmental abnormality. And the gene they identified doesn’t even make a protein.

Trouble with the spliceosome

Most genes include instructions for how to make proteins. That’s true. And yet human genes are not arranged linearly—or rather, they are arranged linearly, but not contiguously. A gene containing the instructions for which amino acids to string together to make a particular protein—hemoglobin, insulin, serotonin, albumin, estrogen, whatever protein you like—is modular. It contains part of the amino acid sequence, then it has a chunk of DNA that is largely irrelevant to that sequence, then a bit more of the protein’s sequence, then another chunk of random DNA, back and forth until the end of the protein. It’s as if each of these prose paragraphs were separated by a string of unrelated letters (but not a meaningful paragraph from a different article).

In order to read this piece through coherently, you’d have to take out the letters interspersed between its paragraphs. And that’s exactly what happens with genes. In order to read the gene through coherently, the cell has machinery that splices out the intervening sequences and links up the protein-making instructions into a continuous whole. (This doesn’t happen in the DNA itself; it happens to an RNA copy of the gene.) The cell’s machinery is obviously called the spliceosome.

There are about a hundred proteins that comprise the spliceosome. But the gene just found to be so strongly associated with neurodevelopmental disorders doesn’t encode any of them. Rather, it encodes one of five RNA molecules that are also part of the spliceosome complex and interact with the RNAs that are being spliced. Mutations in this gene were found to be associated with a syndrome with symptoms that include intellectual disability, seizures, short stature, neurodevelopmental delay, drooling, motor delay, hypotonia (low muscle tone), and microcephaly (having a small head).

Supporting data

The researchers buttressed their finding by examining three other databases; in all of them, they found more people with the syndrome who had mutations in this same gene. The mutations occur in a remarkably conserved region of the genome, suggesting that it is very important. Most of the mutations were new in the affected people—i.e. not inherited from their parents—but there was one case of one particular mutation in the gene that was inherited. Based on this, the researchers concluded that this particular variant may cause a less severe disorder than the other mutations.

Many studies that look for genes associated with diseases have focused on searching catalogs of protein coding genes. These results suggest that we could have been missing important mutations because of this focus.

Nature Medicine, 2024. DOI: 10.1038/s41591-024-03085-5

Mutations in a non-coding gene associated with intellectual disability Read More »

dinosaurs-needed-to-be-cold-enough-that-being-warm-blooded-mattered

Dinosaurs needed to be cold enough that being warm-blooded mattered

Biology, climate change, dinosaurs, evolution, paleontology, Science, warm blooded / /

Some like it less hot —

Two groups of dinosaurs moved to cooler climes during a period of climate change.

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Image of a feathered dinosaur against a white background.

Enlarge / Later theropods had multiple adaptations to varied temperatures.

Dinosaurs were once assumed to have been ectothermic, or cold-blooded, an idea that makes sense given that they were reptiles. While scientists had previously discovered evidence of dinosaur species that were warm-blooded, though what could have triggered this adaptation remained unknown. A team of researchers now think that dinosaurs that already had some cold tolerance evolved endothermy, or warm-bloodedness, to adapt when they migrated to regions with cooler temperatures. They also think they’ve found a possible reason for the trek.

Using the Mesozoic fossil record, evolutionary trees, climate models, and geography, plus factoring in a drastic climate change event that caused global warming, the team found that theropods (predators and bird ancestors such as velociraptor and T. rex) and ornithischians (such as triceratops and stegosaurus) must have made their way to colder regions during the Early Jurassic. Lower temperatures are thought to have selected for species that were partly adapted to endothermy.

“The early invasion of cool niches… [suggests] an early attainment of homeothermic (possibly endothermic) physiology in [certain species], enabling them to colonize and persist in even extreme latitudes since the Early Jurassic,” the researchers said in a study recently published in Current Biology.

Hot real estate

During the Mesozoic Era, which lasted from 230 to 66 million years ago, proto-dinosaurs known as dinosauromorphs began to diversify in hot and dry climates. Early sauropods, ornithischians, and theropods all tended to stay in these regions.

Sauropods (such as brontosaurus and diplodocus) would become the only dinosaur groups to bask in the heat—the fossil record shows that sauropods tended to stay in warmer areas, even if there was less food. This suggests the need for sunlight and heat associated with ectothermy. They might have been capable of surviving in colder temperatures but not adapted enough to make it for long, according to one hypothesis.

It’s also possible that living in cooler areas meant too much competition with other types of dinosaurs, as the theropods and ornithiscians did end up moving into these cooler areas.

Almost apocalypse

Beyond the ecological opportunities that may have drawn dinosaurs to the cooler territories, it’s possible they were driven away from the warm ones. Around 183 million years ago, there was a perturbation in the carbon cycle, along with extreme volcanism that belched out massive amounts of methane, sulfur dioxide, and mercury. Life on Earth suffered through scorching heat, acid rain, and wildfires. Known as the Early Jurassic Jenkyns Event, the researchers now think that these disruptions pushed theropod and ornithischian dinosaurs to cooler climates because temperatures in warmer zones went above the optimal temperatures for their survival.

The theropods and ornithischians that escaped the effects of the Jenkyns event may have had a key adaptation to cooler climes; many dinosaurs from these groups are now thought to have been feathered. Feathers can be used to both trap and release heat, which would have allowed feathered dinosaurs to regulate their body temperature in more diverse climates. Modern birds use their feathers the same way.

Dinosaur species with feathers or special structures that improved heat management could have been homeothermic, which means they would have been able to maintain their body temperature with metabolic activity or even endothermic.

Beyond the dinosaurs that migrated to high latitudes and adapted to a drop in temperature, endothermy might have led to the rise of new species and lineages of dinosaurs. It could have contributed to the rise of Avialae, the clade that includes birds—the only actual dinosaurs still around—and traces all the way back to their earliest ancestors.

“[Our findings] provide novel insights into the origin of avian endothermy, suggesting that this evolutionary trajectory within theropods… likely started in the latest Early Jurassic,” the researchers said in the same study.

That really is something to think about next time a sparrow flies by.

Current Biology, 2024.  DOI: 10.1016/j.cub.2024.04.051

Dinosaurs needed to be cold enough that being warm-blooded mattered Read More »

whale-songs-have-features-of-language,-but-whales-may-not-be-speaking

Whale songs have features of language, but whales may not be speaking

animal behavior, Biology, language, Science, whale song, whales / /
A group of sperm whales and remora idle near the surface of the ocean.

Whales use complex communication systems we still don’t understand, a trope exploited in sci-fi shows like Apple TV’s Extrapolations. That show featured a humpback whale (voiced by Meryl Streep) discussing Mahler’s symphonies with a human researcher via some AI-powered inter-species translation app developed in 2046.

We’re a long way from that future. But a team of MIT researchers has now analyzed a database of Caribbean sperm whales’ calls and has found there really is a contextual and combinatorial structure in there. But does it mean whales have a human-like language and we can just wait until Chat GPT 8.0 to figure out how to translate from English to Sperm-Whaleish? Not really.

One-page dictionary

“Sperm whales communicate using clicks. These clicks occur in short packets we call codas that typically last less than two seconds, containing three to 40 clicks,” said Pratyusha Sharma, a researcher at the MIT Computer Science and Artificial Intelligence Laboratory and the lead author of the study. Her team argues that codas are analogues of words in human language and are further organized in coda sequences that are analogues of sentences. “Sperm whales are not born with this communication system; it’s acquired and changes over the course of time,” Sharma said.

Seemingly, sperm whales have a lot to communicate about. Earlier observational studies revealed that they live a fairly complex social life revolving around family units forming larger structures called clans. They also have advanced hunting strategies and do group decision-making, seeking consensus on where to go and what to do.

Despite this complexity in behavior and relationships, their vocabulary seemed surprisingly sparse.

Sharma’s team sourced a record of codas from the dataset of the Dominica Sperm Whale Project, a long-term study on sperm whales that recorded and annotated 8,719 individual codas made by EC-1, a sperm whale clan living in East Caribbean waters. Those 8,719 recorded codas, according to earlier research on this database, were really just 21 coda types that the whales were using over and over.

A set of 21 words didn’t look like much of a language. “But this [number] is exactly what we found was not true,” Sharma said.

Fine-grained changes

“People doing those earlier studies were looking at the calls in isolation… They were annotating these calls, taking them out of context, shuffling them up, and then tried to figure out what kind of patterns were recurring,” Sharma explained. Her team, by contrast, analyzed the same calls in their full context, basically looking at entire exchanges rather than at separate codas. “One of the things we saw was fine-grained changes in the codas that other whales participating in the exchange were noticing and reacting to. If you looked at all these calls out of context, all these fine-grained changes would be lost; they would be considered noise,” Sharma said.

The first of those newly recognized fine-grained changes was termed “rubato,” borrowed from music, where it means introducing slight variations in the tempo of a piece. Communicating sperm whales could stretch or shrink a coda while keeping the same rhythm (where rhythm describes the spacing between the clicks in a coda).

The second feature the researchers discovered was ornamentation. “An ornament is an extra click added at the end of the coda. And when you have this extra click, it marks a critical point, and the call changes. It either happens toward the beginning or at the end of the call,” said Sharma.

The whales could individually manipulate rubato and ornamentation, as well as previously identified rhythm and tempo features. By combining this variation, they can produce a very large variety of codas. “The whales produce way more combinations of these features than 21—the information-carrying capacity of this system is a lot more capable than that,” Sharma said.

Her team identified 18 types of rhythm, three variants of rubato, five types of tempo, and an ability to add an ornament or not in the sperm whale’s communication system. That adds up to 540 possible codas, of which there are roughly 150 these whales frequently used in real life. Not only were sperm whales’ calls built with distinctive units at a coda level (meaning they were combinatorial), but they were compositional in that a call contained multiple codas.

But does that get us any closer to decoding the whale’s language?

“The combinatoriality at the word level and compositionality at the sentence level in human languages is something that looks very similar to what we found,” Sharma said. But the team didn’t determine whether meaning was being conveyed, she added. And without evidence of meaning, we might be barking up the wrong tree entirely.

Whale songs have features of language, but whales may not be speaking Read More »

beethoven-likely-didn’t-die-from-lead-poisoning,-new-dna-analysis-reveals

Beethoven likely didn’t die from lead poisoning, new DNA analysis reveals

Biology, DNA analysis, forensic DNA, human genetics, Ludwig von Beethoven, Science / /

get the lead out —

There was also mercury and arsenic but none of the toxins likely caused composer’s death.

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(7) Portrait of Beethoven by Joseph Karl Stieler, 1820

Enlarge / Portrait of Beethoven by Joseph Karl Stieler, 1820. Toxocology analysis of the composer’s locks of hair showed high levels of lead.

Beethoven-Haus Bonn

Last year, researchers sequenced the genome of famed composer Ludwig van Beethoven for the first time, based on authenticated locks of hair. The same team has now analyzed two of the locks for toxic substances and found extremely high levels of lead, as well as arsenic and mercury, according to a recent letter published in the journal Clinical Chemistry.

“It definitely shows Beethoven was exposed to high concentrations of lead,” Paul Janetto, co-author and director of the Mayo Clinic’s Department of Laboratory Medicine and Pathology, told The New York Times. “These are the highest values in hair I’ve ever seen. We get samples from around the world, and these values are an order of magnitude higher.” That said, the authors concluded that the lead exposure was not sufficient to actually kill the composer, although Beethoven very likely did suffer adverse health effects because of it.

As previously reported, Beethoven was plagued throughout his life by myriad health problems. The composer began losing his hearing in his mid- to late 20s, experiencing tinnitus and the loss of high-tone frequencies in particular. He claimed the onset began with a fit in 1798 induced by a quarrel with a singer. By his mid-40s, he was functionally deaf and unable to perform public concerts, although he could still compose music.

Beethoven on his deathbed: lithograph by Josef Danhauser after his own drawing.

Enlarge / Beethoven on his deathbed: lithograph by Josef Danhauser after his own drawing.

Beethoven-Haus Bonn

Beethoven also had lifelong chronic gastric ailments, including persistent abdominal pains and prolonged stretches of diarrhea. By 1821, the composer showed signs of liver disease, marked by the first of two severe attacks of jaundice. These issues certainly affected his career and emotional state, so much so that Beethoven requested—via a letter addressed to his brothers—that his favorite physician examine his body after his death to determine the cause of all his suffering.

By December 1826, Beethoven was quite ill, suffering from a second bout of jaundice and swollen limbs, fever, dropsy, and labored breathing. His doctor performed several operations to remove excess fluid from the composer’s abdomen. On March 24, 1827, he purportedly said to visitors, “Plaudite, amici, comoedia finita est” (“Applaud, friends, the comedy is over”). Two days later, he died. According to his good friend Anselm Hüttenbrenner, who was present, lightning and a loud clap of thunder briefly woke Beethoven, who “opened his eyes, lifted his right hand and looked up for several seconds with his fist clenched… not another breath, not a heartbeat more.”

An autopsy identified severe liver damage (evidence of cirrhosis) as the likely cause of death and significant dilation of the auditory nerve. But what caused that liver damage or his hearing loss—or his chronic stomach complaints, for that matter? Medical detectives have been debating possible causes for nearly two centuries, drawing on the composer’s letters, diaries, and physicians’ notes for evidence, as well as reports on skeletal remains from when his body was exhumed in 1863 and 1888. But no general consensus emerged.

Beethoven likely didn’t die from lead poisoning, new DNA analysis reveals Read More »

chemical-tweaks-to-a-toad-hallucinogen-turns-it-into-a-potential-drug

Chemical tweaks to a toad hallucinogen turns it into a potential drug

biochemistry, Biology, hallucinogen, health, neurobiology, psychedelic, Science, toads / /

No licking toads! —

Targets a different serotonin receptor from other popular hallucinogens.

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Image of the face of a large toad.

Enlarge / The Colorado River toad, also known as the Sonoran Desert Toad.

It is becoming increasingly accepted that classic psychedelics like LSD, psilocybin, ayahuasca, and mescaline can act as antidepressants and anti-anxiety treatments in addition to causing hallucinations. They act by binding to a serotonin receptor. But there are 14 known types of serotonin receptors, and most of the research into these compounds has focused on only one of them—the one these molecules like, called 5-HT2A. (5-HT, short for 5-hydroxytryptamine, is the chemical name for serotonin.)

The Colorado River toad (Incilius alvarius), also known as the Sonoran Desert toad, secretes a psychedelic compound that likes to bind to a different serotonin receptor subtype called 5-HT1A. And that difference may be the key to developing an entirely distinct class of antidepressants.

Uncovering novel biology

Like other psychedelics, the one the toad produces decreases depression and anxiety and induces meaningful and spiritually significant experiences. It has been used clinically to treat vets with post-traumatic stress disorder and is being developed as a treatment for other neurological disorders and drug abuse. 5-HT1A is a validated therapeutic target, as approved drugs, including the antidepressant Viibryd and the anti-anxiety med Buspar, bind to it. But little is known about how psychedelics engage with this receptor and which effects it mediates, so Daniel Wacker’s lab decided to look into it.

The researchers started by making chemical modifications to the frog psychedelic and noting how each of the tweaked molecules bound to both 5-HT2A  and 5-HT1A. As a group, these psychedelics are known as “designer tryptamines”—that’s tryp with a “y”, mind you—because they are metabolites of the amino acid tryptophan.

The lab made 10 variants and found one that is more than 800-fold selective about sticking to 5-HT1A as compared to 5-HT2A. That makes it a great research tool for elucidating the structure-activity relationship of the 5-HT1A receptor, as well as the molecular mechanisms behind the pharmacology of the drugs on the market that bind to it. The lab used it to explore both of those avenues. However, the variant’s ultimate utility might be as a new therapeutic for psychiatric disorders, so they tested it in mice.

Improving the lives of mice

The compound did not induce hallucinations in mice, as measured by the “head-twitch response.” But it did alleviate depression, as measured by a “chronic social defeat stress model.” In this model, for 10 days in a row, the experimental mouse was introduced to an “aggressor mouse” for “10-minute defeat bouts”; essentially, it got beat up by a bully at recess for two weeks. Understandably, after this experience, the experimental mouse tended not to be that friendly with new mice, as controls usually are. But when injected with the modified toad psychedelic, the bullied mice were more likely to interact positively with new mice they met.

Depressed mice, like depressed people, also suffer from anhedonia: a reduced ability to experience pleasure. In mice, this manifests in not taking advantage of drinking sugar water when given the opportunity. But treated bullied mice regained their preference for the sweet drink. About a third of mice seem to be “stress-resilient” in this model; the bullying doesn’t seem to phase them. The drug increased the number of resilient mice.

The 5-HT2A receptor has hogged all of the research love because it mediates the hallucinogenic effects of many popular psychedelics, so people assumed that it must mediate their therapeutic effects, too. However, Wacker argues that there is little evidence supporting this assumption. Wacker’s new toad-based psychedelic variant and its preference for the 5-HT1A receptor will help elucidate the complementary roles these two receptor subtypes play in mediating the cellular and psychological effects of psychedelic molecules. And it might provide the basis for a new tryptamine-based mental health treatment as well—one without hallucinatory side effects, disappointing as that may be to some.

Nature, 2024.  DOI: 10.1038/s41586-024-07403-2

Chemical tweaks to a toad hallucinogen turns it into a potential drug Read More »

the-wasps-that-tamed-viruses

The wasps that tamed viruses

Biology, entomology, Parasitic wasps, Science, syndication, virology, viruses / /
Parasitoid wasp

Enlarge / Xorides praecatorius is a parasitoid wasp.

If you puncture the ovary of a wasp called Microplitis demolitor, viruses squirt out in vast quantities, shimmering like iridescent blue toothpaste. “It’s very beautiful, and just amazing that there’s so much virus made in there,” says Gaelen Burke, an entomologist at the University of Georgia.

M. demolitor  is a parasite that lays its eggs in caterpillars, and the particles in its ovaries are “domesticated” viruses that have been tuned to persist harmlessly in wasps and serve their purposes. The virus particles are injected into the caterpillar through the wasp’s stinger, along with the wasp’s own eggs. The viruses then dump their contents into the caterpillar’s cells, delivering genes that are unlike those in a normal virus. Those genes suppress the caterpillar’s immune system and control its development, turning it into a harmless nursery for the wasp’s young.

The insect world is full of species of parasitic wasps that spend their infancy eating other insects alive. And for reasons that scientists don’t fully understand, they have repeatedly adopted and tamed wild, disease-causing viruses and turned them into biological weapons. Half a dozen examples already are described, and new research hints at many more.

By studying viruses at different stages of domestication, researchers today are untangling how the process unfolds.

Partners in diversification

The quintessential example of a wasp-domesticated virus involves a group called the bracoviruses, which are thought to be descended from a virus that infected a wasp, or its caterpillar host, about 100 million years ago. That ancient virus spliced its DNA into the genome of the wasp. From then on, it was part of the wasp, passed on to each new generation.

Over time, the wasps diversified into new species, and their viruses diversified with them. Bracoviruses are now found in some 50,000 wasp species, including M. demolitor. Other domesticated viruses are descended from different wild viruses that entered wasp genomes at various times.

Researchers debate whether domesticated viruses should be called viruses at all. “Some people say that it’s definitely still a virus; others say it’s integrated, and so it’s a part of the wasp,” says Marcel Dicke, an ecologist at Wageningen University in the Netherlands who described how domesticated viruses indirectly affect plants and other organisms in a 2020 paper in the Annual Review of Entomology.

As the wasp-virus composite evolves, the virus genome becomes scattered through the wasp’s DNA. Some genes decay, but a core set is preserved—those essential for making the original virus’s infectious particles. “The parts are all in these different locations in the wasp genome. But they still can talk to each other. And they still make products that cooperate with each other to make virus particles,” says Michael Strand, an entomologist at the University of Georgia. But instead of containing a complete viral genome, as a wild virus would, domesticated virus particles serve as delivery vehicles for the wasp’s weapons.

Here are the steps in the life of a parasitic wasp that harbors a bracovirus.

Enlarge / Here are the steps in the life of a parasitic wasp that harbors a bracovirus.

Those weapons vary widely. Some are proteins, while others are genes on short segments of DNA. Most bear little resemblance to anything found in wasps or viruses, so it’s unclear where they originated. And they are constantly changing, locked in evolutionary arms races with the defenses of the caterpillars or other hosts.

In many cases, researchers have yet to discover even what the genes and proteins do inside the wasps’ hosts or prove that they function as weapons. But they have untangled some details.

For example, M. demolitor  wasps use bracoviruses to deliver a gene called glc1.8  into the immune cells of moth caterpillars. The glc1.8  gene causes the infected immune cells to produce mucus that prevents them from sticking to the wasp’s eggs. Other genes in M. demolitor’s bracoviruses force immune cells to kill themselves, while still others prevent caterpillars from smothering parasites in sheaths of melanin.

The wasps that tamed viruses Read More »

deepmind-adds-a-diffusion-engine-to-latest-protein-folding-software

DeepMind adds a diffusion engine to latest protein-folding software

AI, biochemistry, Biology, deepmind, Google, protein folding, Science / /

Added complexity —

Major under-the-hood changes let AlphaFold handle protein-DNA complexes and more.

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image of a complicated mix of lines and ribbons arranged in a complicated 3D structure.

Enlarge / Prediction of the structure of a coronavirus Spike protein from a virus that causes the common cold.

Google DeepMind

Most of the activities that go on inside cells—the activities that keep us living, breathing, thinking animals—are handled by proteins. They allow cells to communicate with each other, run a cell’s basic metabolism, and help convert the information stored in DNA into even more proteins. And all of that depends on the ability of the protein’s string of amino acids to fold up into a complicated yet specific three-dimensional shape that enables it to function.

Up until this decade, understanding that 3D shape meant purifying the protein and subjecting it to a time- and labor-intensive process to determine its structure. But that changed with the work of DeepMind, one of Google’s AI divisions, which released Alpha Fold in 2021, and a similar academic effort shortly afterward. The software wasn’t perfect; it struggled with larger proteins and didn’t offer high-confidence solutions for every protein. But many of its predictions turned out to be remarkably accurate.

Even so, these structures only told half of the story. To function, almost every protein has to interact with something else—other proteins, DNA, chemicals, membranes, and more. And, while the initial version of AlphaFold could handle some protein-protein interactions, the rest remained black boxes. Today, DeepMind is announcing the availability of version 3 of AlphaFold, which has seen parts of its underlying engine either heavily modified or replaced entirely. Thanks to these changes, the software now handles various additional protein interactions and modifications.

Changing parts

The original AlphaFold relied on two underlying software functions. One of those took evolutionary limits on a protein into account. By looking at the same protein in multiple species, you can get a sense for which parts are always the same, and therefore likely to be central to its function. That centrality implies that they’re always likely to be in the same location and orientation in the protein’s structure. To do this, the original AlphaFold found as many versions of a protein as it could and lined up their sequences to look for the portions that showed little variation.

Doing so, however, is computationally expensive since the more proteins you line up, the more constraints you have to resolve. In the new version, the AlphaFold team still identified multiple related proteins but switched to largely performing alignments using pairs of protein sequences from within the set of related ones. This probably isn’t as information-rich as a multi-alignment, but it’s far more computationally efficient, and the lost information doesn’t appear to be critical to figuring out protein structures.

Using these alignments, a separate software module figured out the spatial relationships among pairs of amino acids within the target protein. Those relationships were then translated into spatial coordinates for each atom by code that took into account some of the physical properties of amino acids, like which portions of an amino acid could rotate relative to others, etc.

In AlphaFold 3, the prediction of atomic positions is handled by a diffusion module, which is trained by being given both a known structure and versions of that structure where noise (in the form of shifting the positions of some atoms) has been added. This allows the diffusion module to take the inexact locations described by relative positions and convert them into exact predictions of the location of every atom in the protein. It doesn’t need to be told the physical properties of amino acids, because it can figure out what they normally do by looking at enough structures.

(DeepMind had to train on two different levels of noise to get the diffusion module to work: one in which the locations of atoms were shifted while the general structure was left intact and a second where the noise involved shifting the large-scale structure of the protein, thus affecting the location of lots of atoms.)

During training, the team found that it took about 20,000 instances of protein structures for AlphaFold 3 to get about 97 percent of a set of test structures right. By 60,000 instances, it started getting protein-protein interfaces correct at that frequency, too. And, critically, it started getting proteins complexed with other molecules right, as well.

DeepMind adds a diffusion engine to latest protein-folding software Read More »

researchers-make-a-plastic-that-includes-bacteria-that-can-digest-it

Researchers make a plastic that includes bacteria that can digest it

bacteria, Biology, chemistry, evolution, materials science, plastics, Science / /

It’s alive! —

Bacterial spores strengthen the plastic, then revive to digest it in landfills.

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Image of two containers of dirt, one with a degraded piece of plastic in it.

Han Sol Kim

One reason plastic waste persists in the environment is because there’s not much that can eat it. The chemical structure of most polymers is stable and different enough from existing food sources that bacteria didn’t have enzymes that could digest them. Evolution has started to change that situation, though, and a number of strains have been identified that can digest some common plastics.

An international team of researchers has decided to take advantage of those strains and bundle plastic-eating bacteria into the plastic. To keep them from eating it while it’s in use, the bacteria is mixed in as inactive spores that should (mostly—more on this below) only start digesting the plastic once it’s released into the environment. To get this to work, the researchers had to evolve a bacterial strain that could tolerate the manufacturing process. It turns out that the evolved bacteria made the plastic even stronger.

Bacteria meet plastics

Plastics are formed of polymers, long chains of identical molecules linked together by chemical bonds. While they can be broken down chemically, the process is often energy-intensive and doesn’t leave useful chemicals behind. One alternative is to get bacteria to do it for us. If they’ve got an enzyme that breaks the chemical bonds of a polymer, they can often use the resulting small molecules as an energy source.

The problem has been that the chemical linkages in the polymers are often distinct from the chemicals that living things have come across in the past, so enzymes that break down polymers have been rare. But, with dozens of years of exposure to plastics, that’s starting to change, and a number of plastic-eating bacterial strains have been discovered recently.

This breakdown process still requires that the bacteria and plastics find each other in the environment, though. So a team of researchers decided to put the bacteria in the plastic itself.

The plastic they worked with is called thermoplastic polyurethane (TPU), something you can find everywhere from bicycle inner tubes to the coating on your ethernet cables. Conveniently, there are already bacteria that have been identified that can break down TPU, including a species called Bacillus subtilis, a harmless soil bacterium that has also colonized our digestive tracts. B. subtilis also has a feature that makes it very useful for this work: It forms spores.

This feature handles one of the biggest problems with incorporating bacteria into materials: The materials often don’t provide an environment where living things can thrive. Spores, on the other hand, are used by bacteria to wait out otherwise intolerable conditions, and then return to normal growth when things improve. The idea behind the new work is that B. subtilis spores remain in suspended animation while the TPU is in use and then re-activate and digest it once it’s disposed of.

In practical terms, this works because spores only reactivate once nutritional conditions are sufficiently promising. An Ethernet cable or the inside of a bike tire is unlikely to see conditions that will wake the bacteria. But if that same TPU ends up in a landfill or even the side of the road, nutrients in the soil could trigger the spores to get to work digesting it.

The researchers’ initial problem was that the manufacturing of TPU products usually involves extruding the plastic at high temperatures, which are normally used to kill bacteria. In this case, they found that a typical manufacturing temperature (130° C) killed over 90 percent of the B. subtilis spores in just one minute.

So, they started out by exposing B. subtilis spores to lower temperatures and short periods of heat that were enough to kill most of the bacteria. The survivors were grown up, made to sporulate, and then exposed to a slightly longer period of heat or even higher temperatures. Over time, B. subtilis evolved the ability to tolerate a half hour of temperatures that would kill most of the original strain. The resulting strain was then incorporated into TPU, which was then formed into plastics through a normal extrusion process.

You might expect that putting a bunch of biological material into a plastic would weaken it. But the opposite turned out to be true, as various measures of its tensile strength showed that the spore-containing plastic was stronger than pure plastic. It turns out that the spores have a water-repelling surface that interacts strongly with the polymer strands in the plastic. The heat-resistant strain of bacteria repelled water even more strongly, and plastics made with these spores was tougher still.

To simulate landfilling or litter with the plastic, the researchers placed them in compost. Even without any bacteria, there were organisms present that could degrade it; by five months in the compost, plain TPU lost nearly half its mass. But with B. subtilis spores incorporated, the plastic lost 93 percent of its mass over the same time period.

This doesn’t mean our plastics problem is solved. Obviously, TPU breaks down relatively easily. There are lots of plastics that don’t break down significantly, and may not be compatible with incorporating bacterial spores. In addition, it’s possible that some TPU uses would expose the plastic to environments that would activate the spores—something like food handling or buried cabling. Still, it’s possible this new breakdown process can provide a solution in some cases, making it worth exploring further.

Nature Communications, 2024. DOI: 10.1038/s41467-024-47132-8  (About DOIs).

Listing image by Han Sol Kim

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High-speed imaging and AI help us understand how insect wings work

AI, Biology, Biomechanics, Computer science, flight, insects, muscles, Science, wings / /
Black and white images of a fly with its wings in a variety of positions, showing the details of a wing beat.

Enlarge / A time-lapse showing how an insect’s wing adopts very specific positions during flight.

Florian Muijres, Dickinson Lab

About 350 million years ago, our planet witnessed the evolution of the first flying creatures. They are still around, and some of them continue to annoy us with their buzzing. While scientists have classified these creatures as pterygotes, the rest of the world simply calls them winged insects.

There are many aspects of insect biology, especially their flight, that remain a mystery for scientists. One is simply how they move their wings. The insect wing hinge is a specialized joint that connects an insect’s wings with its body. It’s composed of five interconnected plate-like structures called sclerites. When these plates are shifted by the underlying muscles, it makes the insect wings flap.

Until now, it has been tricky for scientists to understand the biomechanics that govern the motion of the sclerites even using advanced imaging technologies. “The sclerites within the wing hinge are so small and move so rapidly that their mechanical operation during flight has not been accurately captured despite efforts using stroboscopic photography, high-speed videography, and X-ray tomography,” Michael Dickinson, Zarem professor of biology and bioengineering at the California Institute of Technology (Caltech), told Ars Technica.

As a result, scientists are unable to visualize exactly what’s going on at the micro-scale within the wing hinge as they fly, preventing them from studying insect flight in detail. However, a new study by Dickinson and his team finally revealed the working of sclerites and the insect wing hinge. They captured the wing motion of fruit flies (Drosophila melanogaster) analyzing 72,000 recorded wing beats using a neural network to decode the role individual sclerites played in shaping insect wing motion.

Understanding the insect wing hinge

The biomechanics that govern insect flight are quite different from those of birds and bats. This is because wings in insects didn’t evolve from limbs. “In the case of birds, bats, and pterosaurs we know exactly where the wings came from evolutionarily because all these animals fly with their forelimbs. They’re basically using their arms to fly. In insects, it’s a completely different story. They evolved from six-legged organisms and they kept all six legs. However, they added flapping appendages to the dorsal side of their body, and it is a mystery as to where those wings came from,” Dickinson explained.

Some researchers suggest that insect wings came from gill-like appendages present in ancient aquatic arthropods. Others argue that wings originated from “lobes,” special outgrowths found on the legs of ancient crustaceans, which were ancestors of insects. This debate is still ongoing, so its evolution can’t tell us much about how the hinge and the sclerites operate.

Understanding the hinge mechanics is crucial because this is what makes insects efficient flying creatures. It enables them to fly at impressive speeds relative to their body sizes (some insects can fly at 33 mph) and to demonstrate great maneuverability and stability while in flight.

“The insect wing hinge is arguably among the most sophisticated and evolutionarily important skeletal structures in the natural world,” according to the study authors.

However, imaging the activity of four of the five sclerites that form the hinge has been impossible due to their size and the speeds at which they move. Dickinson and his team employed a multidisciplinary approach to overcome this challenge. They designed an apparatus equipped with three high-speed cameras that recorded the activity of tethered fruit flies at 15,000 frames per second using infrared light.

They also used a calcium-sensitive protein to track changes in the activity of the steering muscles of the insects as they flew (calcium helps trigger muscle contractions). “We recorded a total of 485 flight sequences from 82 flies. After excluding a subset of wingbeats from sequences when the fly either stopped flying or flew at an abnormally low wingbeat frequency, we obtained a final dataset of 72,219 wingbeats,” the researchers note.

Next, they trained a machine-learning-based convolutional neural network (CNN) using 85 percent of the dataset. “We used the CNN model to investigate the transformation between muscle activity and wing motion by performing a set of virtual manipulations, exploiting the network to execute experiments that would be difficult to perform on actual flies,” they explained.

In addition to the neural network, they also developed an encoder-decoder neural network (an architecture used in machine learning) and fed it data related to steering muscle activity. While the CNN model could predict wing motion, the encoder/decoder could predict the action of individual sclerite muscles during the movement of the wings. Now, it was time to check whether the data they predicted was accurate.

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Studies reveal new clues to how tardigrades can survive intense radiation

animals, Biology, Extremophiles, Genetics, proteins, Science, tardigrades / /

It’s in the genes —

Radiation damages their DNA; they’re just able to repair that damage very quickly.

–

SEM Micrograph of a tardigrade, commonly known as a water bear

Enlarge / SEM Micrograph of a tardigrade, more commonly known as a “water bear” or “moss piglet.”

Cultura RM Exclusive/Gregory S. Paulson/Getty Images

Since the 1960s, scientists have known that the tiny tardigrade can withstand very intense radiation blasts 1,000 times stronger than what most other animals could endure. According to a new paper published in the journal Current Biology, it’s not that such ionizing radiation doesn’t damage tardigrades’ DNA; rather, the tardigrades are able to rapidly repair any such damage. The findings complement those of a separate study published in January that also explored tardigrades’ response to radiation.

“These animals are mounting an incredible response to radiation, and that seems to be a secret to their extreme survival abilities,” said co-author Courtney Clark-Hachtel, who was a postdoc in Bob Goldstein’s lab at the University of North Carolina at Chapel Hill, which has been conducting research into tardigrades for 25 years. “What we are learning about how tardigrades overcome radiation stress can lead to new ideas about how we might try to protect other animals and microorganisms from damaging radiation.”

As reported previously, tardigrades are micro-animals that can survive in the harshest conditions: extreme pressure, extreme temperature, radiation, dehydration, starvation—even exposure to the vacuum of outer space. The creatures were first described by German zoologist Johann Goeze in 1773. They were dubbed tardigrada (“slow steppers” or “slow walkers”) four years later by Lazzaro Spallanzani, an Italian biologist. That’s because tardigrades tend to lumber along like a bear. Since they can survive almost anywhere, they can be found in lots of places: deep-sea trenches, salt and freshwater sediments, tropical rain forests, the Antarctic, mud volcanoes, sand dunes, beaches, and lichen and moss. (Another name for them is “moss piglets.”)

When their moist habitat dries up, however, tardigrades go into a state known as “tun”—a kind of suspended animation, which the animals can remain in for as long as 10 years. When water begins to flow again, water bears absorb it to rehydrate and return to life. They’re not technically members of the extremophile class of organisms since they don’t so much thrive in extreme conditions as endure; technically, they belong to the class of extremotolerant organisms. But their hardiness makes tardigrades a favorite research subject for scientists.

For instance, a 2017 study demonstrated that tardigrades use a special kind of disordered protein to literally suspend their cells in a glass-like matrix that prevents damage. The researchers dubbed this a “tardigrade-specific intrinsically disordered protein” (TDP). In other words, the cells become vitrified. The more TDP genes a tardigrade species has, the more quickly and efficiently it goes into the tun state.

In 2021, another team of Japanese scientists called this “vitrification” hypothesis into question, citing experimental data suggesting that the 2017 findings could be attributed to water retention of the proteins. The following year, researchers at the University of Tokyo identified the mechanism to explain how tardigrades can survive extreme dehydration: cytoplasmic-abundant heat soluble (CAHS) proteins that form a protective gel-like network of filaments to protect dried-out cells. When the tardigrade rehydrates, the filaments gradually recede, ensuring that the cell isn’t stressed or damaged as it regains water.

When it comes to withstanding ionizing radiation, a 2016 study identified a DNA damage suppressor protein dubbed “Dsup” that seemed to shield tardigrade genes implanted into human cells from radiation damage. However, according to Clark-Hatchel et al., it still wasn’t clear whether this kind of protective mechanism was sufficient to fully account for tardigrades’ ability to withstand extreme radiation. Other species of tardigrade seem to lack Dsup proteins, yet still have the same high radiation tolerance, which suggests there could be other factors at play.

A team of French researchers at the French National Museum of Natural History in Paris ran a series of experiments in which they zapped water bear specimens with powerful gamma rays that would be lethal to humans. They published their results earlier this year in the journal eLife. The French team found that gamma rays did actually damage the tardigrade DNA, much like they would damage human cells. Since the tardigrades survived, this suggested the tardigrades were able to quickly repair the damaged DNA.

Further experiments with three different species (including one that lacks Dsup proteins) revealed the tardigrades were producing very high amounts of DNA repair proteins. They also found a similar uptick of proteins unique to tardigrades, most notably tardigrade DNA damage response protein 1 (TDR1), which seems to protect DNA from radiation. “We found that TDR1 protein interacts with DNA and forms aggregates at high concentration suggesting it may condensate DNA and act by preserving chromosome organization until DNA repair is accomplished,” the authors wrote.

Clark-Hatchel et al. independently arrived at similar conclusions from their own experiments. Taken together, the two studies confirm that this extremely rapid up-regulation of many DNA repair genes in response to exposure to ionizing radiation should be sufficient to explain the creatures’ impressive resistance to that radiation. It’s possible that there is a “synergy between protective and repair mechanisms” when it comes to tardigrade tolerance of ionizing radiation.

That said, “Why tardigrades have evolved a strong IR tolerance is enigmatic given that it is unlikely that tardigrades were exposed to high doses of ionizing radiation in their evolutionary history,” Clark-Hatchel et al. wrote.  They thought there could be a link to the mechanisms that enable tardigrades to survive extreme dehydration, which can also result in damaged DNA. Revisiting data from desiccation experiments did not show nearly as strong an increase in DNA repair transcripts, but the authors suggest that the uptick could occur later in the process, upon rehydration—an intriguing topic for future research.

Current Biology, 2024. DOI: 10.1016/j.cub.2024.03.019  (About DOIs).

eLife, 2024. DOI: 10.7554/eLife.92621.1

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Sleeping more flushes junk out of the brain

Biology, brain, Neuroscience, Science, sleep / /

Better sleep on it —

Rhythmic activity during sleep may get fluids in the brain moving.

–

Abstract image of a pink brain against a blue background.

As if we didn’t have enough reasons to get at least eight hours of sleep, there is now one more. Neurons are still active during sleep. We may not realize it, but the brain takes advantage of this recharging period to get rid of junk that was accumulating during waking hours.

Sleep is something like a soft reboot. We knew that slow brainwaves had something to do with restful sleep; researchers at the Washington University School of Medicine in St. Louis have now found out why. When we are awake, our neurons require energy to fuel complex tasks such as problem-solving and committing things to memory. The problem is that debris gets left behind after they consume these nutrients. As we sleep, neurons use these rhythmic waves to help move cerebrospinal fluid through brain tissue, carrying out metabolic waste in the process.

In other words, neurons need to take out the trash so it doesn’t accumulate and potentially contribute to neurodegenerative diseases. “Neurons serve as master organizers for brain clearance,” the WUSTL research team said in a study recently published in Nature.

Built-in garbage disposal

Human brains (and those of other higher organisms) evolved to have billions of neurons in the functional tissue, or parenchyma, of the brain, which is protected by the blood-brain barrier.

Everything these neurons do creates metabolic waste, often in the form of protein fragments. Other studies have found that these fragments may contribute to neurodegenerative diseases such as Alzheimer’s.

The brain has to dispose of its garbage somehow, and it does this through what’s called the glymphatic system (no, that’s not a typo), which carries cerebrospinal fluid that moves debris out of the parenchyma through channels located near blood vessels. However, that still left the questions: What actually powers the glymphatic system to do this—and how? The WUSTL team wanted to find out.

To see what told the glymphatic system to dump the trash, scientists performed experiments on mice, inserting probes into their brains and planting electrodes in the spaces between neurons. They then anesthetized the mice with ketamine to induce sleep.

Neurons fired strong, charged currents after the animals fell asleep. While brain waves under anesthesia were mostly long and slow, they induced corresponding waves of current in the cerebrospinal fluid. The fluid would then flow through the dura mater, the outer layer of tissue between the brain and the skull, taking the junk with it.

Just flush it

The scientists wanted to be sure that neurons really were the force that pushed the glymphatic system into action. To do that, they needed to genetically engineer the brains of some mice to nearly eliminate neuronal activity while they were asleep (though not to the point of brain death) while leaving the rest of the mice untouched for comparison.

In these engineered mice, the long, slow brain waves seen before were undetectable. As a result, the fluid was no longer pushed to carry metabolic waste out of the brain. This could only mean that neurons had to be active in order for the brain’s self-cleaning cycle to work.

Furthermore, the research team found that there were fluctuations in the brain waves of the un-engineered mice, with slightly faster waves thought to be targeted at the debris that was harder to remove (at least, this is what the researchers hypothesized). It is not unlike washing a plate and then needing to scrub slightly harder in places where there is especially stubborn residue.

The researchers also found out why previous experiments produced different results. Because the flushing out of cerebrospinal fluid that carries waste relies so heavily on neural activity, the type of anesthetic used mattered—anesthetics that inhibit neural activity can interfere with the results. Other earlier experiments worked poorly because of injuries caused by older and more invasive methods of implanting the monitoring hardware into brain tissues. This also disrupted neurons.

“The experimental methodologies we used here largely avoid acute damage to the brain parenchyma, thereby providing valuable strategies for further investigations into neural dynamics and brain clearance,” the team said in the same study.

Now that neurons are known to set the glymphatic system into motion, more attention can be directed towards the intricacies of that process. Finding out more about the buildup and cleaning of metabolic waste may contribute to our understanding of neurodegenerative diseases. It’s definitely something to think about before falling asleep.

Nature, 2024.  DOI: 10.1038/s41586-024-07108-6

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