Biology

dogs’-brain-activity-shows-they-recognize-the-names-of-objects

Dogs’ brain activity shows they recognize the names of objects

Behavioral science, Biology, Dogs, Science / /
Wired for science!

Enlarge / Wired for science!

Boglárka Morvai

Needle, a cheerful miniature schnauzer I had as a kid, turned into a ball of unspeakable noise and fury each time she saw a dog called Puma. She hated Puma so much she would go ballistic, barking and growling. Merely whispering the name “Puma” set off the same reaction, as though the sound of it and the idea of the dog it represented were clearly connected deep in Needle’s mind.

A connection between a word and a mental representation of its meaning is called “referential understanding,” and for a very long time, we believed dogs lacked this ability. Now, a study published by a team of Hungarian researchers indicates we might have been wrong.

Practice makes perfect

The idea that dogs couldn’t form associations with language in a referential manner grew out of behavioral studies in which dogs were asked to do a selective fetching task. The canines had a few objects placed in front of them (like a toy or a bone) and then had to fetch the one specifically named by their owner.

“In laboratory conditions, the dogs performed at random, fetching whatever they could grab first, even though their owners claimed they knew the names of the objects,” said Marianna Boros, a researcher at Neuroethology of Communication Lab at Eötvös Loránd University in Budapest, Hungary. “But the problem is when the dogs are not trained for the task, there are hundreds of things that can disturb them. They can be more interested in one specific toy, they may be bored, or they may not understand the task. So many distractions.”

To get around the issue of distractions, her team checked to see if the dogs could understand words passively using EEG brain monitoring. In humans, the EEG reading that is considered a telltale sign of semantic reasoning is the N400 effect.

“The work on the N400 was first published in 1981, and hundreds of studies replicated it since then with different stimuli. Typically, you show images of objects to the subject and say matching or mismatching names. When you measure EEG brain activity, you will see it looks different in match and mismatch scenarios,” explained Lilla Magyari, also a scientist at Neuroethology of Communication Lab and co-author of the study. (It’s called the N400 effect because the peak of this difference appears around 400 milliseconds after an object is presented, Magyari explained.)

The only change the team made to adapt a standard N400 test to dogs was switching the order of stimuli—the words were uttered first, and the matching or mismatching objects were shown second. “Because when they hear the word which activates mental representation of the object, they are expecting to see it. The sound made them more attentive,” said Magyari.

Timing is everything

In the experiment, the dogs started out lying on a mat with EEG gear on their heads in a room with an experimenter or the owner of a different dog. The owner of the dog being tested was separated by a glass pane with controllable opaqueness. “It was important because EEG studies [can] very precisely time the moment of presentation of your stimulus,” said Boros.

Oszkár Dániel Gáti

Sentences spoken by the owners that would get the dogs’ attention—things like “Kun-kun, look! The ball!”—were recorded and played to each dog through a loudspeaker. Then, 2,000 milliseconds after each dog heard the sentence, the pane would turn transparent, and the owner would appear holding a matching or mismatching toy. “Each test lasted for as long as the dog was happy to participate. The moment it started to get up or look away, we just stopped the test, and the dog could leave the mat and we just finished by playing sessions. It was all super dog-friendly,” Boros said.

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DNA parasite now plays key role in making critical nerve cell protein

Biology, evolution, Genetics, Genomics, myelin, neurobiology, Science, transposons / /

Domesticated viruses —

An RNA has been adopted to help the production of myelin, a key nerve protein.

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Graphic depiction of a nerve cell with a myelin coated axon.

Human brains (and the brains of other vertebrates) are able to process information faster because of myelin, a fatty substance that forms a protective sheath over the axons of our nerve cells and speeds up their impulses. How did our neurons evolve myelin sheaths? Part of the answer—which was unknown until now—almost sounds like science fiction.

Led by scientists from Altos Labs-Cambridge Institute of Science, a team of researchers has uncovered a bit of the gnarly past of how myelin ended up covering vertebrate neurons: a molecular parasite has been messing with our genes. Sequences derived from an ancient virus help regulate a gene that encodes a component of myelin, helping explain why vertebrates have an edge when it comes to their brains.

Prehistoric infection

Myelin is a fatty material produced by oligodendrocyte cells in the central nervous system and Schwann cells in the peripheral nervous system. Its insulating properties allow neurons to zap impulses to one another at faster speeds and greater lengths. Our brains can be complex in part because myelin enables longer, narrower axons, which means more nerves can be stacked together.

The un-myelinated brain cells of many invertebrates often need to rely on wider—and therefore fewer—axons for impulse conduction. Rapid impulse conduction makes quicker reactions possible, whether that means fleeing danger or capturing prey.

So, how do we make myelin? A key player in its production appears to be a type of molecular parasite called a retrotransposon.

Like other transposons, retrotransposons can move to new locations in the genome through an RNA intermediate. However, most retrotransposons in our genome have picked up too many mutations to move about anymore.

RNLTR12-int is a retrotransposon that is thought to have originally entered our ancestors’ genome as a virus. Rat genomes now have over 100 copies of the retrotransposon.

An RNA made by RNLTR12-int helps produce myelin by binding to a transcription factor or a protein that regulates the activity of other genes. The RNA/protein combination binds to DNA near the gene for myelin basic protein, or MBP, a major component of myelin.

“MBP is essential for the membrane growth and compression of [central nervous system] myelin,” the researchers said in a study recently published in Cell.

Technical knockout

To find out whether RNLTR12-int really was behind the regulation of MBP and, therefore, myelin production, the research team had to knock its level down and see if myelination still happened. They first experimented on rat brains before moving on to zebrafish and frogs.

When they inhibited RNLTR12-int, the results were drastic. In the central nervous system, genetically edited rats produced 98 percent less MBP than those where the gene was left unedited. The absence of RNLTR12-int also caused the oligodendrocytes that produce myelin to develop much simpler structures than they would normally form. When RNLTR12-int was knocked out in the peripheral nervous system, it reduced myelin produced by Schwann cells.

The researchers used a SOX10 antibody to show that SOX10 bound to the RNLTR12-int transcript in vivo. This was an important result, since there are lots of non-coding RNAs made by cells, and it wasn’t clear whether any RNA would work or if it was specific to RNLTR12-int.

Do these results hold up in other jawed vertebrates? Using CRISPR-CAS9 to perform knockout tests with retrotransposons related to RNLTR12-int in frogs and zebrafish showed similar results.

Myelination has enriched the vertebrate brain so it can work like never before. This is why the term “brain food” is literal. Healthy fats are so important for our brains; they help form myelin since it is a fatty acid. Think about that next time you’re pulling an all-nighter while reaching for a handful of nuts.

Cell, 2024. DOI: 10.1016/j.cell.2024.01.011

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seeding-steel-frames-brings-destroyed-coral-reefs-back-to-life

Seeding steel frames brings destroyed coral reefs back to life

Biology, coral, Ecology, Science / /
Image of a large school of fish above a reef.

Coral reefs, some of the most stunningly beautiful marine ecosystems on Earth, are dying. Ninety percent of them will likely be gone by 2050 due to rising ocean temperatures and pollution. “But it’s not that when they are gone, they are gone forever. We can rebuild them,” said Dr. Timothy Lamont, a marine biologist working at Lancaster University.

Lamont’s team evaluated coral reef restoration efforts done through the MARS Coral Reef Restoration Program on the coast of Indonesia and found that planting corals on a network of sand-coated steel frames brought a completely dead reef back to life in just four years. It seems like we can fix something for once.

Growing up in rubble

The restored reef examined by Lamont’s team was damaged by blast fishing done 30–40 years ago. “People were using dynamite to blow up the reef. It kills all the fish, the fish float to the surface, and you can scoop them all up. Obviously, this is very damaging to the habitat and leaves behind loose rubble fields with lots of coral skeletons,” said Lamont.

Because this loose ruble is in constant motion, tumbling and rolling around, coral larvae don’t have enough time to grow before they get squashed. So the first step to bringing damaged reefs back to life was stabilizing the rubble. The people running the MARS program did this using Reef Stars, hexagonal steel structures coated with sand. “These structures are connected into networks and pinned to the seabed to reduce the movement of the rubble,” Lamont said.

Before the reef stars were placed on the seabed, though, the MARS team manually tied little corals around them. This was meant to speed up recovery compared to letting coral larvae settle on the steel structures naturally. Based on some key measures, it worked. But there are questions about whether those measures capture everything we need to know.

Artificial coral reefs

The metric Lamont’s team used to measure the success of the MARS program restoration was a carbonate budget, which describes an overall growth of the whole reef structure. According to Lamont, a healthy coral reef has a positive carbonate budget and produces roughly 20 kilograms of limestone per square meter per year. This is exactly what his team measured in restored sites on the Indonesian reef. But while the recovered reef had the same carbonate budget as a healthy one, the organisms contributing to this budget were different.

An untouched natural reef is a diverse mixture including massive, encrusting, and plating coral species like Isopora or Porites, which contribute roughly a third of the carbonate budget. Restored reefs were almost completely dominated by smaller, branching corals like Stylophora, Acropora, and Pocillopora, which are all fast-growing species initially tied onto reef stars. The question was whether the MARS program achieved its astounding four-year reef recovery time by sacrificing biodiversity and specifically choosing corals that grow faster.

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de-extinction-company-manages-to-generate-first-elephant-stem-cells

De-extinction company manages to generate first elephant stem cells

Biology, colossal, de-extinction, elephants, mammoths, Science, stem cells / /
Large collection of cells with a red outline and white nucleus.

Enlarge / Elephant stem cells turned out to be a hassle to generate. (credit: Colossal.)

A company called Colossal plans on pioneering the de-extinction business, taking species that have died within the past few thousand years and restoring them through the use of DNA editing and stem cells. It’s grabbed headlines recently by announcing some compelling targets: the tylacine, an extinct marsupial predator, and an icon of human carelessness, the dodo. But the company was formed to tackle an even more audacious target: the mammoth, which hasn’t roamed the northern hemisphere for thousands of years.

Obviously, there are a host of ethical and conservation issues that would need to be worked out before Colossal’s plans go forward. But there are some major practical hurdles as well, most of them the product of the distinct and extremely slow reproductive biology of the mammoth’s closest living relatives, the elephants. At least one of those has now been cleared, as the company is announcing the production of the first elephant stem cells. The process turned out to be extremely difficult, suggesting that the company still has a long road ahead of it.

Lots of hurdles

Colossal’s basic road map for de-extinction is pretty straightforward. We have already obtained the genomes of a number of species that have gone extinct recently, as well as those of their closest living relatives. By comparing the two, we can identify key genetic differences that make the extinct species distinct. We can then edit those differences into stem cells obtained from the living species and use that species as a surrogate for embryos produced from these stem cells. This will have to be done using stem cells from a number of individuals to ensure that the resulting population has sufficient genetic diversity to be stable.

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scientists-get-dung-beetles-to-collect-dna-samples-for-biodiversity-studies

Scientists get dung beetles to collect DNA samples for biodiversity studies

beetles, biodiversity, Biology, DNA, peru, Science / /

High tech/low tech solutions —

Researchers are sequencing the DNA of wildlife using dung beetle stomach contents.

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Image of forest-covered hillsides and a river winding through the jungle.

Enlarge / The Manu area of Peru contains a number of ecological zones.

Peru’s Manu Biosphere Reserve is the largest rainforest reserve in the world and one of the most biodiverse spots on the planet. Manu is a UNESCO-protected area the size of Connecticut and Delaware combined, covering an area where the Amazon River Basin meets the Andes Mountain Range. This combination forms a series of unique ecosystems, where species unknown to science are discovered every year. The remoteness of the region has helped preserve its biodiversity but adds to the challenges faced by the scientists who are drawn to study it.

Trapping wildlife for research in the dense jungle is impractical, especially considering the great distances researchers have to travel within Manu, either through the forest or on the waterways. It’s an expensive proposition that inevitably exposes the trapped animals to some amount of risk. Trapping rare and endangered animals is even more difficult and comes with significant risks to the animal.

Trapping beetles, however, does not pose the same challenges. They’re easy to catch, easy to transport, and, most importantly, carry the DNA of many animals in and on them. Any animal a biologist could hope to study leaves tracks and droppings in the forest, and the beetles make a living by cleaning that stuff up.

Beetles as DNA collectors

Beetles are plentiful in the rainforest, and the species that Alejandro Lopera-Toro’s team studies are not endangered. The study does mean that the beetles are killed, but overall, the effect on the ecosystem is minimal.

According to Peruvian biologist and team member Patricia Reyes, “The impact depends on the abundance and reproductive cycle of each species. Reducing the beetle population could have an effect on their predators, such as birds, reptiles, and other insects. The health of the forest depends on the beetles’ function to break down organic matter and disperse seeds. Despite not having found any effect on the ecosystem so far, we still limit how many individual beetles we collect and identify sensitive areas where collecting is prohibited. We promote sustainable methods of collection to mitigate possible impacts in the future.”

Getting beetles to do the work of collecting DNA for researchers took some adjustments. The traps normally used to study beetles cause the beetles to fall into a chemical solution, which kills and preserves them until they are collected. However, those traps contaminate the beetle’s stomach contents, making the DNA unusable. Lopera-Toro’s traps keep them alive, protecting the delicate strands of DNA that the beetles have worked so hard to collect. He and his team also go out into the forest to collect live beetles by hand, carefully recording the time and place each one was collected. Starting in July 2022, the team has been collecting dung beetles across Manu’s diverse ecosystems up and down the altitude gradient, from 500 to 3,500 meters above sea level.

In addition to obtaining DNA from the beetles, researchers also use them as test subjects for metabolic studies.

Enlarge / In addition to obtaining DNA from the beetles, researchers also use them as test subjects for metabolic studies.

Elena Chaboteaux

The Manu Biological Station team is using Nanopore technology to sequence the DNA found in the beetles’ stomachs, with the goal of finding out what animals are represented there. They specifically targeted dung beetles because their feeding habits depend on the feces left by larger animals. The main advantage to the Nanopore minION device is that it can separate long lengths of DNA on-site. “Long nanopore sequencing reads provide enhanced species identification, while real-time data analysis delivers immediate access to results, whether in the field or in the lab,” according to the Nanopore website.

Biologist Juliana Morales acknowledges that Nanopore still has a high rate of error, though as this new technology is refined, that issue is continually decreasing. For the purposes of the Manu Biological Station team, the margin of error is a price they’re willing to pay to have devices they can use in the rainforest. Since they’re not studying one specific species, but rather building a database of the species present in the region, they don’t need to get every nucleotide correct to be able to identify the species. They do, however, need a strand long enough to differentiate between a common woolly monkey and a yellow-tailed woolly monkey.

Though the researchers prefer to sequence DNA on-site with Nanopore minION devices, when they have more than a dozen samples to analyze, they send them to the University of Guelph in Ontario, Canada. It’s a logistical nightmare to send samples from the Peruvian jungle to Canada, but Lopera-Toro says it’s worth it. “The University of Guelph can process hundreds of DNA samples per day. I’m lucky if we can process 10 samples a day at the [Manu] lab.”

In the most recent batch of 76 samples, they analyzed the stomach contents of 27 species from 11 genera of beetles. From those 76 samples, they identified DNA of howler monkeys, spider monkeys, red brocket deer, night monkeys, peccaries, mouse opossum, Rufous-breasted wood quail, and two species of armadillos. Oddly, the beetles had also eaten about a dozen species of fruit, and one had consumed pollen from a tropical plant called syngonium.

The implications could be vast. “The dung beetle that ate the jaguar’s excrement will tell us not only the DNA of the jaguar but also what the jaguar is eating,” said Lopera-Toro. “If the jaguar kills a peccary and eats 80 percent of the peccary, beetles will eat some of the other 20 percent. If a beetle walks over a jaguar print or saliva, there could be traces of jaguar DNA on the beetle. We analyze the stomach contents and the outside of the beetle. We have an endless number of options, opportunities, and questions we can answer from studying these small insects. We can see the bigger picture of what is happening in the jungle.”

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brutally-bludgeoned-“vittrup-man”-went-from-forager-to-farmer-before-his-death

Brutally bludgeoned “Vittrup Man” went from forager to farmer before his death

anthropology, Archaeology, Biology, bog bodies, forensic archaeology, Science, Vitrup man / /

From forager to farmer —

The skull was shattered by at least eight blows before the body was tossed into a peat bog.

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reconstructed skull showing fractures

Enlarge / The cranial remains of Vittrup Man, who was bludgeoned to death and tossed in a peat bog between 3300-3100 BCE.

Stephen Freiheit via Fischer A., et al./PLoS ONE

In 1915, peat diggers recovered the fragmented skeletal remains of a man with a severely fractured skull in a peat bog near the village of Vittrup in Denmark. The remains were kept in a museum for the next century, but scientists have now conducted an in-depth analysis of the remains using various techniques to learn more about the so-called Vittrup Man’s life and violent death. They described their findings in a recent paper published in the journal PLoS ONE—including the surprising fact that Vittrup Man grew up in a coastal foraging community along the Scandinavian coast before his murder as an adult in a farming culture in Neolithic Denmark.

Vittrup Man is one of numerous “bog bodies” unearthed from peat bogs in northwestern Europe. These are human cadavers that have been naturally preserved and frequently mummified by the unique chemistry of the bogs. As peat ages, it releases humic acid, which has a pH level similar to vinegar. The bog bodies are basically pickled, and decomposition is dramatically slowed because of the anaerobic conditions of the bog. The best-preserved bog bodies are those that were put there during the winter or early spring when the water is very cold—less than 4° Celsius (39° F), i.e., too cold for bacteria to thrive—because the bog acids were able to saturate the tissues before decay could begin.

Peat has been a common fuel source since the Iron Age, and there are records of peat diggers coming across bog bodies dating back to 1640 in Germany. Bog bodies became of interest to antiquarians in the 19th century and archaeologists in the 20th century. One of the most famous examples is Tollund Man, a bog body found in the 1950s and dating back to the 5th century BCE. Tollund Man was so exquisitely mummified that he was originally mistaken for a recent murder victim, although only the head was preserved for posterity; the rest of the body was allowed to desiccate, given the less advanced state of preservation techniques in the 1950s.

But many bog bodies are only partially preserved, or only the skeletons (or parts thereof) survive. Vittrup Man falls into the latter category, consisting of a right ankle bone, the left tibia, the fractured skull, and a jawbone. He was discovered along with a wooden club, which archaeologists believe may have been the weapon used to bludgeon him to death. Various radiocarbon dating and isotope analyses confirmed that the bones all belonged to the same individual, while genetic analysis confirmed the remains were those of a male. He was likely deposited in the peat bog sometime between 3300–3100 BCE.

  • Left lower leg bone and right ankle bone of Vittrup Man.

    Marie Louise Jorkov/Fischer A., et al./PLoS ONE

  • The jawbone of Vittrup Man showing several worn teeth.

    Arnold Mikkelsen/Fischer A., et al./PLoS ONE

  • Drawing of Vittrup Man’s cranium showing front and back views of impact lesions and radiating fracture lines.

    Fischer A., et al./PLoS ONE

  • Drawing of Vittrup Man’s cranium showing right and left side views of impact lesions and radiating fracture lines.

    Fischer A., et al./PLoS ONE

Vittrup Man was included in a sweeping 2014 genomic project to learn more about Eurasia’s Mesolithic and Neolithic gene pools, but the resulting genetic profile was markedly different from other remains from the same region and time period. This intrigued University of Gothenburg (Sweden) archaeologist Karl-Göran Sjögren and his co-authors, and they decided to take a closer look, integrating data collected with various genetic, isotopic, physical, anthropological, and archaeological techniques. “To our knowledge, this is the first time that research has been able to map a north European inhabitant’s life history in such a high degree of detail and in such a high distance of time,” the authors wrote.

The size and distinctive characteristics of the skull, lower leg bones, and teeth indicate that at the time of his death, Vittrup Man was an adult male in his 30s. The cranium was shattered by at least eight blows delivered by a blunt object (like the wooden club), and the injuries were fatal, with no signs of healing post-trauma. There are no marks on the surviving bones indicating dismemberment, so the authors believe the body may have come apart while decomposing in the bog. It’s possible more Vittrup Man fragments have yet to be recovered.

But the clues gleaned from two of Vittrup Man’s teeth (sacrificed to science) are what provided the most interesting insights. Sjögren et al. found isotopes of strontium, carbon, and oxygen and concluded that the man had grown up along the coast of the Scandinavian Peninsula. Genetic analysis showed commonalities with Mesolithic people of Norway and Sweden; Vittrup Man had blue eyes and darker skin than the usual Neolithic farmer. The teeth and bones also had proteins and isotopes indicating a shift in diet from marine mammals and fish as a child, to sheep, goat, cereals, and dairy as an adult—the latter more typical of a farming community as opposed to a coastal foraging community.

Why Vittrup Man left the Scandinavian coast and ended up in Denmark remains a mystery. He may have been captured and enslaved or immigrated, or he may have been a foreign merchant selling goods like flint axes between foraging and farming communities. Either way, he eventually integrated into the farming community—at least until they killed him.

As for why he was killed, “At that time, it was commonplace in present-day Denmark to sacrifice humans in bogs, and these acts were often conducted in violent ways,” the authors concluded. “Evidently, such dubious honor was also given to persons of nonlocal provenance.”

PLoS ONE, 2024. DOI: 10.1371/journal.pone.0297032  (About DOIs).

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New E. coli strain will accelerate evolution of the genes of your choice

biochemistry, Biology, E. coli, evolution, mutation rate, mutations, Science / /

Making mutants —

Strain eliminates the trade-offs of a high mutation rate.

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Woman holding a plate of bacteria with clusters of bacteria on it.

Genetic mutations are essential for innovation and evolution, yet too many—or the wrong ones—can be fatal. So researchers at Cambridge established a synthetic “orthogonal” DNA replication system in E. coli that they can use as a risk-free way to generate and study such mutations. It is orthogonal because it is completely separate from the system that E. coli uses to copy its actual genome, which contains the genes E. coli needs to survive.

The genes in the orthogonal system are copied with an extraordinarily error-prone DNA replication enzyme, which spurs rapid evolution by generating many random mutations. This goes on while E. coli’s genes are replicated by its normal high-fidelity DNA copying enzyme. The two enzymes work alongside each other, each doing their own thing but not interfering with the other’s genes.

Engineering rapid mutation

Such a cool idea, right? The scientists stole it from nature. Yeast already has a system like this, with a set of genes copied by a dedicated enzyme that doesn’t replicate the rest of the genome. But E. coli is much easier to work with than yeast, and its population can double in 20 minutes, so you can get a lot of rounds of replication and evolution done fast.

The researchers generated the system by pillaging a phage—a virus that infects E. coli. They took out all of the phage genes that allow the phage to grow uncontrollably until it bursts the E. coli cell it infected open. The engineering left only a cassette containing the genes responsible for copying the phage genome. Once this cassette was inserted into the E. coli genome, it could simultaneously replicate at least three different strings of genes placed next to it in the DNA, maintaining them for over a hundred generations—all while leaving the rest of the E. coli genome to be copied by other enzymes.

The scientists then tweaked the mutation rate of the orthogonal DNA-replicating enzyme, eventually enhancing it 1,000-fold. To test if the system could be used to evolve new functions, they inserted a gene for resistance to one antibiotic and saw how long it took for that gene to mutate into one conferring resistance to a different antibiotic. Within twelve days, they got 150 times more resistance to the new antibiotic. They also inserted the gene encoding green fluorescent protein and increased its fluorescence over 1,000-fold in five days.

Evolving detoxification

Not 20 pages later, in the same issue of Science, Frances Arnold’s lab has a paper that provides evidence of how powerful this approach could be. This team directed the evolution of an enzyme the old-fashioned way: through sequential rounds of random mutagenesis and selection for the desired trait. Arnold won The Nobel Prize in Chemistry 2018 for the directed evolution of enzymes, so she knows what she’s about. In this recent work, her lab generated an enzyme that can biodegrade volatile methyl siloxanes. We make megatons of these compounds every year to stick in cleaning products, shampoos and lotions, and industrial products, but they linger in the environment. They contain carbon-silicon bonds, which were never a thing until humans made them about 80 years ago; since nature never made these bonds, there is no natural way to break them, either.

“Directed evolution with siloxane was particularly challenging,” the authors note in their introduction, for various technical reasons. “We started from an enzyme we had previously engineered for other chemistry on siloxanes—that enzyme, unlike the natural enzyme, showed a tiny bit of activity for siloxane Si-C bond cleavage. The overall project, however, from initial discovery to figuring out how to measure what we wanted, took several years,” Arnold said. And it is only the first step in possibly rendering siloxanes biodegradable. The accelerated continuous evolution that the new orthologous system allows will hopefully greatly facilitate the development of enzymes and other proteins like this that will have applications in research, medicine, and industry.

We do not (yet) have machines that can efficiently assemble long stretches of DNA or make proteins. But cells do these things extremely efficiently, and E. coli cells have long been the ones used in the lab as little factories, churning out whatever genes or proteins researchers program into them. Now E. coli can be used for one more molecular task—they can be little hotbeds of evolution.

Science, 2024.  DOI: 10.1126/science.adi5554, 10.1126/science.adk1281

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humans-are-living-longer-than-ever-no-matter-where-they-come-from 

Humans are living longer than ever no matter where they come from 

Biology, health, Longevity, public health, Science / /

Live long and prosper? —

Disease outbreaks and human conflicts help dictate regional differences in longevity.

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An older person drinking coffee in an urban environment.

Most of us want to stay on this planet as long as possible. While there are still differences depending on sex and region, we are now living longer as a species—and it seems life spans will only continue to grow longer.

Researcher David Atance of Universidad de Alcalá, Spain, and his team gathered data on the trends of the past. They then used their findings to project what we can expect to see in the future. Some groups have had it harder than others because of factors such as war, poverty, natural disasters, or disease, but the researchers found that morality and longevity trends are becoming more similar regardless of disparities between sexes and locations.

“The male-female gap is decreasing among the [clusters],” they said in a study recently published in PLOS One.

Remembering the past

The research team used specific mortality indicators—such as life expectancy at birth and most common age at death–to identify five global clusters that reflect the average life expectancy in different parts of the world. The countries in these clusters changed slightly from 1990 to 2010 and are projected to change further by 2030 (though 2030 projections are obviously tentative). Data for both males and females was considered when deciding which countries belonged in which cluster during each period. Sometimes, one sex thrived while the other struggled within a cluster—or even within the same country.

Clusters that included mostly wealthier countries had the best chance at longevity in 1990 and 2010. Low-income countries predictably had the worst mortality rate. In 1990, these countries, many of which are in Africa, suffered from war, political upheaval, and the lethal spread of HIV/AIDS. Rwanda endured a bloody civil war during this period. Around the same time, Uganda had tensions with Rwanda, as well as Sudan and Zaire. In the Middle East, the Gulf War and its aftermath inevitably affected 1990 male and female populations.

Along with a weak health care system, the factors that gave most African countries a high mortality rate were still just as problematic in 2010. In all clusters, male life spans tended to differ slightly less between countries than female life spans. However, in some regions, there were differences between how long males lived compared to females. Mortality significantly increased in 1990 male populations from former Soviet countries after the dissolution of the Soviet Union, and this trend continued in 2010. Deaths in those countries were attributed to violence, accidents, cardiovascular disease, alcohol, an inadequate healthcare system, poverty, and psychosocial stress.

Glimpsing the future

2030 predictions must be taken with caution. Though past trends can be good indicators of what is to come, trends do not always continue. While things may change between now and 2030 (and those changes could be drastic), these estimates project what would happen if past and current trends continue into the relatively near future.

Some countries might be worse off in 2030. The lowest-income, highest-mortality cluster will include several African countries that have been hit hard with wars as well as political and socioeconomic challenges. The second low-income, high-mortality cluster, also with mostly African countries, will now add some Eastern European and Asian countries that suffer from political and socioeconomic issues most have recently been involved in conflicts and wars or still are, such as Ukraine.

The highest-income, lowest-mortality cluster will gain some countries. These include Chile, which has made strides in development that are helping people live longer.

Former Soviet countries will probably continue to face the same issues they did in 1990 and 2010. They fall into one of the middle-income, mid-longevity clusters and will most likely be joined by some Latin American countries that were once in a higher bracket but presently face high levels of homicide, suicide, and accidents among middle-aged males. Meanwhile, there are some other countries in Latin America that the research team foresees as moving toward a higher income and lower mortality rate.

Appearances can be deceiving

The study places the US in the first or second high-income, low-mortality bracket, depending on the timeline. This could make it look like it is doing well on a global scale. While the study doesn’t look at the US specifically, there are certain local issues that say otherwise.

A 2022 study by the Centers for Disease Control and Prevention suggests that pregnancy and maternal care in the US is abysmal, with a surprisingly high (and still worsening) maternal death rate of about 33 deaths per 100,000 live births. This is more than double what it was two decades ago. In states like Texas, which banned abortion after the overturn of Roe v. Wade, infant deaths have also spiked. The US also has the most expensive health care system among high-income countries, which was only worsened by the pandemic.

The CDC also reports that life expectancy in the US keeps plummeting. Cancer, heart disease, stroke, drug overdose, and accidents are the culprits, especially in middle-aged Americans. There has also been an increase in gun violence and suicides. Guns have become the No. 1 killer of children and teens, which used to be car accidents.

Whether the US will stay in that top longevity bracket is also unsure, especially if maternal death rates keep rising and there aren’t significant improvements made to the health care system. There and elsewhere, there’s no way of telling what will actually happen between now and 2030, but Atance and his team want to revisit their study then and compare their estimates to actual data. The team is also planning to further analyze the factors that contribute to longevity and mortality, as well as conduct surveys that could support their predictions. We will hopefully live to see the results.

PLOS One, 2024. DOI:  10.1371/journal.pone.0295842

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Our oldest microbial ancestors were way ahead of their time

Biology, eukaryotes, evolution, paleontology, Science / /

Going Golgi —

Specialized internal structures were present over 1.5 billion years ago.

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computer generated image of membrane structures inside a cell

Enlarge / The Golgi apparatus, shown here in light green, may have been involved in building internal structures in cells.

ARTUR PLAWGO / SCIENCE PHOTO LIBRARY

Before Neanderthals and Denisovans, before vaguely humanoid primates, proto-mammals, or fish that crawled out of the ocean to become the first terrestrial animals, our earliest ancestors were microbes.

More complex organisms like ourselves descend from eukaryotes, which have a nuclear membrane around their DNA (as opposed to prokaryotes, which don’t). Eukaryotes were thought to have evolved a few billion years ago, during the late Palaeoproterozoic period, and started diversifying by around 800 million years ago. Their diversification was not well understood. Now, a team of researchers led by UC Santa Barbara paleontologist Leigh Ann Riedman discovered eukaryote microfossils that are 1.64 billion years old, yet had already diversified and had surprisingly sophisticated features.

“High levels of eukaryotic species richness and morphological disparity suggest that although late Palaeoproterozoic [fossils] preserve our oldest record of eukaryotes, the eukaryotic clade has a much deeper history,” Riedman and her team said in a study recently published in Papers in Paleontology.

Really, really, really old tricks

During the late Palaeoproterozoic, eukaryotes most likely evolved in the wake of several major changes on Earth, including a drastic increase in atmospheric oxygen and shifts in ocean chemistry. This could have been anywhere from 3 billion to 2.3 billion years ago. Riedman’s team explored the layers of sedimentary rock in the Limbunya region of Australia’s Birrindudu basin. The fossils they unearthed included a total of 26 taxa, as well as 10 species that had not been described before. One of them is Limbunyasphaera operculata, a species of the new genus Limbunyasphera.

What makes L. operculata so distinct is that it has a feature that appears to be evidence of a survival mechanism used by modern eukaryotes. There are some extant microbes that form a protective cyst so they can make it through harsh conditions. When things are more tolerable, they produce an enzyme that dissolves a part of the cyst wall into an opening, or pylome, that makes it possible for them to creep out. This opening also has a lid, or operculum. These were both observed in L. operculata.

While splits in fossilized single-cell organisms may be the result of taphonomic processes that break the cell wall, complex structures such as a pylome and operculum are not found in prokaryotic organisms, and therefore suggest that a species must be eukaryotic.

Didn’t know they could do that

Some of the previously known species of extinct eukaryotes also surprised the scientists with unexpectedly advanced features. Satka favosa had a vesicle in the cell that was enclosed by a membrane with platelike structures. Another species, Birrindudutuba brigandinia, also had plates identified around its vesicles, although none of its plates were as diverse in shape as those seen in different S. favosa individuals. Those plates came in a large variety of shapes and sizes, which could mean that what has been termed S. favosa is more than one species.

The plated vesicle of S. favosa is what led Riedman to determine that the species must have been eukaryotic, because the plates are possible indicators that Golgi bodies existed in these organisms. After the endoplasmic reticulum of a cell synthesizes proteins and lipids, Golgi bodies process and package those substances depending on where they have to go next. Riedman and her team think that Golgi or Golgi-like bodies transported materials within the cell to form plates around vesicles, such as the ones seen in S. favosa. The hypothetical Golgi bodies themselves are not thought to have had these plates.

This sort of complex sorting of cellular contents is a feature of all modern eukaryotes. “Taxa including Satka favosa… are considered [eukaryotes] because they have a complex, platy vesicle construction,” the researchers said in the study. These new fossils suggest that it arose pretty early in their history.

Eukaryotes have evidently been much more complex and diverse than we thought for hundreds of millions of years longer than we thought. There might be even older samples out there. While fossil evidence of eukaryotes from near their origin eludes us, samples upwards of a billion years old, such as those found by Riedman and her team, are telling us more than ever about their—and therefore our—evolution.

Papers in Paleontology, 2023.  DOI: 10.1002/spp2.1538

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Clownfish “count” white stripes to determine if an invader is friend or foe

animal cognition, animals, Biology, clownfish, numerosity, Science / /

Counting Nemo —

They attacked similar fish with three stripes more often than those with one or two stripes.

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Clown anemonefish (Amphiprion ocellaris) photographed in the wild.

Enlarge / Clown anemonefish (Amphiprion ocellaris) seem to recognize different species of clownfish by counting white stripes.

Kina Hayashi

Many people tend to think of clownfish, with their distinctive white bars against an orange, red, or black background, as a friendly sort of fish, perhaps influenced to some extent by the popular Pixar film Finding Nemo. But clownfish can be quite territorial when it comes to defending their host anemone from intrusion by others, particularly those from their own species. A new paper published in the Journal of Experimental Biology describes how clownfish determine if a fish approaching their home is friend or foe by “counting” the number of white bars or stripes on their bodies.

As previously reported, mathematical ability is often considered uniquely human, but in fact, scientists have found that many animal species—including lions, chimpanzees, birds, bees, ants, and fish—seem to possess at least a rudimentary counting ability or number sense. Crows can understand the concept of zero. So can bees, which can also add and subtract, as can both stingrays and cichlids—at least for a small number of objects (in the range of one to five). Some ants count their steps.

This so-called “numerosity” simply refers to the number of things in a set, according to cognitive psychologist Brian Butterworth, an emeritus professor at University College London and author of Can Fish Count? What Animals Reveal About Our Uniquely Mathematical Minds. It has nothing to do with reasoning or logical mathematical intelligence. This is information that will be in the environment, and counting animals must have some mechanism for extracting this numerical information from the environment. But it nonetheless makes for a fascinating field of study.

In 2022, Kina Hayashi of the Okinawa Institute of Science and Technology (OIST) and several colleagues found that clownfish display more aggressive behavior (e.g., chasing or biting) toward fish (or fish toys) with vertical bar patterns compared with fish with horizontal stripe patterns and that this aggressive behavior lasted longer when directed at fish with vertical bars versus horizontal bars. This behavior appears to influence the position of fish species between host anemones and coral reefs: No fish with vertical bars sought shelter in host anemones, while several species with vertical bars were found in the surrounding coral reefs. But it wasn’t clear how the fish recognized the color patterns or what basic rules controlled this signaling. The study results suggested that it wasn’t based on the mere presence of white bars or how much white color was present on a given fish’s body.

The plastic models used to measure the clown anemonefish’s aggressive behavior.

Enlarge / The plastic models used to measure the clown anemonefish’s aggressive behavior.

This new study builds on that earlier work. This time around, Kayashi and co-authors raised a school of young common clownfish (A. ocellaris) from eggs to ensure that the fish had never set eyes on other species of anemonefish. At six months old, the fish were introduced to several other clownfish species, including Clarke’s anemonefish (A. clarkii), orange skunk clownfish (A. sandaracinos), and saddleback clownfish (A. polymnus).

The researchers placed different species of clownfish, with different numbers of white bars, in small cases inside a tank with a clownfish colony and filmed their reaction. Because they were in a controlled tank environment, there was no chasing or biting. Rather, aggressive behavior was defined as staring aggressively at the other fish and circling the case in which the other fish were held.

They followed up with a second set of experiments in which they presented a colony of clownfish with different plastic models painted with accurate clownfish coloration, with differing numbers of white stripes. The researchers also filmed and measured the degree of aggressive behavior directed at the different plastic models.

Clownfish showing aggression toward another fish with similar stripes. Credit: Kina Hayashi

The results: “The frequency and duration of aggressive behaviors in clown anemonefish was highest toward fish with three bars like themselves,” said Hayashi, “while they were lower with fish with one or two bars, and lowest toward those without vertical bars, which suggests that they are able to count the number of bars in order to recognize the species of the intruder.”

Hayashi et al. cautioned that one limitation of their study is that all the fish used in the experiments were hatched and raised in an environment where they had only encountered other fish of their own species. So, they could not conclusively determine whether the observed behavior was innate or learned. Other species of clownfish also use the same anemone species as hosts, so aggressive behavior toward those species might be more frequent in the wild than observed in the laboratory tank environment.

Journal of Experimental Biology, 2024. DOI: 10.1242/jeb.246357  (About DOIs).

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should-you-flush-with-toilet-lid-up-or-down?-study-says-it-doesn’t-matter

Should you flush with toilet lid up or down? Study says it doesn’t matter

bacteria, Biology, cross contamination, epidemiology, fluid dynamics, hygiene, sanitation, Science, toilet plumes, toilets, viral aerosols / /
Whether the toilet lid is up or down doesn't make much difference in the spread of airborne bacterial and viral particles.

Enlarge / Whether the toilet lid is up or down doesn’t make much difference in the spread of airborne bacterial and viral particles.

File this one under “Studies We Wish Had Let Us Remain Ignorant.” Scientists at the University of Arizona decided to investigate whether closing the toilet lid before flushing reduces cross-contamination of bathroom surfaces by airborne bacterial and viral particles via “toilet plumes.” The bad news is that putting a lid on it doesn’t result in any substantial reduction in contamination, according to their recent paper published in the American Journal of Infection Control. The good news: Adding a disinfectant to the toilet bowl before flushing and using disinfectant dispensers in the tank significantly reduce cross-contamination.

Regarding toilet plumes, we’re not just talking about large water droplets that splatter when a toilet is flushed. Even smaller droplets can form and be spread into the surrounding air, potentially carrying bacteria like E. coli or a virus (e.g., norovirus) if an infected person has previously used said toilet. Pathogens can linger in the bowl even after repeated flushes, just waiting for their chance to launch into the air and spread disease. That’s because larger droplets, in particular, can settle on surfaces before they dry, while smaller ones travel further on natural air currents.

The first experiments examining whether toilet plumes contained contaminated particles were done in the 1950s, and the notion that disease could be spread this way was popularized in a 1975 study. In 2022, physicists and engineers at the University of Colorado, Boulder, managed to visualize toilet plumes of tiny airborne particles ejected from toilets during a flush using a combination of green lasers and cameras. It made for some pretty vivid video footage:

Colorado researchers managed to visualize toilet plumes in 2022 using green lasers and strategically placed cameras.

“If it’s something you can’t see, it’s easy to represent it doesn’t exist,” study co-author John Grimaldi said at the time. They found that the ejected airborne particles could travel up to 6.6 feet per second, reaching heights of 4.9 feet above the toilet within 8 seconds. And if those particles were smaller (less than 5 microns), they could hang around in that air for over a minute.

More relevant to this latest paper, it’s been suggested that closing the lid before flushing could substantially reduce the airborne spread of contaminants. For example, in 2019, researchers at University College Cork deployed bioaerosol sensors in a shared lavatory for a week to monitor the number and size of contaminant particles. They concluded that flushing with the toilet lid down reduced airborne droplets between 30 and 60 percent. But this scenario also increased the diameter of the droplets and bacteria concentration. Leaving the lid down also means the airborne microdroplets are still detectable 16 minutes after flushing, 11 minutes longer than if one flushed with the lid up.

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gotta-go?-we’ve-finally-found-out-what-makes-urine-yellow

Gotta go? We’ve finally found out what makes urine yellow

biochemistry, Biology, Genomics, Science, urine / /

It isn’t from eating corn —

The yellow color comes from bacteria metabolizing waste from red blood cells.

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Image of a series of scientific sample tubes filled with yellow liquids.

There are many mysteries in life that we end up shrugging off. Why is urine yellow? It just is, right? Rather than flush that 125-year-old question down the toilet, scientists sought out the answer, discovering a previously unknown microbial enzyme was to blame.

The enzyme that has eluded us for so long is now known as bilirubin reductase. It was identified by researcher and assistant professor Brantley Hall of the University of Maryland, who was part of a team based at the university and the National Institutes of Health.

Bilirubin is an orange pigment released by red blood cells after they die. Gut microbes then use bilirubin reductase to break down bilirubin into colorless urobilinogen, which degrades into yellowish urobilin, giving urine that infamous hue. While urobilin previously had an association with the color of urine, the enzyme that starts the process by producing urobilinogen was unknown until now.

“Though it was previously thought that multiple enzymes were involved in the reduction of bilirubin, our results support the finding that a single enzyme performs the reduction of bilirubin to urobilinogen,” the research team said in a study recently published in Nature Microbiology.

Gut feeling

Because some gut bacteria had been known to reduce bilirubin, Hall and his team knew where to start but wanted to fill in the unknowns by finding out which particular species actually do this—and how. This meant they had to find the gene responsible for encoding bilirubin reductase.

Previous studies had found that the species Clostridiodes difficile was capable of reducing bilirubin (though the mechanism it used was unknown). Using C. difficile as a basis for comparison, the team cultured different species of gut bacteria and exposed them to bilirubin to see whether that bacteria could produce urobilinogen, detecting its presence using a fluorescence assay.

The fluorescence assay told Hall and his colleagues that there were nine strains within the tested species that they thought were capable of reducing bilirubin, although how these bacteria were breaking it down was still unclear.  After the fluorescence assay, the genomes of the most closely related strains were analyzed,  and several turned out to share a gene that encoded an enzyme that could reduce bilirubin—bilirubin reductase.

Bacterial strains that metabolized bilirubin using bilirubin reductase all came from species that were found to belong to a single clade (the researchers informally referred to it as the bilirubin reductase clade). Within that clade, most of these species are from the class Clostridia in the phylum Firmicutes, a phylum of bacteria important to gut health.

More than … you know

The discovery of bilirubin reductase goes beyond the origin of urine color. After identifying the enzyme, the researchers found out that, while bilirubin reductase is present in healthy adults, there is a deficit in newborns and adults with inflammatory bowel disease, which could eventually influence future treatments

By sequencing infant gut genomes, Hall and his team saw that bilirubin reductase was often missing during the first few months of life. Too much bilirubin building up in the blood turns the skin and the whites of the eyes yellow, a symptom known as jaundice. Most infants have some level of jaundice, but it usually goes away on its own.

The absence of bilirubin reductase is also associated with pigmented gallstones in adults with inflammatory bowel disease (inflammatory bowel disease or IBD is a general term that can refer to several different diagnoses). Sequencing adult gut genomes showed that there was a deficit of this enzyme in most patients with Crohn’s disease or ulcerative colitis whose gut genomes were sequenced.

“With the knowledge of the species, genes, and enzymes involved in bilirubin reduction, future research can now focus on the extent to which gut microbial bilirubin metabolism affects…the role of bilirubin reduction in health and disease,” the researchers said in the same study.

There is still more research to be done on bilirubin reductase and the health implications it could have. The team thinks there may be a link between the amount of urobilin produced in the body and insulin resistance, obesity, heart disease, and even heart failure. Next to that, we finally know why urine is yellow.

Nature Microbiology, 2023. DOI: 10.1038/s41564-023-01549-x

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