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      New algorithm finds lots of gene-editing enzymes in environmental DNA

      news.movim.eu / ArsTechnica · Saturday, 2 December - 13:00 · 1 minute

    A dark blue background with light blue ribbons, and yellow nucleic acids in front.

    Enlarge / The protein structure of CAS, shown with nucleic acids bound. (credit: Bang Wong, Broad Institute )

    CRISPR—Clustered Regularly Interspaced Short Palindromic Repeats—is the microbial world’s answer to adaptive immunity. Bacteria don’t generate antibodies when they are invaded by a pathogen and then hold those antibodies in abeyance in case they encounter that same pathogen again, the way we do. Instead, they incorporate some of the pathogen’s DNA into their own genome and link it to an enzyme that can use it to recognize that pathogenic DNA sequence and cut it to pieces if the pathogen ever turns up again.

    The enzyme that does the cutting is called Cas, for CRISPR associated. Although the CRISPR-Cas system evolved as a bacterial defense mechanism, it has been harnessed and adapted by researchers as a powerful tool for genetic manipulation in laboratory studies. It also has demonstrated agricultural uses, and the first CRISPR-based therapy was just approved in the UK to treat sickle-cell disease and transfusion-dependent beta-thalassemia.

    Now, researchers have developed a new way to search genomes for CRISPR-Cas-like systems. And they’ve found that we may have a lot of additional tools to work with.

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      Study: The serotine bat uses its super-large penis as an arm when mating

      news.movim.eu / ArsTechnica · Monday, 27 November - 16:45 · 1 minute

    closeup of a serotine bat

    Enlarge / "That's not my arm": Male serotine bats have such large penises, they can use them as an arm while mating. (credit: Alona Shulenko)

    Little is known about the mating habits of the serotine bat ( Eptesicus serotinus ), but the males of the species boast unusually large penises—much larger than the vaginas of the females. The purpose of such an enormous organ has long baffled scientists. But a recent paper published in the journal Current Biology revealed that the males of this bat species use their gigantic members not for penetrating females while mating, but as an arm to push the female's tail sheath aside, thereby improving the odds of successful insemination.

    Eurasian serotine bats can be recognized by their long smoky-brown fur (with pale yellow-brown underbelly), large triangular ears, and distinctive flight pattern: bouts of flapping interspersed with brief glides. They typically roost in older buildings like churches that have high gables and cavity walls, or abandoned mines. The male bats are largely solitary until fall mating season arrives, when they seek out females. Females set up maternity colonies around late May in Europe and remain there throughout the breeding season, usually giving birth to a single offspring (pup) in late summer.

    Female bats have unusually long cervixes, the better to store sperm. The males have penises that are seven times longer than the females' vaginas, with a heart-shaped head seven times wider than the vaginal opening. “By chance, we had observed that these bats have disproportionately long penises, and we were always wondering, ‘How does that work?’” said co-author Nicolas Fasel of the University of Lausanne. “We thought maybe it's like in the dog where the penis engorges after penetration so that they are locked together, or alternatively maybe they just couldn't put it inside, but that type of copulation hasn’t been reported in mammals until now.”

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      How these parasitic worms turn brown shrimp into bright orange “zombies”

      news.movim.eu / ArsTechnica · Thursday, 7 September - 21:02 · 1 minute

    a bright orange shrimp

    Enlarge / Orange amphipods caught the eye (and interest) of Brown University graduate students conducting field research. (credit: David Johnson)

    Scour the salt marshes of Plum Island Estuary in Massachusetts and you're likely to spot bright orange shrimp lurking among the vegetation and detritus. That unusual hue is a sign that a shrimp has been infected with a parasitic worm, which also seems to affect the shrimp's behavior. Infected shrimp typically become sluggish and spend more time exposed in the open marsh, easy pickings for hungry birds. Now biologists at Brown University have sequenced the DNA of these shrimp to hone in on the molecular mechanisms behind the changes, according to a recent paper published in the journal Molecular Ecology.

    “This may be an example of a parasite manipulating an intermediate host to ensure its own transmission between hosts,” said co-author David Rand of Brown University, drawing an analogy to how malaria spreads to humans via the intermediary of mosquito bites. “Rabies could be another relevant example: it drives infected individuals ‘mad’ so they bite others and infect the next host. Learning the molecular mechanisms of these kinds of host-parasite interactions can have important implications for how to manage pathogens generally, and in humans.”

    Parasites that control and alter the behavior of their hosts are well-known in nature. Most notably, there is a family of zombifying parasitic fungi called Cordyceps —more than 400 different species , each targeting a particular insect species, whether it be ants, dragonflies, cockroaches, aphids, or beetles. In fact, The Last of Us game co-creator Neil Druckmann has said the premise was partly inspired by an episode of the BBC nature documentary Planet Earth (narrated by Sir David Attenborough) portraying the "zombification" of an ant in vivid detail . Scientists are keen to study Cordyceps to learn more about the origins and intricate mechanisms behind these kinds of pathogen-based diseases.

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      Vlad the Impaler may have shed tears of blood, study finds

      news.movim.eu / ArsTechnica · Monday, 21 August, 2023 - 21:58 · 1 minute

    This letter written by Vlad the Impaler in 1475 contains proteins that suggest he suffered from respiratory problems and bloodied tears.

    Enlarge / This 1475 letter written by Vlad the Impaler contains proteins suggesting he suffered from respiratory problems, bloodied tears. (credit: Adapted from M.G.G. Pittala et al., 2023/CC BY )

    The eponymous villain of Bram Stoker's classic 1897 novel Dracula was partly inspired by a real historical person: Vlad III, a 15th century prince of Wallachia (now southern Romania), known by the moniker Vlad the Impaler because of his preferred method of execution: impaling his victims on spikes. Much of what we know about Vlad III comes from historical documents, but scientists have now applied cutting-edge proteomic analysis to three of the prince's surviving letters, according to a recent paper published in the journal Analytical Chemistry. Among their findings: the Romanian prince was not a vampire, but he may have wept tears of blood, consistent with certain legends about Vlad III.

    Vlad III was the second son of Vlad Dracul ("the Dragon"), who became the voivode of Wallachia in 1436. Vlad III was also known as Vlad Dracula ("son of the Dragon"), and it was this name that Stoker used for his fictional vampire— dracul means "the devil" in modern Romanian—along with a few historical details he was able to glean about Wallachia. This was a brutal, bloody period of political instability. Vlad spent several years as a prisoner of the Ottoman Empire, along with his younger brother Radu, and his father and older brother, Mircea, were murdered in 1447. Eventually, Vlad became voivode of Wallachia himself—three times, in fact, interrupted by periods of exile or captivity.

    Vlad was constantly at war, and it was his brutal treatment of his enemies that led to his reputation as a monster, particularly in German-speaking territories, where books detailing his atrocities became bestsellers. These accounts described how Vlad executed men, women, and children taken prisoner from a Saxon village and impaled them. The more accurate, eye-witness-based accounts also included details about the churches Vlad's army destroyed during plundering raids in Transylvania. Other stories (many likely exaggerated) claimed he burned the lazy and the poor, and had women impaled along with their nursing babies. A well-known woodcut shows Vlad dining while surrounded by impaled people on poles. He died in battle in January 1477, having killed an estimated 80,000 people in his lifetime.

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      Dinosaurs and the evolution of breathing through bones

      news.movim.eu / ArsTechnica · Wednesday, 26 July, 2023 - 11:00

    Image of a dinosaur looming over some small mammals, potentially about to eat them.

    Enlarge / It takes careful study and the right kind of bones to determine how something like this breathed. (credit: Tito Aureliano et. al. )

    Somewhere in Earth’s past, some branches on the tree of life adopted a body plan that made breathing and cooling down considerably more efficient than how mammalian bodies like ours do it. This development might not seem like much on the surface, until you consider that it may have ultimately enabled some of the largest dinosaurs this planet has ever known. It was so successful that it was maintained by three different groups of extinct species and continues to exist today in the living descendants of dinosaurs.

    Because lungs don’t usually survive fossilization, one might wonder how scientists are able to ascertain anything about the breathing capabilities of extinct species. The answer lies within their bones.

    In a suite of papers published in late 2022 and early 2023 , paleontologists examined fossil microstructure within some of the earliest known dinosaurs to determine just how early parts of this system evolved.

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      Understanding the octopus and its relationships with humans

      news.movim.eu / ArsTechnica · Sunday, 23 July, 2023 - 11:07

    A giant Pacific octopus shows its colors at the Monterey Bay Aquarium.

    A giant Pacific octopus shows its colors at the Monterey Bay Aquarium. (credit: Monterey Bay Aquarium)

    While other octopus books study the animal's behavior in aquaria or tropical waters worldwide, Dr. David Scheel, a professor of Marine Biology at Alaska Pacific University, takes a unique approach in his first book , Many Things Under a Rock. He travels to extreme places in the Pacific Northwest where one may not expect these creatures to live, but they have for approximately 330 million years

    “I think it is a little surprising to some people that octopuses live in cold water,” Scheel told Ars. “It might be because we're used to seeing them in aquariums, and we think of aquariums as tropical locations, although you can run cold water aquariums as well.”

    Personal experience

    In Many Things Under a Rock, Scheel regales the reader with anecdotes of his time researching cephalopods in Alaska and Canada. From yearly tracking of octopus dens to discovering new octopus “cities,” Scheel’s chapters give engaging and informative stories on marine biology. Between these chapters are Indigenous stories about octopuses in the Pacific Northwest, revealing their influence on the area's native tribes.

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      A calculated risk: How ants judge when to commit their bodies to a ladder

      news.movim.eu / ArsTechnica · Wednesday, 12 July, 2023 - 12:08

    a group of reddish ants forming a bridge between two green leaves with their body.

    Enlarge (credit: grass-lifeisgood )

    Social insects, which don't have very large nervous systems, are capable of remarkably sophisticated behavior, such as the direction-giving dance by bees or the lifesaving rafts formed by fire ants. In these cases, the benefits of this behavior—more food or survival, respectively—are pretty obvious. But there are also cases where the benefits are less than obvious, so how do insects collectively decide to engage in a risky activity?

    Researchers are studying a species of ant, the weaver ant Oecophylla smaragdina , that can move vertically amid trees by building a ladder using its own body. The effort takes a lot of workers away from foraging for as long as the ladder is in place, making it a major investment. But in most cases, the rewards will be uncertain; there's only a payoff if the ants find a significant food source at the newly accessed level.

    To make the decision, ants appear to judge the distance between their location and the destination. But not every ant makes the same judgment, and it's possible to trick the ants into building longer ladders by moving the destination.

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      The physics of how gentoo penguins can swim speedily underwater

      news.movim.eu / ArsTechnica · Thursday, 6 July, 2023 - 22:33 · 1 minute

    A gentoo penguin swimming

    Enlarge / Gentoo penguins are the world's fastest swimming birds, thanks to the unique shape and structure of their wings. (credit: Priya Venkatesh/CC BY-SA 3.0 )

    Gentoo penguins are the world's fastest swimming birds, clocking in at maximum underwater speeds of up to 36 km/h (about 22 mph). That's because their wings have evolved into flippers ideal for moving through water (albeit pretty much useless for flying in the air). Physicists have now used computational modeling of the hydrodynamics of penguin wings to glean additional insight into the forces and flows that those wings create underwater. They concluded that the penguin's ability to change the angle of its wings while swimming is the most important variable for generating thrust, according to a recent paper published in the journal Physics of Fluids.

    “Penguins’ superior swimming ability to start/brake, accelerate/decelerate, and turn swiftly is due to their freely waving wings," said co-author Prasert Prapamonthon of King Mongkut‘s Institute of Technology Ladkrabang in Bangkok, Thailand. "They allow penguins to propel and maneuver in the water and maintain balance on land. Our research team is always curious about sophisticated creatures in nature that would be beneficial to mankind.”

    Scientists have long been interested in the study of aquatic animals. Such research could lead to new designs that reduce drag on aircraft or helicopters. Or it can help build more efficient bio-inspired robots for exploring and monitoring underwater environments—such as RoboKrill , a small, one-legged, 3D-printed robot designed to mimic the leg movement of krill so it can move smoothly in underwater environments.

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      Smelling in stereo—a surprising find on a fossilized shark

      news.movim.eu / ArsTechnica · Thursday, 6 July, 2023 - 20:58 · 1 minute

    Image of an odd looking shark swallowing a smaller fish.

    Enlarge / Artist's reconstruction of the shark as it once lived. (credit: Klug et. al. )

    Sharks are largely cartilaginous, a body structure that often doesn’t survive fossilization. But in a paper published in the Swiss Journal of Paleontology, scientists describe an entirely new species of primitive shark from the Late Devonian period, a time when they were just beginning to proliferate in ancient oceans.

    The team found several exceptionally well-preserved fossils that include soft tissues such as scales, musculature, digestive tract, liver, and blood vessel imprints. Also preserved: the species’ most distinct feature, widely separated nasal organs, somewhat akin to those on today’s hammerhead sharks. The find suggests that sharks’ finely tuned sense of smell, the subject of urban legends, was already being selected for just as these predators were becoming established.

    A key time and a rare find

    Christian Klug is the lead author and curator of the Paleontological Institute and Museum at Zurich University. He explained the significance of the Devonian period in the oceans’ history, when life was flourishing and an evolutionary arms race was in full swing. “With increasing competition among predators inhabiting the water column, the entire organism was selected for more efficiency,” he explained. “This affected swimming abilities, feeding apparatus, but also the sensory systems, which are essential to detect prey, to orient themselves in space, and to escape from even larger predators such as the huge placoderm Dunkleosteus and the equally large shark Ctenacanthus .”

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