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      New algorithm finds lots of gene-editing enzymes in environmental DNA / 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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      New effort IDs the genes that made the mammoth / ArsTechnica · Friday, 7 April, 2023 - 17:40 · 1 minute

    Artist's view of a mammoth superimposed over DNA sequencing data.

    Enlarge (credit: Beth Zaiken)

    An international team of scientists has published the results of their research into 23 woolly mammoth genomes in Current Biology . As of today, we have even more tantalizing insights into their evolution, including indications that, while the woolly mammoth was already predisposed to life in a cold environment, it continued to make further adaptations throughout its existence.

    Years of research, as well as multiple woolly mammoth specimens, enabled the team to build a better picture of how this species adapted to the cold tundra it called home. Perhaps most significantly, they included a genome they had previously sequenced from a woolly mammoth that lived 700,000 years ago, around the time its species initially branched off from other types of mammoth. Ultimately, the team compared that to a remarkable 51 genomes—16 of which are new woolly mammoth genomes: the aforementioned genome from Chukochya, 22 woolly mammoth genomes from the Late Quaternary, one genome of an American mastodon (a relative of mammoths), and 28 genomes from extant Asian and African elephants.

    From that dataset, they were able to find more than 3,000 genes specific to the woolly mammoth. And from there, they focused on genes where all the woolly mammoths carried sequences that altered the protein compared to the version found in their relatives. In other words, genes where changes appear to have been naturally selected.

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      Beethoven’s genome, sequenced for first time, yields clues on cause of death / ArsTechnica · Wednesday, 22 March, 2023 - 16:35 · 1 minute

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

    Enlarge / Portrait of Beethoven by Joseph Karl Stieler, 1820 (credit: Beethoven-Haus Bonn)

    Ludwig van Beethoven is one of the greatest composers of all time, but he was plagued throughout his life by myriad health problems, most notably going mostly deaf by 1818. 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.

    Nearly two centuries after the composer's demise, scientists say they have sequenced his genome based on preserved locks of hair. While the analysis of that genome failed to pinpoint a definitive cause of Beethoven's hearing loss or chronic digestive problems, he did have numerous risk factors for liver disease and was infected with hepatitis B, according to a new paper published in the journal Current Biology. The researchers also found genetic evidence that somewhere in the Beethoven paternal line, an ancestor had an extramarital affair.

    “We cannot say definitely what killed Beethoven, but we can now at least confirm the presence of significant heritable risk and an infection with hepatitis B virus,” said co-author Johannes Krause , an expert in ancient DNA at the Max Planck Institute of Evolutionary Anthropology. “We can also eliminate several other less plausible genetic causes.” The fully sequenced genome will be made publicly available so other researchers can have access to conduct future studies.

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      National Academies: We can’t define “race,” so stop using it in science / ArsTechnica · Wednesday, 15 March, 2023 - 22:50

    Image of two women's eyes.

    Enlarge (credit: National Academies of Science )

    With the advent of genomic studies, it's become ever more clear that humanity's genetic history is one of churn. Populations migrated, intermingled, and fragmented wherever they went, leaving us with a tangled genetic legacy that we often struggle to understand. The environment—in the form of disease, diet, and technology—also played a critical role in shaping populations.

    But this understanding is frequently at odds with the popular understanding, which often views genetics as a determinative factor and, far too often, interprets genetics in terms of race . Worse still, even though race cannot be defined or quantified scientifically, popular thinking creeps back into scientific thought, shaping the sort of research we do and how we interpret the results.

    Those are some of the conclusions of a new report produced by the National Academies of Science. Done at the request of the National Institutes of Health (NIH), the report calls for scientists and the agencies that fund them to stop thinking of genetics in terms of race, and instead to focus on things that can be determined scientifically.

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      Million-year-old mammoth DNA rewrites animal’s evolutionary tree

      John Timmer · / ArsTechnica · Wednesday, 17 February, 2021 - 18:10 · 1 minute

    Image of a fractured, white post partially embedded in the soil.

    Enlarge / A mammoth tusk thaws out of the ground in Siberia.

    Ancient DNA has revolutionized how we understand human evolution, revealing how populations moved and interacted and introducing us to relatives like the Denisovans, a "ghost lineage" that we wouldn't realize existed if it weren't for discovering their DNA. But humans aren't the only ones who have left DNA behind in their bones, and the same analyses that worked for humans can work for any other group of species.

    Today, the mammoths take their turn in the spotlight, helped by what appears to be the oldest DNA ever sequenced. DNA from three ancient molars, one likely to be over a million years old, has revealed that there is a ghost lineage of mammoths that interbred with distant relatives to produce the North American mammoth population.

    Dating and the mammoth family tree

    Mammoths share something with humans: like us, they started as an African population but spread across much of the planet. Having spread out much earlier, mammoth populations spent enough time separated from each other to form different species. After branching off from elephants, the mammoths first split into what are called southern and steppe species. Later still, adaptations to ice age climates produced the woolly mammoth and its close relative, the North American mammoth, called the Columbian mammoth. All of those species, however, are extinct, and the only living relatives are the elephants.

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