Mar 18, 2021 06:50 PM
(This post was last modified: Mar 18, 2021 06:58 PM by C C.)
Why does DNA spontaneously mutate? Quantum physics might explain.
https://www.livescience.com/quantum-phys...tions.html
INTRO: Quantum mechanics, which rules the world of the teensy-tiny, may help explain why genetic mutations spontaneously crop up in DNA as it makes copies of itself, a recent study suggests. Quantum mechanics describes the strange rules that govern atoms and their subatomic components. When the rules of classical physics, which describe the big world, break down, quantum comes in to explain. In the case of DNA, classical physics offers one explanation for why changes can suddenly appear in a single rung of the spiraling ladder of DNA, resulting in what's called a point mutation.
In a recent study, published Jan. 29 in the journal Physical Chemistry Chemical Physics, researchers explore another explanation, showing that a quantum phenomenon called proton tunneling can cause point mutations by allowing positively charged protons in DNA to leap from place-to-place. This, in turn, can subtly change the hydrogen bridges that bind the two sides of DNA's double helix, which can lead to errors when it's time for DNA to make copies of itself.
In particular, this subtle change can potentially cause misprints in the DNA sequence, where the wrong "letters" get paired together as the strand replicates, the study authors note. These letters, known as bases, usually pair up in a certain way: A to T and G to C. But proton tunneling could cause some bases to mix-and-match.
"There has been quite a lot of computational work looking at hydrogen bonding [and] proton transfer in DNA base pairs," said Sam Hay, a professor of computational and theoretical chemistry at the University of Manchester, who was not involved in the study. "This paper uses quite high-level calculations to reexamine this phenomenon," he told Live Science in an email.
However, due to the calculations used, the authors could model only small portions of a DNA strand, at the level of single bases and base pairs. That means the model doesn't include the two sides of the DNA double-helix, nor the pairs located elsewhere in the strand, Hay noted. These nearby structures may have a "significant effect" on how proton tunneling unfolds, but to model the entire DNA strand would have required an enormous amount of computational power, he said.
"We may have to wait until computing power or methodology improves further before this can be addressed," he said... (MORE)
How microbes in permafrost could trigger a massive carbon bomb
https://www.nature.com/articles/d41586-021-00659-y
EXCERPTS: Several decades ago, Stordalen Mire was covered in permafrost. But today, thanks to rising global temperatures, most of it has degraded into a patchwork of bogs and grassy wetlands, leaving behind raised mounds known as palsas, in which permafrost remains partially insulated by dry peat. As the palsas continue to thaw, scientists are eager to document changes to the microbial communities within.
For most of human history, permafrost has been Earth’s largest terrestrial carbon sink, trapping plant and animal material in its frozen layers for centuries. It currently stores about 1,600 billion tonnes of carbon — more than twice the amount in the atmosphere today. But thanks to rising temperatures, permafrost is fracturing and disappearing, leaving behind dramatic changes in the landscape (see ‘The big thaw’).
[...] Scientists are becoming increasingly worried that the thaw will lead to an epic feast for bacteria and archaea that produce carbon dioxide and methane. And although climate models have long accounted for the carbon-emitting capacity of Arctic permafrost and Arctic lakes, the microbial activity within has largely been treated as a black box, changing in sync with the physical properties of the ecosystem, including temperature and moisture. That’s a problem, says Carmody McCalley, a biogeochemist at the Rochester Institute of Technology in New York. “If your model doesn’t get the mechanism right, it’s probably not going to do a great job of making predictions,” she says.
[...] Relating the observations at Stordalen Mire and a few other research sites around the Arctic to permafrost carbon stores elsewhere will not be straightforward. The size, variety and remoteness of these landscapes pose a challenge for scientists. In fact, it is estimated that almost one-third of all Arctic research has been conducted within 50 kilometres of just two sites — Abisko and Toolik Lake in the North Slope. Mark Waldrop, a microbial ecologist at the US Geological Survey in Menlo Park, California, has spent more than a decade studying the Alaskan permafrost, and thinks there is a lot of value in learning how the microbiology there works at local and regional scales, but he points out that there are still many unknowns about what will happen to different permafrost habitats as they thaw across the Arctic. To combat this sampling bias, he is working with NASA to amass the largest pan-Arctic database of permafrost microbe samples. Waldrop is excited about using this database to study under-sampled regions of the Arctic.
[...] researchers at the Abisko research station showed that, as microbes thaw and awaken, the presence of iron in the soil could actually hasten the release of carbon dioxide.
Going forward [... there is interest...] in studying the viruses that infect many of these soil microbes and unpicking their role in carbon processing. Some viruses will kill off their hosts, altering the balance of microbes in the community. Others contain auxiliary metabolic genes that encode proteins that will release carbon locked up in plant matter. “It’s not a normal thing that you would expect a virus to do well, and we have a lot of unpublished data showing that they can do a lot more than that, potentially,” she says.
As temperatures rise in the Northern Hemisphere, scientists are preparing to return to the Arctic research sites... (MORE - details)
https://www.livescience.com/quantum-phys...tions.html
INTRO: Quantum mechanics, which rules the world of the teensy-tiny, may help explain why genetic mutations spontaneously crop up in DNA as it makes copies of itself, a recent study suggests. Quantum mechanics describes the strange rules that govern atoms and their subatomic components. When the rules of classical physics, which describe the big world, break down, quantum comes in to explain. In the case of DNA, classical physics offers one explanation for why changes can suddenly appear in a single rung of the spiraling ladder of DNA, resulting in what's called a point mutation.
In a recent study, published Jan. 29 in the journal Physical Chemistry Chemical Physics, researchers explore another explanation, showing that a quantum phenomenon called proton tunneling can cause point mutations by allowing positively charged protons in DNA to leap from place-to-place. This, in turn, can subtly change the hydrogen bridges that bind the two sides of DNA's double helix, which can lead to errors when it's time for DNA to make copies of itself.
In particular, this subtle change can potentially cause misprints in the DNA sequence, where the wrong "letters" get paired together as the strand replicates, the study authors note. These letters, known as bases, usually pair up in a certain way: A to T and G to C. But proton tunneling could cause some bases to mix-and-match.
"There has been quite a lot of computational work looking at hydrogen bonding [and] proton transfer in DNA base pairs," said Sam Hay, a professor of computational and theoretical chemistry at the University of Manchester, who was not involved in the study. "This paper uses quite high-level calculations to reexamine this phenomenon," he told Live Science in an email.
However, due to the calculations used, the authors could model only small portions of a DNA strand, at the level of single bases and base pairs. That means the model doesn't include the two sides of the DNA double-helix, nor the pairs located elsewhere in the strand, Hay noted. These nearby structures may have a "significant effect" on how proton tunneling unfolds, but to model the entire DNA strand would have required an enormous amount of computational power, he said.
"We may have to wait until computing power or methodology improves further before this can be addressed," he said... (MORE)
How microbes in permafrost could trigger a massive carbon bomb
https://www.nature.com/articles/d41586-021-00659-y
EXCERPTS: Several decades ago, Stordalen Mire was covered in permafrost. But today, thanks to rising global temperatures, most of it has degraded into a patchwork of bogs and grassy wetlands, leaving behind raised mounds known as palsas, in which permafrost remains partially insulated by dry peat. As the palsas continue to thaw, scientists are eager to document changes to the microbial communities within.
For most of human history, permafrost has been Earth’s largest terrestrial carbon sink, trapping plant and animal material in its frozen layers for centuries. It currently stores about 1,600 billion tonnes of carbon — more than twice the amount in the atmosphere today. But thanks to rising temperatures, permafrost is fracturing and disappearing, leaving behind dramatic changes in the landscape (see ‘The big thaw’).
[...] Scientists are becoming increasingly worried that the thaw will lead to an epic feast for bacteria and archaea that produce carbon dioxide and methane. And although climate models have long accounted for the carbon-emitting capacity of Arctic permafrost and Arctic lakes, the microbial activity within has largely been treated as a black box, changing in sync with the physical properties of the ecosystem, including temperature and moisture. That’s a problem, says Carmody McCalley, a biogeochemist at the Rochester Institute of Technology in New York. “If your model doesn’t get the mechanism right, it’s probably not going to do a great job of making predictions,” she says.
[...] Relating the observations at Stordalen Mire and a few other research sites around the Arctic to permafrost carbon stores elsewhere will not be straightforward. The size, variety and remoteness of these landscapes pose a challenge for scientists. In fact, it is estimated that almost one-third of all Arctic research has been conducted within 50 kilometres of just two sites — Abisko and Toolik Lake in the North Slope. Mark Waldrop, a microbial ecologist at the US Geological Survey in Menlo Park, California, has spent more than a decade studying the Alaskan permafrost, and thinks there is a lot of value in learning how the microbiology there works at local and regional scales, but he points out that there are still many unknowns about what will happen to different permafrost habitats as they thaw across the Arctic. To combat this sampling bias, he is working with NASA to amass the largest pan-Arctic database of permafrost microbe samples. Waldrop is excited about using this database to study under-sampled regions of the Arctic.
[...] researchers at the Abisko research station showed that, as microbes thaw and awaken, the presence of iron in the soil could actually hasten the release of carbon dioxide.
Going forward [... there is interest...] in studying the viruses that infect many of these soil microbes and unpicking their role in carbon processing. Some viruses will kill off their hosts, altering the balance of microbes in the community. Others contain auxiliary metabolic genes that encode proteins that will release carbon locked up in plant matter. “It’s not a normal thing that you would expect a virus to do well, and we have a lot of unpublished data showing that they can do a lot more than that, potentially,” she says.
As temperatures rise in the Northern Hemisphere, scientists are preparing to return to the Arctic research sites... (MORE - details)