5 ms·

Ushikuvirus: Newly discovered virus may offer clues to the origin of eukaryotes

131 points by rustoo 9mo ago

Chance-Device 9mo ago
Incidentally, anyone know what is going on with this image - “Cryo-EM map of a center slice of the ushikuvirus particle”: https://journals.asm.org/cms/10.1128/jvi.01206-25/asset/1357dcfc-5856-4bd3-a7f6-f96db6c2bcd4/assets/images/large/jvi.01206-25.f011.jpg https://journals.asm.org/cms/10.1128/jvi.01206-25/asset/1357... It’s one quarter of an image flipped horizontally and then vertically, you can see the patterns. It’s a bit odd to do that? Shouldn’t it just be the original EM image?
- jiggawatts 9mo ago
  Rampant fraud in science papers has reached the point where hobbyists can point out obviously fake charts and graphics even in prestigious journals. Publish or perish needs to end.
  - jibal 9mo ago
    This isn't fraud ... see the informative comments nearby.
- RicoElectrico 9mo ago
  According to this article the image is computed and not really directly captured https://www.chemistryworld.com/news/explainer-what-is-cryo-electron-microscopy/3008091.article https://www.chemistryworld.com/news/explainer-what-is-cryo-e...
- observationist 9mo ago
  https://www.sciencedirect.com/science/article/pii/S104784772100085X https://www.sciencedirect.com/science/article/pii/S104784772... - there are similar results in this paper, too. After a bit of digging - it looks like it's done to sharpen features as one of the standard steps in producing these images. Where there are rotational symmetries in the things they're looking at, they focus on the smallest unit, and then rotate accordingly. If you had a trilateral symmetry, or hexagonal structure, they'd rotate 3 or 6 times around the center. You're not getting a real image of the thing, but apparently it's got data from those other segments mixed in with the rotations, so you're getting a kind of idealized structure, to make the details being studied pop out, but if you have some sort of significant deviation, damage, or non symmetric feature it'll show up as well. It's called "imposed symmetry" https://discuss.cryosparc.com/t/what-is-actually-occuring-when-symmetry-is-imposed/11733 https://discuss.cryosparc.com/t/what-is-actually-occuring-wh... Neat stuff, cool thing to catch!
  - Terr_ 9mo ago
    So kind of like taking a picture of a human, and then taking each half, flipping along the midline, and blending to get an idealized Symmetrical Human?
    - deleted 9mo ago
      [deleted]
    - hnlmorg 9mo ago
      Humans aren’t symmetrical though. This would more like zooming into one edge of a snowflake and then rotating it.
      - Terr_ 9mo ago
        > Humans aren’t symmetrical though. Perhaps you assumed a "radially" which wasn't part of my analogy? :p Land animals have a pretty consistent trend of exterior bilateral symmetry which is very noticeable. (Naturally, a completely normal Hunam such as myself cannot speak for how it may work in places other than my home planet Dirt.)
        hnlmorg 9mo ago
        I understood you meant bilateral symmetry. And yes, there are similarities, but we are not bilaterally symmetric. At least not to the extent where you can flip an image and have that look normal. Even faces look weird when flipped that way (there have been studies on this effect too). And that’s before you get into the issue that it’s common to have differently shaped breasts, different sized hands or feet. Ears shaped differently. Non-uniform teeth. And so on and so forth.
        yencabulator 9mo ago
        Only superficially. https://en.wikipedia.org/wiki/Axial_twist_theory https://en.wikipedia.org/wiki/Axial_twist_theory
- Bjartr 9mo ago
  I think that might just be the original and it simply is symmetrical to that degree. I found a few more examples of "cryo-em center slices" and I've yet to find one that doesn't have really strong symmetry down to the small dot patterns. A different paper, this figure shows a number of cryo-em images, including a simulation, and they all show the same degree of pattern symmetry https://www.researchgate.net/figure/Central-sections-through-cryo-EM-density-maps-of-Fab-labeled-and-control-HBV-capsids_fig2_10583392 https://www.researchgate.net/figure/Central-sections-through... First figure in this third paper also shows symmetry of small patterns https://journals.asm.org/doi/10.1128/jvi.00990-22 https://journals.asm.org/doi/10.1128/jvi.00990-22
  - Chance-Device 9mo ago
    Thanks, those examples make it pretty clear. I still think it’s super weird that it looks exactly like an EM image, but is generated. Anyway, good to know!
possiblelion 9mo ago
Interesting, hope that these discoveries can be used to fight those amoeba's which cause infections as well!
embedding-shape 9mo ago
I remember someone talking about "last universal common ancestor" at some point, the single "origin of the cells" or something. Is that the same as the "archaeal ancestor" they're referring to here? And is the "archaeal ancestor" the same as the "Primitive archael cell" mentioned in the last image in the article? (https://www.tus.ac.jp/en/mediarelations/20251219_9539_03.png https://www.tus.ac.jp/en/mediarelations/20251219_9539_03.png)
- Tagbert 9mo ago
  From what I know - There are two sister groups, the Archae and Bacteria. Their ancestor would be LUCA. The first Archae would be the archaeal ancestor. There should be a first bacteria to match that. I believe that Eukaryotes then from Archae.
  - adrian_b 9mo ago
    For now, it is still not certain whether Archaea is the sister group of all Bacteria, or only of one branch of Bacteria. There are some very important differences between Archaea and Bacteria, in membrane composition and in the nucleic acid replication and protein synthesis mechanisms, but there are several hypotheses about how these differences could have evolved and there is not enough evidence yet to be sure which of them is true, i.e. whether the distinctive membranes, ribosomes and certain enzymes of Archaea have never been like those of Bacteria, or they have evolved from those of Bacteria. The eukaryotes are hybrids, mainly between some Archaea and some bacteria (the ancestors of mitochondria). It is not completely certain whether the ancestor of the eukaryotes from Archaea belonged to a branch that was sister to all still existing Archaea or only of one branch of Archaea, but here the evidence makes it very likely that the ancestor of the eukaryotes belonged to an interior branch that was nested within the existing Archaea, i.e. it was sister to only one branch of the present Archaea. In the history of life, there have been many events of hybridization between very distant living beings, so the tree of evolution is only approximately a tree, while actually being a more general directed graph. A part of these events have been the results of symbiosis, the most frequent cases being of symbiosis with some phototrophic organism able to capture solar light or with some bacteria able to consume some unusual substance from the environment. Other such hybridization events have been with viruses, when the genes for some enzymes have been transferred permanently from viruses to their hosts and they have been retained, presumably for being better than the versions used by the hosts for the same function, previously. Even vertebrates and humans have a small fraction of their genome that originates from viruses.
thangalin 9mo ago
My brief, illustrated history of Microbial Mats (p.10) to Multicellular Eukaryotes (p.13) may be of interest: https://impacts.to/downloads/lowres/impacts.pdf https://impacts.to/downloads/lowres/impacts.pdf
- BitwiseFool 9mo ago
  This is quite well made, thank you for sharing. I appreciate the relevance and knowledge section on each page's subject.
advl343 9mo ago
[dead]
avadodin 9mo ago
We have discovered a new giant DNA virus that may help us fight life-threatening amoebae was good enough.
adityaathalye 9mo ago
Lends a whole other colour to that scene from The Matrix... Agent Smith monologuing at Morpheus bound to the chair. > Agent Smith: I’d like to share a revelation during my time here. It came to me when I tried to classify your species. I realized that you’re not actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment but you humans do not. You move to an area and you multiply and multiply until every natural resource is consumed. The only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus. ref: "Smith Interrogates Morpheus Transcript" https://scottmanning.com/content/smith-interrogates-morpheus-transcript/ https://scottmanning.com/content/smith-interrogates-morpheus... --- Edit: Maybe it takes virulence to colonise the galaxy. A sobering thought.
- Erlangen 9mo ago
  > Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment but you humans do not. Though it's an interesting quote, I have to disagree. The reindeers on St. Matthew Island continued to multiply and depleted their food resources without any predators, until an extreme snow storms struck. They don't "instinctively" develops a natural equilibrium. https://www.adn.com/features/article/what-wiped-out-st-matthew-islands-reindeer/2010/01/17/ https://www.adn.com/features/article/what-wiped-out-st-matth...
  - kakacik 9mo ago
    Yeah 'instincts' are in real world just enough external pressure and death to keep the equilibrium going, whatever grisly happens behind the curtains. Hunters hunt as much as they can. Wolves regularly kill 10 or 20 sheep while eating one if they get the chance. Foxes do similar stuff with chickens. Nature is brutal and without empathy.
    - cestith 9mo ago
      Housecats let outdoors often don’t even eat what they hunt, because they have a steady supply of their favorite food in the house. They just hunt and kill because they are furry little murder machines. They really shouldn’t be let outside unsupervised.

131 points by rustoo 9mo ago

Incidentally, anyone know what is going on with this image - “Cryo-EM map of a center slice of the ushikuvirus particle”: https://journals.asm.org/cms/10.1128/jvi.01206-25/asset/1357dcfc-5856-4bd3-a7f6-f96db6c2bcd4/assets/images/large/jvi.01206-25.f011.jpg https://journals.asm.org/cms/10.1128/jvi.01206-25/asset/1357... It’s one quarter of an image flipped horizontally and then vertically, you can see the patterns. It’s a bit odd to do that? Shouldn’t it just be the original EM image?

jiggawatts 9mo ago
Rampant fraud in science papers has reached the point where hobbyists can point out obviously fake charts and graphics even in prestigious journals. Publish or perish needs to end.
- jibal 9mo ago
  This isn't fraud ... see the informative comments nearby.
RicoElectrico 9mo ago
According to this article the image is computed and not really directly captured https://www.chemistryworld.com/news/explainer-what-is-cryo-electron-microscopy/3008091.article https://www.chemistryworld.com/news/explainer-what-is-cryo-e...
observationist 9mo ago
https://www.sciencedirect.com/science/article/pii/S104784772100085X https://www.sciencedirect.com/science/article/pii/S104784772... - there are similar results in this paper, too. After a bit of digging - it looks like it's done to sharpen features as one of the standard steps in producing these images. Where there are rotational symmetries in the things they're looking at, they focus on the smallest unit, and then rotate accordingly. If you had a trilateral symmetry, or hexagonal structure, they'd rotate 3 or 6 times around the center. You're not getting a real image of the thing, but apparently it's got data from those other segments mixed in with the rotations, so you're getting a kind of idealized structure, to make the details being studied pop out, but if you have some sort of significant deviation, damage, or non symmetric feature it'll show up as well. It's called "imposed symmetry" https://discuss.cryosparc.com/t/what-is-actually-occuring-when-symmetry-is-imposed/11733 https://discuss.cryosparc.com/t/what-is-actually-occuring-wh... Neat stuff, cool thing to catch!
- Terr_ 9mo ago
  So kind of like taking a picture of a human, and then taking each half, flipping along the midline, and blending to get an idealized Symmetrical Human?
  - deleted 9mo ago
    [deleted]
  - hnlmorg 9mo ago
    Humans aren’t symmetrical though. This would more like zooming into one edge of a snowflake and then rotating it.
    - Terr_ 9mo ago
      > Humans aren’t symmetrical though. Perhaps you assumed a "radially" which wasn't part of my analogy? :p Land animals have a pretty consistent trend of exterior bilateral symmetry which is very noticeable. (Naturally, a completely normal Hunam such as myself cannot speak for how it may work in places other than my home planet Dirt.)
      - hnlmorg 9mo ago
        I understood you meant bilateral symmetry. And yes, there are similarities, but we are not bilaterally symmetric. At least not to the extent where you can flip an image and have that look normal. Even faces look weird when flipped that way (there have been studies on this effect too). And that’s before you get into the issue that it’s common to have differently shaped breasts, different sized hands or feet. Ears shaped differently. Non-uniform teeth. And so on and so forth.
      - yencabulator 9mo ago
        Only superficially. https://en.wikipedia.org/wiki/Axial_twist_theory https://en.wikipedia.org/wiki/Axial_twist_theory
Bjartr 9mo ago
I think that might just be the original and it simply is symmetrical to that degree. I found a few more examples of "cryo-em center slices" and I've yet to find one that doesn't have really strong symmetry down to the small dot patterns. A different paper, this figure shows a number of cryo-em images, including a simulation, and they all show the same degree of pattern symmetry https://www.researchgate.net/figure/Central-sections-through-cryo-EM-density-maps-of-Fab-labeled-and-control-HBV-capsids_fig2_10583392 https://www.researchgate.net/figure/Central-sections-through... First figure in this third paper also shows symmetry of small patterns https://journals.asm.org/doi/10.1128/jvi.00990-22 https://journals.asm.org/doi/10.1128/jvi.00990-22
- Chance-Device 9mo ago
  Thanks, those examples make it pretty clear. I still think it’s super weird that it looks exactly like an EM image, but is generated. Anyway, good to know!

possiblelion 9mo ago

Interesting, hope that these discoveries can be used to fight those amoeba's which cause infections as well!

embedding-shape 9mo ago

I remember someone talking about "last universal common ancestor" at some point, the single "origin of the cells" or something. Is that the same as the "archaeal ancestor" they're referring to here? And is the "archaeal ancestor" the same as the "Primitive archael cell" mentioned in the last image in the article? (https://www.tus.ac.jp/en/mediarelations/20251219_9539_03.png https://www.tus.ac.jp/en/mediarelations/20251219_9539_03.png)

Tagbert 9mo ago
From what I know - There are two sister groups, the Archae and Bacteria. Their ancestor would be LUCA. The first Archae would be the archaeal ancestor. There should be a first bacteria to match that. I believe that Eukaryotes then from Archae.
- adrian_b 9mo ago
  For now, it is still not certain whether Archaea is the sister group of all Bacteria, or only of one branch of Bacteria. There are some very important differences between Archaea and Bacteria, in membrane composition and in the nucleic acid replication and protein synthesis mechanisms, but there are several hypotheses about how these differences could have evolved and there is not enough evidence yet to be sure which of them is true, i.e. whether the distinctive membranes, ribosomes and certain enzymes of Archaea have never been like those of Bacteria, or they have evolved from those of Bacteria. The eukaryotes are hybrids, mainly between some Archaea and some bacteria (the ancestors of mitochondria). It is not completely certain whether the ancestor of the eukaryotes from Archaea belonged to a branch that was sister to all still existing Archaea or only of one branch of Archaea, but here the evidence makes it very likely that the ancestor of the eukaryotes belonged to an interior branch that was nested within the existing Archaea, i.e. it was sister to only one branch of the present Archaea. In the history of life, there have been many events of hybridization between very distant living beings, so the tree of evolution is only approximately a tree, while actually being a more general directed graph. A part of these events have been the results of symbiosis, the most frequent cases being of symbiosis with some phototrophic organism able to capture solar light or with some bacteria able to consume some unusual substance from the environment. Other such hybridization events have been with viruses, when the genes for some enzymes have been transferred permanently from viruses to their hosts and they have been retained, presumably for being better than the versions used by the hosts for the same function, previously. Even vertebrates and humans have a small fraction of their genome that originates from viruses.

thangalin 9mo ago

My brief, illustrated history of Microbial Mats (p.10) to Multicellular Eukaryotes (p.13) may be of interest: https://impacts.to/downloads/lowres/impacts.pdf https://impacts.to/downloads/lowres/impacts.pdf

BitwiseFool 9mo ago
This is quite well made, thank you for sharing. I appreciate the relevance and knowledge section on each page's subject.

advl343 9mo ago

[dead]

avadodin 9mo ago

We have discovered a new giant DNA virus that may help us fight life-threatening amoebae was good enough.

adityaathalye 9mo ago

Lends a whole other colour to that scene from The Matrix... Agent Smith monologuing at Morpheus bound to the chair. > Agent Smith: I’d like to share a revelation during my time here. It came to me when I tried to classify your species. I realized that you’re not actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment but you humans do not. You move to an area and you multiply and multiply until every natural resource is consumed. The only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus. ref: "Smith Interrogates Morpheus Transcript" https://scottmanning.com/content/smith-interrogates-morpheus-transcript/ https://scottmanning.com/content/smith-interrogates-morpheus... --- Edit: Maybe it takes virulence to colonise the galaxy. A sobering thought.

Erlangen 9mo ago
> Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment but you humans do not. Though it's an interesting quote, I have to disagree. The reindeers on St. Matthew Island continued to multiply and depleted their food resources without any predators, until an extreme snow storms struck. They don't "instinctively" develops a natural equilibrium. https://www.adn.com/features/article/what-wiped-out-st-matthew-islands-reindeer/2010/01/17/ https://www.adn.com/features/article/what-wiped-out-st-matth...
- kakacik 9mo ago
  Yeah 'instincts' are in real world just enough external pressure and death to keep the equilibrium going, whatever grisly happens behind the curtains. Hunters hunt as much as they can. Wolves regularly kill 10 or 20 sheep while eating one if they get the chance. Foxes do similar stuff with chickens. Nature is brutal and without empathy.
  - cestith 9mo ago
    Housecats let outdoors often don’t even eat what they hunt, because they have a steady supply of their favorite food in the house. They just hunt and kill because they are furry little murder machines. They really shouldn’t be let outside unsupervised.