8 ms·

New viruslike entities found in human gut microbes

156 points by drooby 3y ago

abirch 3y ago
It'll be great to learn more about these and see what diseases are associated with them. I still think it's crazy that an anti-fungal drug is very good therapeutic for Multiple Sclerosis: https://en.m.wikipedia.org/wiki/Dimethyl_fumarate https://en.m.wikipedia.org/wiki/Dimethyl_fumarate
- Paul-Craft 3y ago
  Are you lost? You don't seem to have read the same article I just did.
  - abirch 3y ago
    "It’s not yet known whether obelisks affect human health, says Matthew Sullivan, an integrative biologist at Ohio State University" We have no idea what these do. What if they could cause MS? Then drugs could kill these things and prevent MS. Now that we know some cancers are caused by viruses, we've created vaccines to stop the viruses and the cancer.
    - a_gnostic 3y ago
      It is probably best to destroy obelisks, and deny their utility to the Necrontyr.
  - hinkley 3y ago
    We don’t know why human digestion is such a (pun not intended) shitshow right now. There are microbes that don’t culture in agar. There are histamine reactions from allergies. Detergents and rinse agents messing up protective layers. Or maybe the right bacteria are there but they’re sick with a virus and misbehaving. We don’t know. My brain went the same place as GP but without the anecdote. So I suspect did the people who greyed out your reply before I got here.
    - deleted 3y ago
      [deleted]
  - coldtea 3y ago
    Or he just paid attention to it: "It’s not yet known whether obelisks affect human health, says Matthew Sullivan, an integrative biologist at Ohio State University, but they could alter the genetic activity of their bacterial hosts, which in turn could affect human genes." And of course, even if there wasn't an explicit reference to that question, wondering how those new entities might affect our health is 100% compatible with the article.
- panabee 3y ago
  not fungal, but pathogen related: stanford researchers in 2022 identified how epstein-barr virus (EBV) could be one cause of MS. essentially, EBV proteins may mimic a human protein and induce the immune system to mistakenly attack the body’s nerve cells. https://med.stanford.edu/news/all-news/2022/01/epstein-barr-virus-multiple-sclerosis.html https://med.stanford.edu/news/all-news/2022/01/epstein-barr-...
- atombender 3y ago
  Dimethyl fumarate is not an antifungal drug. It's an immunomodulator.
  - abirch 3y ago
    You're correct it's not an antifungal drug, it's a substance used for its antifungal properties. Furniture companies today still use it for that: https://www.leatherusa.org/dimethyl-fumarate-dmf https://www.leatherusa.org/dimethyl-fumarate-dmf you can Google "Dimethyl fumarate furniture". I'm not sure if it's mechanism of action is known. It was originally used to prevent mold on furniture. The Germans notices that treated psoriasis when it was applied topically. After which the swiss(Fumapharm) was noticed that people who took it for psoriasis and had MS, had fewer MS symptoms. https://en.wikipedia.org/wiki/Dimethyl_fumarate https://en.wikipedia.org/wiki/Dimethyl_fumarate ==== https://pubmed.ncbi.nlm.nih.gov/36641891 https://pubmed.ncbi.nlm.nih.gov/36641891 Dimethyl fumarate ameliorates fungal keratitis by limiting fungal growth and inhibiting pyroptosis
j16sdiz 3y ago
This sentence captured my mind: > Scientists still debate whether viruses are alive—they can’t replicate independent of a host cell’s molecules—but there are even simpler “creatures.” We have varies "definition" and "categorization" saying virus is not "alive".. you can see many biologist saying this definition does not capture the essence and need changes... There are published paper for that every few other years. Look like this is what the "AI is sentient" thing going... We will get a textbook definition for sentient AI, but nothing could end that debate.
- Tagbert 3y ago
  People like definitions that have clearly defined boundaries but biology is not like that. There can be a messy continuum between is and is not. Things can match a definition strongly by some measures but miss some that are critical to how other things meet the definition. At best, a definition is a constellation of semi-related characteristic where some organism meet some subset and other meet another subset, but there isn’t a 100% match and may not even be an overlap.
  - yowzadave 3y ago
    > There can be a messy continuum between is and is not. Exactly--concepts like "life" were invented long before we had an inkling of what viruses were...is it surprising that it's not a perfect abstraction for what we find in reality?
  - PeterStuer 3y ago
    I think people have no qualms about fuzzy boundaries or continuities. The problem arises when those get subsequently mapped onto discrete sets with wildly different consequences. My work in computational ontology led me to believe people are fast to come to a conceptual joint agreement in a given model when the outcome is not consequential, but find it nearly impossible to settle when there are strong implications attached to a labeling. Language only works between people that ultimatly want to agree.
    - vjk800 3y ago
fieryskiff17 3y ago
[dead]
dopylitty 3y ago
It’s amazing how RNA pops up everywhere we look. As our tools get better and better we find simpler and simpler RNA based things floating around, apparently being replicated by some chemical or biological processes. It’s hard to see the trillions of other planets in the known universe along with its age and apparently limited chemistry and not imagine how similar RNAs should’ve have popped up over and over again.
- iraqmtpizza 3y ago
  >we find simpler and simpler RNA based things >In the early 20th century, plant pathologists came across viroids >some of the obelisk sequences encoded proteins involved in RNA replication, making them more complex than standard viroids I don't mean to interrupt your narrative but you seem to be getting information from other sources and I was wondering what they are.
- sfjailbird 3y ago
  "Some chemichal or biological processes" seem to always be living cells, isn't it. So any kind of RNA depends on already existing living cells.
  - contravariant 3y ago
    I mean it's a bit more complicated, since ribosomes are themselves mostly made of RNA. Which gives RNA a kind of unique property that it can not only be transcribed into new proteins but also build the machinery to do this transcription. Given a bath of amino acids you can easily use RNA to bootstrap a whole self-replicating system, which is probably what happened by accident at some point.
    - DiffEq 3y ago
      "Probably" - yet the real calculations of probability say it is not going to happen at all, ever. And then when we observe the natural world...lets take things that are alive and then die. Well, are they not essentially a soup of everything one would possibly need for life to arise, even with external energy source from the sun (think road kill as an example)...and yet we know of no instance in which life, by chance formed out of it; all the dead bodies seem to degrade into dirt. Of course if it did happen even once - how would we know as we can't possibly observe all occasions of such things. Anyway - just some thoughts I had on the matter.
atleastoptimal 3y ago
Doesn't this support the theory that viruses are rogue cellular messengers that left their hosts and started a genealogy on their own
- adrian_b 3y ago
  It is possible that some viruses have appeared in this way, though not very likely. A large part of the viruses (if not all) appears to have an ancestor that was significantly further in the past than the common ancestor of all present cellular life forms, so they are much more distantly related to us than any bacteria. While a part of the viral genomes has this distinct origin, many viruses have combined with various pieces of nucleic acids extracted from their hosts, so these can be considered hybrids that include fragments of DNA or RNA of various origins, possibly even human DNA for some.
adrian_b 3y ago
The research paper (preprint): https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1 https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1
lukeschlather 3y ago
I skimmed the paper, and it's interesting that this seems like these were identified purely from scanning public RNA sequencing datasets and then finding things that look like they would make circles. As someone with only a rudimentary understanding of biology and bioinformatics, I'm wondering: * Has anyone experimentally demonstrated that these RNA sequences actually form circles? * Is it possible that these are the result of some reaction in the transcription process? (My understanding of RNA transcription is that we sequentially dump some enzymes into a petri dish, so it seems plausible that we could generate novel DNA/RNA not present in the source.) * Is it possible these are actually ubiquitous, exist in every cell, but we don't have any reliable way to detect them?
- jcims 3y ago
  I can't watch it right now but IIRC this (amazing) video of the life cycle of an HIV viral particle demonstrates an RNA that forms a ring: https://vimeo.com/260291607 https://vimeo.com/260291607
- COGlory 3y ago
  >Is it possible that these are the result of some reaction in the transcription process? (My understanding of RNA transcription is that we sequentially dump some enzymes into a petri dish, so it seems plausible that we could generate novel DNA/RNA not present in the source.) Even if this was plausible, it wouldn't be there at a high enough copy level when using a DNA-dependent RNA polymerase. Let's say the RNA polymerase goes haywire and creates a random string of RNA. Well, you'd just get one exact copy of that string, it'd be unable to use it as a template to duplicate the string, since it requires a DNA template, not an RNA one. A single copy wouldn't be detectable above the noise, and so wouldn't show up in any datasets. (or would be discarded if it did, as noise). >Is it possible these are actually ubiquitous, exist in every cell, but we don't have any reliable way to detect them? There is so much more to the RNA world, especially the RNA virus world, than we realize, because RNA is so hard to work with. Humans secrete enzymes that degrade, and those enzymes are extremely durable and wind up everywhere. Also, RNA is generally not good for DNA processing, so lots of DNA prep kits degrade the RNA intentionally. So the overwhelming majority of nucleic acid work is done with just DNA, and RNA viruses are a huge blind spot. That's not to say no one is doing RNA work, just far fewer.
ycjspjh 3y ago
Are obelisks supposed to be circular? I thought they were like towers or something.
jojobas 3y ago
RNA world is alive and well.

156 points by drooby 3y ago

It'll be great to learn more about these and see what diseases are associated with them. I still think it's crazy that an anti-fungal drug is very good therapeutic for Multiple Sclerosis: https://en.m.wikipedia.org/wiki/Dimethyl_fumarate https://en.m.wikipedia.org/wiki/Dimethyl_fumarate

Paul-Craft 3y ago
Are you lost? You don't seem to have read the same article I just did.
- abirch 3y ago
  "It’s not yet known whether obelisks affect human health, says Matthew Sullivan, an integrative biologist at Ohio State University" We have no idea what these do. What if they could cause MS? Then drugs could kill these things and prevent MS. Now that we know some cancers are caused by viruses, we've created vaccines to stop the viruses and the cancer.
  - a_gnostic 3y ago
    It is probably best to destroy obelisks, and deny their utility to the Necrontyr.
- hinkley 3y ago
  We don’t know why human digestion is such a (pun not intended) shitshow right now. There are microbes that don’t culture in agar. There are histamine reactions from allergies. Detergents and rinse agents messing up protective layers. Or maybe the right bacteria are there but they’re sick with a virus and misbehaving. We don’t know. My brain went the same place as GP but without the anecdote. So I suspect did the people who greyed out your reply before I got here.
  - deleted 3y ago
    [deleted]
- coldtea 3y ago
  Or he just paid attention to it: "It’s not yet known whether obelisks affect human health, says Matthew Sullivan, an integrative biologist at Ohio State University, but they could alter the genetic activity of their bacterial hosts, which in turn could affect human genes." And of course, even if there wasn't an explicit reference to that question, wondering how those new entities might affect our health is 100% compatible with the article.
panabee 3y ago
not fungal, but pathogen related: stanford researchers in 2022 identified how epstein-barr virus (EBV) could be one cause of MS. essentially, EBV proteins may mimic a human protein and induce the immune system to mistakenly attack the body’s nerve cells. https://med.stanford.edu/news/all-news/2022/01/epstein-barr-virus-multiple-sclerosis.html https://med.stanford.edu/news/all-news/2022/01/epstein-barr-...
atombender 3y ago
Dimethyl fumarate is not an antifungal drug. It's an immunomodulator.
- abirch 3y ago
  You're correct it's not an antifungal drug, it's a substance used for its antifungal properties. Furniture companies today still use it for that: https://www.leatherusa.org/dimethyl-fumarate-dmf https://www.leatherusa.org/dimethyl-fumarate-dmf you can Google "Dimethyl fumarate furniture". I'm not sure if it's mechanism of action is known. It was originally used to prevent mold on furniture. The Germans notices that treated psoriasis when it was applied topically. After which the swiss(Fumapharm) was noticed that people who took it for psoriasis and had MS, had fewer MS symptoms. https://en.wikipedia.org/wiki/Dimethyl_fumarate https://en.wikipedia.org/wiki/Dimethyl_fumarate ==== https://pubmed.ncbi.nlm.nih.gov/36641891 https://pubmed.ncbi.nlm.nih.gov/36641891 Dimethyl fumarate ameliorates fungal keratitis by limiting fungal growth and inhibiting pyroptosis

j16sdiz 3y ago

This sentence captured my mind: > Scientists still debate whether viruses are alive—they can’t replicate independent of a host cell’s molecules—but there are even simpler “creatures.” We have varies "definition" and "categorization" saying virus is not "alive".. you can see many biologist saying this definition does not capture the essence and need changes... There are published paper for that every few other years. Look like this is what the "AI is sentient" thing going... We will get a textbook definition for sentient AI, but nothing could end that debate.

Tagbert 3y ago
People like definitions that have clearly defined boundaries but biology is not like that. There can be a messy continuum between is and is not. Things can match a definition strongly by some measures but miss some that are critical to how other things meet the definition. At best, a definition is a constellation of semi-related characteristic where some organism meet some subset and other meet another subset, but there isn’t a 100% match and may not even be an overlap.
- yowzadave 3y ago
  > There can be a messy continuum between is and is not. Exactly--concepts like "life" were invented long before we had an inkling of what viruses were...is it surprising that it's not a perfect abstraction for what we find in reality?
- PeterStuer 3y ago
  I think people have no qualms about fuzzy boundaries or continuities. The problem arises when those get subsequently mapped onto discrete sets with wildly different consequences. My work in computational ontology led me to believe people are fast to come to a conceptual joint agreement in a given model when the outcome is not consequential, but find it nearly impossible to settle when there are strong implications attached to a labeling. Language only works between people that ultimatly want to agree.
  - vjk800 3y ago

fieryskiff17 3y ago

[dead]

dopylitty 3y ago

It’s amazing how RNA pops up everywhere we look. As our tools get better and better we find simpler and simpler RNA based things floating around, apparently being replicated by some chemical or biological processes. It’s hard to see the trillions of other planets in the known universe along with its age and apparently limited chemistry and not imagine how similar RNAs should’ve have popped up over and over again.

iraqmtpizza 3y ago
>we find simpler and simpler RNA based things >In the early 20th century, plant pathologists came across viroids >some of the obelisk sequences encoded proteins involved in RNA replication, making them more complex than standard viroids I don't mean to interrupt your narrative but you seem to be getting information from other sources and I was wondering what they are.
sfjailbird 3y ago
"Some chemichal or biological processes" seem to always be living cells, isn't it. So any kind of RNA depends on already existing living cells.
- contravariant 3y ago
  I mean it's a bit more complicated, since ribosomes are themselves mostly made of RNA. Which gives RNA a kind of unique property that it can not only be transcribed into new proteins but also build the machinery to do this transcription. Given a bath of amino acids you can easily use RNA to bootstrap a whole self-replicating system, which is probably what happened by accident at some point.
  - DiffEq 3y ago
    "Probably" - yet the real calculations of probability say it is not going to happen at all, ever. And then when we observe the natural world...lets take things that are alive and then die. Well, are they not essentially a soup of everything one would possibly need for life to arise, even with external energy source from the sun (think road kill as an example)...and yet we know of no instance in which life, by chance formed out of it; all the dead bodies seem to degrade into dirt. Of course if it did happen even once - how would we know as we can't possibly observe all occasions of such things. Anyway - just some thoughts I had on the matter.

atleastoptimal 3y ago

Doesn't this support the theory that viruses are rogue cellular messengers that left their hosts and started a genealogy on their own

adrian_b 3y ago
It is possible that some viruses have appeared in this way, though not very likely. A large part of the viruses (if not all) appears to have an ancestor that was significantly further in the past than the common ancestor of all present cellular life forms, so they are much more distantly related to us than any bacteria. While a part of the viral genomes has this distinct origin, many viruses have combined with various pieces of nucleic acids extracted from their hosts, so these can be considered hybrids that include fragments of DNA or RNA of various origins, possibly even human DNA for some.

adrian_b 3y ago

The research paper (preprint): https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1 https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1

lukeschlather 3y ago

I skimmed the paper, and it's interesting that this seems like these were identified purely from scanning public RNA sequencing datasets and then finding things that look like they would make circles. As someone with only a rudimentary understanding of biology and bioinformatics, I'm wondering: * Has anyone experimentally demonstrated that these RNA sequences actually form circles? * Is it possible that these are the result of some reaction in the transcription process? (My understanding of RNA transcription is that we sequentially dump some enzymes into a petri dish, so it seems plausible that we could generate novel DNA/RNA not present in the source.) * Is it possible these are actually ubiquitous, exist in every cell, but we don't have any reliable way to detect them?

jcims 3y ago
I can't watch it right now but IIRC this (amazing) video of the life cycle of an HIV viral particle demonstrates an RNA that forms a ring: https://vimeo.com/260291607 https://vimeo.com/260291607
COGlory 3y ago
>Is it possible that these are the result of some reaction in the transcription process? (My understanding of RNA transcription is that we sequentially dump some enzymes into a petri dish, so it seems plausible that we could generate novel DNA/RNA not present in the source.) Even if this was plausible, it wouldn't be there at a high enough copy level when using a DNA-dependent RNA polymerase. Let's say the RNA polymerase goes haywire and creates a random string of RNA. Well, you'd just get one exact copy of that string, it'd be unable to use it as a template to duplicate the string, since it requires a DNA template, not an RNA one. A single copy wouldn't be detectable above the noise, and so wouldn't show up in any datasets. (or would be discarded if it did, as noise). >Is it possible these are actually ubiquitous, exist in every cell, but we don't have any reliable way to detect them? There is so much more to the RNA world, especially the RNA virus world, than we realize, because RNA is so hard to work with. Humans secrete enzymes that degrade, and those enzymes are extremely durable and wind up everywhere. Also, RNA is generally not good for DNA processing, so lots of DNA prep kits degrade the RNA intentionally. So the overwhelming majority of nucleic acid work is done with just DNA, and RNA viruses are a huge blind spot. That's not to say no one is doing RNA work, just far fewer.

ycjspjh 3y ago

Are obelisks supposed to be circular? I thought they were like towers or something.

jojobas 3y ago

RNA world is alive and well.