Are you keeping your backups too?
March 23, 2005 3:59 AM Subscribe
(A)bort, (I)gnore, (R)evert to Grandma's DNA A jaw-dropping revision to Mendelian inheritance: bad genes can be replaced from a secret ancestral stash. (The same researchers have previously mentioned other ways to get around Mendel.) Also, DNA gets a fake fifth letter.
As a biologist, let me just say: What. The. Fuck. Arabidopsis???
This will certainly make things interesting the next time I teach genetics.
posted by caution live frogs at 5:47 AM on March 23, 2005
This will certainly make things interesting the next time I teach genetics.
posted by caution live frogs at 5:47 AM on March 23, 2005
I don't quite buy it.
I can imagine how this could be a (very small) hotspot for reversion, and there is some developmental selection for that particular reversion. They note that there isn't an occurence of silent mutations around the reverted base, but what if that whole region is highly sensitive to mutation? Then you'd be selecting against events that didn't specifically cause the reversion.
and
IF THEY THINK IT HAS AN RNA TEMPLATE, WHY DIDN'T THEY TRY TO BLOT FOR THAT RNA
maybe I'm being hasty here. Someone explain it to me.
Here's the online paper, by the way
posted by rxrfrx at 6:17 AM on March 23, 2005
I can imagine how this could be a (very small) hotspot for reversion, and there is some developmental selection for that particular reversion. They note that there isn't an occurence of silent mutations around the reverted base, but what if that whole region is highly sensitive to mutation? Then you'd be selecting against events that didn't specifically cause the reversion.
and
IF THEY THINK IT HAS AN RNA TEMPLATE, WHY DIDN'T THEY TRY TO BLOT FOR THAT RNA
maybe I'm being hasty here. Someone explain it to me.
Here's the online paper, by the way
posted by rxrfrx at 6:17 AM on March 23, 2005
Wouldn't the plant using the gene "backup" not also end up with a greater susceptibility to mutate in the same way as its parent though?
posted by clevershark at 6:23 AM on March 23, 2005
posted by clevershark at 6:23 AM on March 23, 2005
er, I meant "as great a susceptibility", not "greater"...
posted by clevershark at 6:24 AM on March 23, 2005
posted by clevershark at 6:24 AM on March 23, 2005
There's probably more going on than a simple RNA backup. Either that or our understanding of the relative lack of stability of RNA is way off. Either one works for me.
I love the way an editor at Nature describes backup RNA as "the least mad" hypothesis to explain the discovery. I'm just sitting here waiting for someone to demonstrate the occasional inheritence of acquired traits next.
posted by mediareport at 6:28 AM on March 23, 2005
I love the way an editor at Nature describes backup RNA as "the least mad" hypothesis to explain the discovery. I'm just sitting here waiting for someone to demonstrate the occasional inheritence of acquired traits next.
posted by mediareport at 6:28 AM on March 23, 2005
mediareport writes "I'm just sitting here waiting for someone to demonstrate the occasional inheritence [sic] of acquired traits next."
Depending on how you're willing to define "trait", see this from the first link in the post: "Imprinting, an odd feature of inheritance of which Dr. Haig is a leading student, involves inherited changes to the way certain genes are activated, not to the genes themselves."
posted by orthogonality at 6:34 AM on March 23, 2005
Depending on how you're willing to define "trait", see this from the first link in the post: "Imprinting, an odd feature of inheritance of which Dr. Haig is a leading student, involves inherited changes to the way certain genes are activated, not to the genes themselves."
posted by orthogonality at 6:34 AM on March 23, 2005
[sic]
I keep telling myself it's not worth posting just to correct a misspelling, but dammit it still bugs the shit out of me when I do it.
posted by mediareport at 6:37 AM on March 23, 2005
I keep telling myself it's not worth posting just to correct a misspelling, but dammit it still bugs the shit out of me when I do it.
posted by mediareport at 6:37 AM on March 23, 2005
Excellent post...with good followup links. Kudos.
The 2003 abstract (abstract #34 btw) suggests that the team had known about the mutation-fixing properties of Arabidopsis (cress family) for some time. I suppose Nature published the Pruitt/Lolle findings in only 6 weeks because the gist of the findings had been in the scientific community for these last couple of years and had been publically vetted.
I guess I'm not surprised to learn of a radical DNA integrity system being found in plants. Between their nuclear genetic material, plastids (organelles such as chloroplasts) and mitochondria (both of which have their own genetic material) as well as contributions and exchanges from viruses, I've always found plant molecular biology to be more complex than animals.
I note they think that there may be some as yet undiscovered RNA species in Arabidopsis which will have provided the template for this new genetic integrity system. (I agree with mediareport: goes against the normally easily degraded/unstable nature of RNA)
Personally, I've always been fascinated by the idea of prions: non-genetic infectious proteins said to cause madcow disease. Could there be a hidden protein in the Arabidopsis cells that is the bona fide product from the wildtype Hothead gene? With no accepted accounting for the Arabidopsis phenomenon established, I'm claiming copyright on a proteinous product being reverse scripted into a polymerase integrity system.
posted by peacay at 6:51 AM on March 23, 2005
The 2003 abstract (abstract #34 btw) suggests that the team had known about the mutation-fixing properties of Arabidopsis (cress family) for some time. I suppose Nature published the Pruitt/Lolle findings in only 6 weeks because the gist of the findings had been in the scientific community for these last couple of years and had been publically vetted.
I guess I'm not surprised to learn of a radical DNA integrity system being found in plants. Between their nuclear genetic material, plastids (organelles such as chloroplasts) and mitochondria (both of which have their own genetic material) as well as contributions and exchanges from viruses, I've always found plant molecular biology to be more complex than animals.
I note they think that there may be some as yet undiscovered RNA species in Arabidopsis which will have provided the template for this new genetic integrity system. (I agree with mediareport: goes against the normally easily degraded/unstable nature of RNA)
Personally, I've always been fascinated by the idea of prions: non-genetic infectious proteins said to cause madcow disease. Could there be a hidden protein in the Arabidopsis cells that is the bona fide product from the wildtype Hothead gene? With no accepted accounting for the Arabidopsis phenomenon established, I'm claiming copyright on a proteinous product being reverse scripted into a polymerase integrity system.
posted by peacay at 6:51 AM on March 23, 2005
My problem with that is: Where in the cell do you store previous generations worth of RNA? Obviously that's a large amount of RNA to store (if it is RNA....). I find the logicstics of this hard to imagine. It's not like there's a lot of free spce inside a cell. So would it be in the nucleolus? That's full of RNA but I can't imagine storing a whole other genome's worth of info inside something that is already in the nucleus (which is already packed full of a genome's worth of DNA). I'm having a "space" issue.
I'm not sure I believe those results. I'm gonna bet that rxrfrx's theory is correct and the HOTHEAD gene is in a highly unstable area of the genome.
posted by LunaticFringe at 6:59 AM on March 23, 2005
I'm not sure I believe those results. I'm gonna bet that rxrfrx's theory is correct and the HOTHEAD gene is in a highly unstable area of the genome.
posted by LunaticFringe at 6:59 AM on March 23, 2005
I agree about the blotting rxrfrx ........ I was thinking about that when I read about their techniques to ensure their experiements were valid.
Seemed like a job for a northern blot or one of its variations.
There are some serious geneticists giving these published findings validity Lunaticfringe/mediareport. Pruitt etc have answered all queries to date. My guess is that the Hothead gene was chosen because it is conserved through generations as a very very stable gene and known NOT to be subject to point mutations.
I can't get through for access to the whole article at Nature. Damn shame.
posted by peacay at 7:08 AM on March 23, 2005
Seemed like a job for a northern blot or one of its variations.
There are some serious geneticists giving these published findings validity Lunaticfringe/mediareport. Pruitt etc have answered all queries to date. My guess is that the Hothead gene was chosen because it is conserved through generations as a very very stable gene and known NOT to be subject to point mutations.
I can't get through for access to the whole article at Nature. Damn shame.
posted by peacay at 7:08 AM on March 23, 2005
LunaticFringe writes "I'm gonna bet that rxrfrx's theory is correct and the HOTHEAD gene is in a highly unstable area of the genome."
Except, they've apparently seen reversion for genes other than Hothead, including genes without other homologous genes in Arabidosis, from which to copy repairs.
So it's not just hothead, and it's not just genes that have a similar copy (like two correct, four pseudogene, and one zeta copy of alpha globin next to each other on chromosome 11 in humans, or the similar run of six various versions of beta globin on chromosome 16, any of which is a close, and depending on the repair required, possibly close enough homologue of another).
So if it's not just that Hothead wiggles back and forth a bit too easily from bad allele to good, and if it's not a copy from a homologous gene, well well well, somebody may have a trip to Sweden to look forward to.
posted by orthogonality at 7:11 AM on March 23, 2005
Except, they've apparently seen reversion for genes other than Hothead, including genes without other homologous genes in Arabidosis, from which to copy repairs.
So it's not just hothead, and it's not just genes that have a similar copy (like two correct, four pseudogene, and one zeta copy of alpha globin next to each other on chromosome 11 in humans, or the similar run of six various versions of beta globin on chromosome 16, any of which is a close, and depending on the repair required, possibly close enough homologue of another).
So if it's not just that Hothead wiggles back and forth a bit too easily from bad allele to good, and if it's not a copy from a homologous gene, well well well, somebody may have a trip to Sweden to look forward to.
posted by orthogonality at 7:11 AM on March 23, 2005
>(I agree with mediareport: goes against the normally easily degraded/unstable nature of RNA)
Mmm, you mean mRNA is quite unstable. There's always other forms that can remain stable if protected by Proteins, like the Ribosome, some small nuclear RNAs in splicing and lots of other itty bitty pieces.
And as far as space goes, if it's transcribed and spliced RNA packaged in some form then there's plenty of space.
The Northern blot is a reasonable idea, and I bet they tried it, but probably had little or no signal.
OK. I go with what rfrxrf says. The presence of silent mutations is a nice giveaway to a mechanism that could include a non-template directed event. If it's a direct copy of the RNA *somehow* stored in the cell, then the error-prone nature of the replication points to something else -- or at least a combination of things.
Anyway, it's all highly sexed-up theory. I'd like to see some Biochemistry here, eventually.
posted by gsb at 7:11 AM on March 23, 2005
Mmm, you mean mRNA is quite unstable. There's always other forms that can remain stable if protected by Proteins, like the Ribosome, some small nuclear RNAs in splicing and lots of other itty bitty pieces.
And as far as space goes, if it's transcribed and spliced RNA packaged in some form then there's plenty of space.
The Northern blot is a reasonable idea, and I bet they tried it, but probably had little or no signal.
OK. I go with what rfrxrf says. The presence of silent mutations is a nice giveaway to a mechanism that could include a non-template directed event. If it's a direct copy of the RNA *somehow* stored in the cell, then the error-prone nature of the replication points to something else -- or at least a combination of things.
Anyway, it's all highly sexed-up theory. I'd like to see some Biochemistry here, eventually.
posted by gsb at 7:11 AM on March 23, 2005
I'm wondering why they only see these reversions (or whatever they're calling them) on a whole-plant scale? Do they discuss the possibility and/or reasons why this mechanism only works during fertilization?
posted by nprigoda at 7:49 AM on March 23, 2005
posted by nprigoda at 7:49 AM on March 23, 2005
nprigoda writes "Do they discuss the possibility and/or reasons why this mechanism only works during fertilization?"
I'm presuming because swapping nucleotides early on means that, after one or a few cells are repaired, the corrected gene is copied to all other cells as part of the normal process of cell division and growth. Correcting a grown plant's entire complement of cells, after development, would be a much much larger undertaking. But what argues against my understanding is the contention that reversion is caused by stress. Stress before the plant has grown beyond a few cells??
There's much here I don't understand -- not that that's anything new for me.
posted by orthogonality at 8:15 AM on March 23, 2005 [1 favorite]
I'm presuming because swapping nucleotides early on means that, after one or a few cells are repaired, the corrected gene is copied to all other cells as part of the normal process of cell division and growth. Correcting a grown plant's entire complement of cells, after development, would be a much much larger undertaking. But what argues against my understanding is the contention that reversion is caused by stress. Stress before the plant has grown beyond a few cells??
There's much here I don't understand -- not that that's anything new for me.
posted by orthogonality at 8:15 AM on March 23, 2005 [1 favorite]
Fascinating stuff. I can't wait to dive into all these links.
posted by blendor at 8:17 AM on March 23, 2005
posted by blendor at 8:17 AM on March 23, 2005
Wow, that's incredible! Great post.
On another note, now I have a great reason to go visit the office of that bio prof I have a crush on. Thanks!
posted by arcticwoman at 8:21 AM on March 23, 2005
On another note, now I have a great reason to go visit the office of that bio prof I have a crush on. Thanks!
posted by arcticwoman at 8:21 AM on March 23, 2005
Mmmm, sorry to barge in again. I've just realized that error-prone replication is entirely possible if the RNA "backup" used some kind of reverse transcriptase, that's kinda radical and fun.
posted by gsb at 8:32 AM on March 23, 2005
posted by gsb at 8:32 AM on March 23, 2005
orthogonality: I guess what I was thinking but not saying out loud was "Why do we only see this on a whole plant level, and not in small pockets of cells in an otherwise mutant plant?"
I could imagine that if this event could happen during any cellular division that we should see some plants with stalks of normal flowers amongst a majority of hothead flowers.
posted by nprigoda at 8:41 AM on March 23, 2005
I could imagine that if this event could happen during any cellular division that we should see some plants with stalks of normal flowers amongst a majority of hothead flowers.
posted by nprigoda at 8:41 AM on March 23, 2005
Oh, and the stress you're trying to think of might be the unique pressures that occurr during the fusion of pollen nucleus and egg nucleus. We're talking genetic stress here, not whole organism stress!
posted by nprigoda at 8:43 AM on March 23, 2005
posted by nprigoda at 8:43 AM on March 23, 2005
I haven't had time to fully read the article, but isn't it more likely that the observed reversion is in a mutational 'hotspot' and the 'unfuxored' version of the sequence is more stable?
Plants tend to polyploidy; maybe the reversion is a swap from another copy? Transposons jumping around?
posted by PurplePorpoise at 8:46 AM on March 23, 2005
Plants tend to polyploidy; maybe the reversion is a swap from another copy? Transposons jumping around?
posted by PurplePorpoise at 8:46 AM on March 23, 2005
PurplePorpoise: The authors discuss your exact concerns. There don't appear to be any related sequences for this gene in the A. thaliana genome. However, they aren't as convincing on the mutational hotspot question, in my opinion.
posted by nprigoda at 8:48 AM on March 23, 2005
posted by nprigoda at 8:48 AM on March 23, 2005
there 's much here i don't understand
ditto here.........and I studied Mol. Biology (albeit a few moons ago)
I presume that the selfpollinating mutant produces mutant diploid seeds which are dormant until planted. Once planted they produce a faulty protein product from the Hothead gene. That product is the stressor. This in turn activates our hidden (?)RNA integrity system to continue off-chromosome transcription/translation.
But it wasn't only the Hothead gene. Others genes reverted to the ancestral type (not sure how this was verified) - so they are hypothesizing that under stress, there is a reversion to a separate genetic system.
So I agree Orthogonality, I can't see how such a system would work if the stressor was introduced after the plant had grown to any extent. I conclude that is at the seed germination stage that this system kicks in [or perhaps as long as the plant hadn't yet produced flowers/leaves?]. Someone explain please if/where I'm wrong.
on prev: polypoloidy doesn't matter: they are selfpollinators so won't have anything but mutant Hothead genes.
posted by peacay at 8:56 AM on March 23, 2005
ditto here.........and I studied Mol. Biology (albeit a few moons ago)
I presume that the selfpollinating mutant produces mutant diploid seeds which are dormant until planted. Once planted they produce a faulty protein product from the Hothead gene. That product is the stressor. This in turn activates our hidden (?)RNA integrity system to continue off-chromosome transcription/translation.
But it wasn't only the Hothead gene. Others genes reverted to the ancestral type (not sure how this was verified) - so they are hypothesizing that under stress, there is a reversion to a separate genetic system.
So I agree Orthogonality, I can't see how such a system would work if the stressor was introduced after the plant had grown to any extent. I conclude that is at the seed germination stage that this system kicks in [or perhaps as long as the plant hadn't yet produced flowers/leaves?]. Someone explain please if/where I'm wrong.
on prev: polypoloidy doesn't matter: they are selfpollinators so won't have anything but mutant Hothead genes.
posted by peacay at 8:56 AM on March 23, 2005
My problem with that is: Where in the cell do you store previous generations worth of RNA? Obviously that's a large amount of RNA to store...I'm having a "space" issue.
I wonder if only expressed, or highly expressed, sequence might be backed up, which would reduce the size considerably. The mechanism wouldn't necessarily need to restrict the backup to the coding region but could also include the neighbouring regulatory regions of the genes.
posted by Turtles all the way down at 10:03 AM on March 23, 2005
I wonder if only expressed, or highly expressed, sequence might be backed up, which would reduce the size considerably. The mechanism wouldn't necessarily need to restrict the backup to the coding region but could also include the neighbouring regulatory regions of the genes.
posted by Turtles all the way down at 10:03 AM on March 23, 2005
This is a great set of links, thanks. I've been more and more interested in evolution and genetics lately, in part because of discussions that both you and I have been involved in here, orthogonality.
I also really like that Pruitt's title is "Associate Professor of Weed Genetics." Childish of me, I know, but I can't help it. hehe
posted by OmieWise at 10:17 AM on March 23, 2005
I also really like that Pruitt's title is "Associate Professor of Weed Genetics." Childish of me, I know, but I can't help it. hehe
posted by OmieWise at 10:17 AM on March 23, 2005
nprigoda writes " PurplePorpoise: The authors discuss your exact concerns. There don't appear to be any related sequences for this gene in the A. thaliana genome. However, they aren't as convincing on the mutational hotspot question, in my opinion."
You seem to have read more in depth than I have been able to (perhaps you have a subscription to Nature? and you probably know more about this sort of thing). If you have a moment, could you give a (suitably dumbed-down for me to follow) overview of the author's claims, for those of us who don't haven't read the actual paper?
posted by orthogonality at 10:20 AM on March 23, 2005
You seem to have read more in depth than I have been able to (perhaps you have a subscription to Nature? and you probably know more about this sort of thing). If you have a moment, could you give a (suitably dumbed-down for me to follow) overview of the author's claims, for those of us who don't haven't read the actual paper?
posted by orthogonality at 10:20 AM on March 23, 2005
OmieWise writes " I also really like that Pruitt's title is 'Associate Professor of Weed Genetics.'"
Duuude. Pruitt is like, sooo mellow. And uh, where'd my cheetos go, because I'm really hungry. (In all seriousness, yeah, it's a fascinating subject all around. And thank you for the Lewontin links in the other thread.)
posted by orthogonality at 10:23 AM on March 23, 2005
Duuude. Pruitt is like, sooo mellow. And uh, where'd my cheetos go, because I'm really hungry. (In all seriousness, yeah, it's a fascinating subject all around. And thank you for the Lewontin links in the other thread.)
posted by orthogonality at 10:23 AM on March 23, 2005
Odd - I can't seem to find the paper - news.nature sez that it's published online in 2004 in the reference but states that it was published this week online; pubmed searches for Pruitt and Lolle returns something from 2003 about HotHead but it's in Plant Journal not Nature - and the link above to the purported article is dead.
nprigoda - lend a hand?
Caution Live Frogs - what do you have against A. thaliana?
posted by PurplePorpoise at 10:34 AM on March 23, 2005
nprigoda - lend a hand?
Caution Live Frogs - what do you have against A. thaliana?
posted by PurplePorpoise at 10:34 AM on March 23, 2005
Okay, I've got the paper in front of me. It's from Nature Vol434 p.505-509.
The authors found several mutations of the hothead locus that appear to revert to normal in the absence of a normal template for error-repair. To evaluate this paper, there are a couple things you need to know about A. thaliana. First, it has a very small genome, and is generally considered to have very little duplicated sequence. The ecotype used in this study is a known diploid (not polyploid). Second, most ecotypes of A. thaliana are capable of self-fertilization and in fact are nearly incapable of cross-fertilization.
The researchers allowed hth/hth plants to self-fertilize and got between 8% and 16% phenotypically normal progeny. Of those, most were HTH/hth genotypically, but a very small proportion were HTH/HTH. Interestingly, they found 11 different mutations (hth-1 to hth-11) of this gene that revert in this way.
To cover the possibility that these revertants were actually contaminants, they actually dissected developing seeds and genotyped the incompletely developed embryos and found the same proportion of revertants as seen in mature progeny.
To determine if these reversions are as a result of an unusually high rate of mutation at this locus, they analyzed the occurrence of silent mutations in these reverted sequences. As they explain: “Given the frequency with which the mutant nucleotide is observed to revert to wild-type and the 1,226 possible silent nucleotide substitutions in the HTH coding sequence, we would expect to see between 49 and 100 other changes […] in the reverted alleles[…]”. What they found instead was that the sequence of the reverted HTH allele exactly matched the parental allele except for the reverted position.
They also searched the genome for a possible duplicate copy of the HTH gene and found no such copy, nor did they find amongst the HOTHEAD-like genes sequence relating to some of the hth mutations.
There’s a lot more interesting stuff in there, but this is the gist of the info you need to evaluate the science. Evaluating the theory to explain the results is another story! Hope this helps!
posted by nprigoda at 11:12 AM on March 23, 2005
The authors found several mutations of the hothead locus that appear to revert to normal in the absence of a normal template for error-repair. To evaluate this paper, there are a couple things you need to know about A. thaliana. First, it has a very small genome, and is generally considered to have very little duplicated sequence. The ecotype used in this study is a known diploid (not polyploid). Second, most ecotypes of A. thaliana are capable of self-fertilization and in fact are nearly incapable of cross-fertilization.
The researchers allowed hth/hth plants to self-fertilize and got between 8% and 16% phenotypically normal progeny. Of those, most were HTH/hth genotypically, but a very small proportion were HTH/HTH. Interestingly, they found 11 different mutations (hth-1 to hth-11) of this gene that revert in this way.
To cover the possibility that these revertants were actually contaminants, they actually dissected developing seeds and genotyped the incompletely developed embryos and found the same proportion of revertants as seen in mature progeny.
To determine if these reversions are as a result of an unusually high rate of mutation at this locus, they analyzed the occurrence of silent mutations in these reverted sequences. As they explain: “Given the frequency with which the mutant nucleotide is observed to revert to wild-type and the 1,226 possible silent nucleotide substitutions in the HTH coding sequence, we would expect to see between 49 and 100 other changes […] in the reverted alleles[…]”. What they found instead was that the sequence of the reverted HTH allele exactly matched the parental allele except for the reverted position.
They also searched the genome for a possible duplicate copy of the HTH gene and found no such copy, nor did they find amongst the HOTHEAD-like genes sequence relating to some of the hth mutations.
There’s a lot more interesting stuff in there, but this is the gist of the info you need to evaluate the science. Evaluating the theory to explain the results is another story! Hope this helps!
posted by nprigoda at 11:12 AM on March 23, 2005
nprigoda writes " Oh, and the stress you're trying to think of might be the unique pressures that occurr [sic] during the fusion of pollen nucleus and egg nucleus. We're talking genetic stress here, not whole organism stress!"
Yeah, but the problem with Hothead is the petals clump together, right? Surely that deleterious effects of that aren't noticed until the plant has developed beyond a single cell? (I guess, shooting totally in the dark here. Pardon me if I'm being, hotheaded in my speculation.)
posted by orthogonality at 11:15 AM on March 23, 2005
Yeah, but the problem with Hothead is the petals clump together, right? Surely that deleterious effects of that aren't noticed until the plant has developed beyond a single cell? (I guess, shooting totally in the dark here. Pardon me if I'm being, hotheaded in my speculation.)
posted by orthogonality at 11:15 AM on March 23, 2005
Another issue I have with the RNA-theory is this: Does arabidopsis express reverse transcriptase? If it does then the RNA->DNA theory will hold but if it doesn't then there is no way for the RNA to be incorporated into the genome.
My friends are all looking at this and we're discussing possible mechanisms for this occurence. (I'm a grad student in a cancer research lab - we know lots about mutation and recombination - we don't know lots about plant mol bio) Our theory is that there are pseudogenes in the genome that are providing the template for the reversion. Not much but its the best we can come up with without more info on Arabidopsis.
posted by LunaticFringe at 11:28 AM on March 23, 2005
My friends are all looking at this and we're discussing possible mechanisms for this occurence. (I'm a grad student in a cancer research lab - we know lots about mutation and recombination - we don't know lots about plant mol bio) Our theory is that there are pseudogenes in the genome that are providing the template for the reversion. Not much but its the best we can come up with without more info on Arabidopsis.
posted by LunaticFringe at 11:28 AM on March 23, 2005
Thanks nprigoda for the volume information.
Scanned it (I feel so guilty) - that RNA is involved is only a postulate; speculation without any hypothesis testing. An interesting hypothesis, but no data to back it up.
It might be interesting to take a look at the sequence in question on an atomic level as well as A. thaliana's polymerase.
An easier experiment would be to put a bunch of point mutations (of the similar kind as in HTH) in another part of the plant's genome. If it reverts, then it lends credence to sequence stability (but doesn't discount 'backup RNA'), if it doesn't, it lends credence to, but still doesn't prove, the 'backup RNA' hypothesis.
A. thaliana has been sequenced for a long time now - I wonder if there are any sequences that have been overlooked (as in with the human genome) because it's a duplicate of another part of the genome....?
posted by PurplePorpoise at 11:59 AM on March 23, 2005
Scanned it (I feel so guilty) - that RNA is involved is only a postulate; speculation without any hypothesis testing. An interesting hypothesis, but no data to back it up.
It might be interesting to take a look at the sequence in question on an atomic level as well as A. thaliana's polymerase.
An easier experiment would be to put a bunch of point mutations (of the similar kind as in HTH) in another part of the plant's genome. If it reverts, then it lends credence to sequence stability (but doesn't discount 'backup RNA'), if it doesn't, it lends credence to, but still doesn't prove, the 'backup RNA' hypothesis.
A. thaliana has been sequenced for a long time now - I wonder if there are any sequences that have been overlooked (as in with the human genome) because it's a duplicate of another part of the genome....?
posted by PurplePorpoise at 11:59 AM on March 23, 2005
Why did it take a generation for them to see this reversion? Were they just not looking for it in the generation that they bred for hth/hth? The same stresses should have been present in the parent generation.
And thanks nprigoda for the gloss.
posted by OmieWise at 1:08 PM on March 23, 2005
And thanks nprigoda for the gloss.
posted by OmieWise at 1:08 PM on March 23, 2005
I really don't think they're talking about the same sort of whole organism stress everyone here is talking about. Genetic stress, or stress on the genome is very different than physiological stress.
I'm glad my summary helped. I did grad work in evolutionary genetics of plants, but I'm working in medical molecular genetics, so it is really cool for me to have a chance to discuss this paper.
It's a really well written paper, and very well designed experiments. I guess it had to be, you only get one shot at a paper like this!
posted by nprigoda at 1:21 PM on March 23, 2005
I'm glad my summary helped. I did grad work in evolutionary genetics of plants, but I'm working in medical molecular genetics, so it is really cool for me to have a chance to discuss this paper.
It's a really well written paper, and very well designed experiments. I guess it had to be, you only get one shot at a paper like this!
posted by nprigoda at 1:21 PM on March 23, 2005
LunaticFringe -- I seem to remember a virology prof mentioning that there was evidence of native reverse transcriptase activity in plants, so the answer could very well be yes...
posted by greatgefilte at 1:26 PM on March 23, 2005
posted by greatgefilte at 1:26 PM on March 23, 2005
nprigoda writes " I really don't think they're talking about the same sort of whole organism stress everyone here is talking about. Genetic stress, or stress on the genome is very different than physiological stress."
I'm willing to accept that, since I'm quite sure I don't know what I'm talking about, but why would that stress be present on the second generation under discussion here, and not the hth/hth generation? Simply because of the existence of that mutation? This might be so basic that I'm even asking the wrong question.
posted by OmieWise at 1:34 PM on March 23, 2005
I'm willing to accept that, since I'm quite sure I don't know what I'm talking about, but why would that stress be present on the second generation under discussion here, and not the hth/hth generation? Simply because of the existence of that mutation? This might be so basic that I'm even asking the wrong question.
posted by OmieWise at 1:34 PM on March 23, 2005
Two armchair theories:
(1) Some mutations are more likely than others, given the typical conditions inside the cell. Notable/persistent genes will often be the product of many likely mutations, a sort of 'local minimum'. Thus any mutation that has a (say) 1% chance of happening may have a (say) 10% chance of fixing itself.
(2) Beneficial viruses, floating about with spare copies of important genes, or just sequences that bias mutations in a certain way, which are either in the environment or lingering in out-of-the-way parts of the cell since reproduction.
posted by gojomo at 1:14 AM on March 24, 2005
(1) Some mutations are more likely than others, given the typical conditions inside the cell. Notable/persistent genes will often be the product of many likely mutations, a sort of 'local minimum'. Thus any mutation that has a (say) 1% chance of happening may have a (say) 10% chance of fixing itself.
(2) Beneficial viruses, floating about with spare copies of important genes, or just sequences that bias mutations in a certain way, which are either in the environment or lingering in out-of-the-way parts of the cell since reproduction.
posted by gojomo at 1:14 AM on March 24, 2005
Since no one's mentioned the bdelliod rotifers, I'd like to pimp this page's flash animation (scroll down) again.
If the reproductive mechanism the flash animation presents is accurate, there's a subtle but fascinating detail in it that underscores the interrelation of life on earth, by the conservation by evolution of unnecessary details. The human coccyx demonstrates that we are descended from other vertebrates, because like all vertebrates we have a tail that extends past the anus. The the human "blind-spot" underscores both the unplanned construction of eyes cones with nerves that counter-productively exit forward rather than back and that our eyes evolved separately from, for instance, the eyes of octopuses (which sensibly exit the nerves from the back, avoiding any blind spot).
Like these examples, the little detail in the flash (again, if accurate) implies that, rather than having been asexual throughout its entire evolutionary history, the bdelloid rotifer has an ancestor that reproduced sexually.
Take a look at the flash animation, and see if you see it too. Your reward is that beautiful sensation of "aha!"
posted by orthogonality at 3:18 AM on March 24, 2005
If the reproductive mechanism the flash animation presents is accurate, there's a subtle but fascinating detail in it that underscores the interrelation of life on earth, by the conservation by evolution of unnecessary details. The human coccyx demonstrates that we are descended from other vertebrates, because like all vertebrates we have a tail that extends past the anus. The the human "blind-spot" underscores both the unplanned construction of eyes cones with nerves that counter-productively exit forward rather than back and that our eyes evolved separately from, for instance, the eyes of octopuses (which sensibly exit the nerves from the back, avoiding any blind spot).
Like these examples, the little detail in the flash (again, if accurate) implies that, rather than having been asexual throughout its entire evolutionary history, the bdelloid rotifer has an ancestor that reproduced sexually.
Take a look at the flash animation, and see if you see it too. Your reward is that beautiful sensation of "aha!"
posted by orthogonality at 3:18 AM on March 24, 2005
roti's just remind me that some of us have kept up sexual reproduction coz we like it.
posted by peacay at 7:00 AM on March 24, 2005
posted by peacay at 7:00 AM on March 24, 2005
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posted by orthogonality at 4:28 AM on March 23, 2005