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Genome of Controversial Arsenic Bacterium Sequenced

timothy posted more than 2 years ago | from the there's-gotta-be-some-arsenic-somewhere dept.

NASA 56

Med-trump writes "One year ago a media controversy was ignited when Felisa Wolfe-Simon and her colleagues held a press conference to announce the discovery of a bacterium that not only survived high levels of arsenic in its environment but also seemed to use that element in its DNA. Last week, the genome of the bacterium, known as GFAJ-1, which gets its name from the acronym for 'Give Felisa a Job.' (No joke!), was posted in Genbank, the public repository of DNA sequences for all who care to take a look. But it doesn't settle the debate over whether arsenic is used in DNA."

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Shouldn't it be fairly simple to determine that? (0)

bobwrit (1232148) | more than 2 years ago | (#38303670)

Two words: Mass Spectrometry. Back in High School, I remember when I took a class in genetics, and we had actively extracted DNA from cell's(both human and wheat). Considering that it is fairly simple to do that(just the right chemicals), you can then take the DNA, and run it through a mass spectrometer. Based off of the relative amounts of Arsenic vs the rest of the bacterium, you can determine if there is Arsenic in its genome or not... It seems sort of ridiculous that there is a debate over it.

Re:Shouldn't it be fairly simple to determine that (5, Insightful)

quarterbuck (1268694) | more than 2 years ago | (#38303708)

Not enough in this case.
They know that this bacteria lives in an environment of Arsenic and may use it in its cell process. So any Spectrometric study will show Arsenic as contamination. Even if you clean up for that, there might be bits of Arsenic stuck in the DNA, but which do not do anything. I believe what they are trying to do is to see if Arsenic is a "functional" part of DNA. ie would the DNA without Arsenic be the same as arsenic without it.

Re:Shouldn't it be fairly simple to determine that (1)

captainkoloth (99341) | more than 2 years ago | (#38303780)

Indeed. How much of Human DNA is actually useful? How mUch is just aking up space?

Re:Shouldn't it be fairly simple to determine that (1)

Anonymous Coward | more than 2 years ago | (#38303864)

More than you think. Most of that "junk" dna serves additional purposes that we have only started realizing. Sometimes it is just filler, which is great and allows for genetic flexibility. Sometimes it is used in creation of the immune system, even if it is normally inactive.

Re:Shouldn't it be fairly simple to determine that (-1)

Anonymous Coward | more than 2 years ago | (#38304836)

Exactly. There's so much more to explore in the complexity of inner space than the simplicity of outer space. Oh look, another dead rock.

Re:Shouldn't it be fairly simple to determine that (5, Interesting)

Anonymous Coward | more than 2 years ago | (#38304408)

Mass spectrometry using ESI ionisation should be able to detect DNA bases with arsenium replacing phosphor in the 5' phosphoester bound to ribose. It should be trivial to distinguish free arsenic from incorporated arsenic.

Re:Shouldn't it be fairly simple to determine that (1)

Anonymous Coward | more than 2 years ago | (#38304934)

Enhance!

Re:Shouldn't it be fairly simple to determine that (0)

Anonymous Coward | more than 2 years ago | (#38306524)

Why ESI specifically? Couldn't you use MALDI or any other ionization method? (Just curious...)

Re:Shouldn't it be fairly simple to determine that (0)

Anonymous Coward | more than 2 years ago | (#38312300)

MALDI will not fragment the DNA. Optimal ionisation protocol should break down the DNA into fragments with masses in the range of several thousands Da. But they may opt to fragment the DNA with an enzyme or a chemical agent before MS analysis, and then MALDI might be a better option.

In any case, free aresenic (As2O5?) will have a mass 1-2 orders of magnitude smaller than the DNA fragments. Under such conditions the m/z values should allow to conclude if arsenic is incorporated, possibly even the ratio to phosphor. My background is biochemistry, don't really know the less common ionisation methods. Someone from the physical chemistry field may be more helpful.

Re:Shouldn't it be fairly simple to determine that (0)

Anonymous Coward | more than 2 years ago | (#38336374)

Mass spectrometry using ESI ionisation should be able to detect DNA bases with arsenium replacing phosphor in the 5' phosphoester bound to ribose. It should be trivial to distinguish free arsenic from incorporated arsenic.

Yeah, but preparing samples for ESI while unequivocally *not* altering it substantially seems impossible currently.

Re:Shouldn't it be fairly simple to determine that (5, Informative)

Hatta (162192) | more than 2 years ago | (#38304824)

They know that this bacteria lives in an environment of Arsenic and may use it in its cell process. So any Spectrometric study will show Arsenic as contamination.

What matters is whether the arsenic is covalently bound to functional groups like adenosine, which mass spectrometry is able to detect.

Re:Shouldn't it be fairly simple to determine that (4, Insightful)

osu-neko (2604) | more than 2 years ago | (#38304274)

Two words: Mass Spectrometry [...] It seems sort of ridiculous that there is a debate over it.

OMG, how is it they never thought of this?! /sarcasm

Why is it the stupider someone is, the most certain they are other people are overlooking "the obvious"? I can understand not knowing the details of why a particular idea wouldn't work, but how oblivious to your own ignorance do you have to be to figure that when the experts aren't using a particular idea, it can't be there are reasons it won't work that you aren't aware of, and rather you instead come to the conclusion that the experts understand their own field less well than you do based on what you learned "Back in High School"? The mind boggles...

Re:Shouldn't it be fairly simple to determine that (5, Insightful)

networkBoy (774728) | more than 2 years ago | (#38304740)

The counterpoint of this is that if *everyone* assumed someone smarter than them was already "on it", then the forward progress of our society would grind to a halt.
Calling someone out on it is counter productive because it discourages asking questions, thus making you simply a troll.
Science is all about asking questions. In fact I learned something because of their question. It is something that had I thought about it I likely could have come up with the answer, but having it elucidated for me was helpful, and that was about not being able to tell (and ways you could possibly tell) whether the arsenic was merely sticking to the DNA strand, or if it was actually in place of the phosphorous.

Remember the greatest discoveries are not usually preceded by "eureka!", but rahter "hmmm... that's funny".
-nB

Re:Shouldn't it be fairly simple to determine that (0)

Anonymous Coward | more than 2 years ago | (#38307414)

Science is about asking questions and challenging results. I think the issue here is not the challenge itself, but the attitude and form of challenge. There is a big difference between asking why something wasn't used versus saying something is so obviously trivial that the only reason scientist didn't do it was stupidity. The post at the top of the thread here is pretty mild, but could be read by some as having that attitude issue. There certainly enough other, more extreme cases to embitter people over the problem though.

Re:Shouldn't it be fairly simple to determine that (3, Informative)

neonKow (1239288) | more than 2 years ago | (#38304438)

It seems like someone is trying to do exactly that:
http://cosmiclog.msnbc.msn.com/_news/2011/12/02/9168255-arsenic-life-debate-still-percolates [msn.com]

Correct me if I'm wrong, but the linked article seems to suggest that the problem has been that no one else has tried to replicate the experiment until now.

Re:Shouldn't it be fairly simple to determine that (3, Informative)

geekoid (135745) | more than 2 years ago | (#38304664)

If only they had thought of that~

"Redfield has sent purified DNA samples to collaborators at Princeton University for mass spectrometry analysis — to see whether any arsenic was really taken up into the molecular structure. "We just got the DNA from Rosie Redfield," one of those collaborators, Leonid Kruglyak, told me this week. A graduate student in Kruglyak's lab, Marshall Louis Reaves, is currently working out the protocols for analyzing the DNA."

Re:Shouldn't it be fairly simple to determine that (0)

Anonymous Coward | more than 2 years ago | (#38310234)

Yes, the point is the original authors on the paper didn't think of that.

Rosie is not an author on the original paper. Actually, she was one of the first to do a very in-depth critique on the original paper.

Of course it isn't a joke (4, Informative)

ByOhTek (1181381) | more than 2 years ago | (#38303678)

We geneticists come up with some of the most goofy names for genes.

Smaug is a fun one.
So is "MADD", which stands for "Mothers Against Dumpy Drosophela"

Re:Of course it isn't a joke (3, Informative)

jinushaun (397145) | more than 2 years ago | (#38303774)

Don't forgot Sonic Hedgehog (SHH), an important protein used in development.

Re:Of course it isn't a joke (4, Interesting)

Guppy (12314) | more than 2 years ago | (#38304142)

Don't forgot Sonic Hedgehog (SHH), an important protein used in development.

Which ends up being an unfunny problem for doctors, that have to explain to a mom that her baby's congenital malformation is caused by a "Sonic Hedgehog Mutation": http://www.nature.com/nature/journal/v439/n7074/full/439266d.html [nature.com]

Re:Of course it isn't a joke (3, Insightful)

nedlohs (1335013) | more than 2 years ago | (#38305040)

Of they could not be stupid and say "caused by an SHH Mutation".

Re:Of course it isn't a joke (1)

Brian Feldman (350) | more than 2 years ago | (#38305056)

Don't forgot Sonic Hedgehog (SHH), an important protein used in development.

Which ends up being an unfunny problem for doctors, that have to explain to a mom that her baby's congenital malformation is caused by a "Sonic Hedgehog Mutation": http://www.nature.com/nature/journal/v439/n7074/full/439266d.html [nature.com]

I think Shakespeare may have had a particular point about the meaning of names... hmm.

Re:Of course it isn't a joke (1)

Anonymous Coward | more than 2 years ago | (#38305722)

I also like the "I'm Not Dead Yet" (INDY) gene that they had found in fruit flies.

Re:Of course it isn't a joke (1)

izomiac (815208) | more than 2 years ago | (#38307138)

OTOH, humorless names also become problems because they're not memorable. Most patients give an admirable effort in pronouncing or remembering the name of their prior illnesses, but there are limits. "Mysthenia Gravis" or "Lambert-Eaton syndrome" are simply beyond what many people can tell their future doctors, and they have even a rougher time trying to spell them for Google. Latin is a bit better than an eponym, but neither is useful when forgotten. OTOH, if a mother mentions a "hedgehog" then any doctor will know what she's talking about. Contrast this with an apyrase deficiency. Every doctor learns that pathway, it's taught just as much or more than the hedgehog system, but you'd be hard-pressed to find many that remember what that enzyme does.

Now, this is a non-issue for most doctors. Unless they just learned English they'll be able to describe a disease in at least three or four ways and pick the most appropriate for the individual patient. Not too many patients care to learn the molecular biology specifics of their genetic defect, e.g. the term "Cystic Fibrosis" is vastly preferred to "a F508 deletion".

Re:Of course it isn't a joke (1)

RockDoctor (15477) | more than 2 years ago | (#38317050)

"Mysthenia Gravis" or "Lambert-Eaton syndrome" are simply beyond what many people can tell their future doctors, and they have even a rougher time trying to spell them for Google.

I almost hate to say this, and certainly hesitate before typing this, but "Darwin Award, anyone?"

Remove (from your gene pool) the ones with spelling and/or writing problems (or thinking problems, to not realise this might be a problem in the future), and eventually the number of people with such problems will decrease. If we were breeding Drosophila or Equus, we'd call it a cull, but people seem to treat (some) hominids differently.

Re:Of course it isn't a joke (1)

zarmanto (884704) | more than 2 years ago | (#38304144)

Funny; I thought caffeine was the most important compound used in development...

Re:Of course it isn't a joke (5, Informative)

Niedi (1335165) | more than 2 years ago | (#38304336)

Anything that involves Drosophila in gerneral and especially Christiane Nüsslein Vollhard is just plain silly....
examples (along with the translation if necessary)
Spätzle (a swabian kind of noodle), wingless, toll (either great or crazy), Gurke (cucumber), tube, Pelle (husk/peel), Krüppel (cripple) etc....

Basically they tried to destroy/deactivate/mutate random genes necessary for the development of the fly, without knowing what they'd hit. Then they looked for larvae or flies that looked weird or behaved funky and named them with whatever they associated with it. Finally they took the animal and tried to find the gene they deactivated. If successful, they'd give that original name to the gene, no matter how stupid the name was and no matter how important the gene is. Hilarity ensued.

Re:Of course it isn't a joke (4, Informative)

mwfischer (1919758) | more than 2 years ago | (#38304094)

I googled Mothers Against Dumpy Drosphela and this site came up.

http://jpetrie.myweb.uga.edu/genes.html [uga.edu]

You people are strange. I like you.

Re:Of course it isn't a joke (1)

marcosdumay (620877) | more than 2 years ago | (#38308230)

When he says that the table does not align on Firefox, well, he's not kidding. Not even ordering seems to be preserved!

Re:Of course it isn't a joke (1)

sandytaru (1158959) | more than 2 years ago | (#38310010)

I knew it would involve UGA somehow. My anatomy teacher in high school worked on Drosophila there and had some of the funniest stories about her times in the lab.

Re:Of course it isn't a joke (0)

Anonymous Coward | more than 2 years ago | (#38304512)

So is "MADD", which stands for "Mothers Against Dumpy Drosophela"

MAD is Mothers Against Decapentaplegic. More often seen in the mammalian ortholog: SMAD (Small Mothers Against Decapentaplegic).

Fly people...

Arsenic should be banned (-1, Troll)

For a Free Internet (1594621) | more than 2 years ago | (#38303694)

These bacterias are illegal and they smell and they are bad and illegal and they should be sent back to the moon where they came from. I approved thjis message using my iphone!!!!!!!! DOGFART

Iron Lisa (0)

Anonymous Coward | more than 2 years ago | (#38304020)

I watched the NASA press conference, and "Iron Lisa" (FeLisa, get it?) came across as one seriously arrogant young lady; arrogant to the point of me wishing her claim of arsenic-based DNA was wrong and she'd have to eat crow.

Well, she got the job. (4, Interesting)

zarmanto (884704) | more than 2 years ago | (#38304078)

While the rest of this is intriguing and all, I was actually more interested in whether or not she ever got the job... it seems that she did, from a note in the title article:

Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.

Good for her.

Re:Well, she got the job. (2, Insightful)

Anonymous Coward | more than 2 years ago | (#38304394)

Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.

Good for her.

Please don't hold it against LBL - most of the people I've spoken to here think the paper was bullshit. I'm not sure what Tainer was thinking; his lab normally does crystallography and small-angle X-ray scattering (SAXS), which rarely stray into controversial territory. We do have the necessary equipment to verify her claims, however, if that's possible. I'm just not looking forward to the inevitable public reaction if she holds another hand-waving press conference; the DOE doesn't need that kind of publicity.

- a Berkeley Lab scientist

Re:Well, she got the job. (5, Informative)

geekoid (135745) | more than 2 years ago | (#38304772)

The paper was fine. Her handling of some of the samples may not have been what one would want.
The sensationalism is the problem. Her conclusion, while unexpected and quite possible wrong, are fine based on the experiment.
This will be worked out like science is worked out. People will try to recreate it, and the DNA will be put under a Mass Spec.

All of which is in the article.

Shit. I just realized you posted AC. So, you are crap. Normally I don't bother with AC, but since I wrote it, I'll post it.

Re:Well, she got the job. (1)

Anonymous Coward | more than 2 years ago | (#38304782)

Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.

Good for her.

Please don't hold it against LBL - most of the people I've spoken to here think the paper was bullshit. I'm not sure what Tainer was thinking; his lab normally does crystallography and small-angle X-ray scattering (SAXS), which rarely stray into controversial territory. We do have the necessary equipment to verify her claims, however, if that's possible. I'm just not looking forward to the inevitable public reaction if she holds another hand-waving press conference; the DOE doesn't need that kind of publicity.

- a Berkeley Lab scientist

I would be tempted to hold YOUR comment against LBNL, except you might not actually be a scientist there and just a troll (I hope so), and even if you are, your attitude might actually not be representative.

She published a paper, and put her data out there. She drew a conclusion from the data that others don't agree with, but she explained her reasoning with supporting data. Working in "controversial territory" is nothing to be ashamed of. She may be right, she may be wrong, let actual data settle the question.

Now, if she had turned out to have falsified any of the data, you'd have good reason to dislike her a scientist. As far as I know, she's done nothing of the sort.

Re:Well, she got the job. (2)

captainkoloth (99341) | more than 2 years ago | (#38305122)

My concern is that it appears that she seems to have been ostracized and punished by members of the scientific community for publishing her paper. Science and peer review aren't supposed to inject personal feelings into research. It's not supposed to be a case of liking or disliking her data but, whether or not it's accurate.

Re:Well, she got the job. (4, Insightful)

Anonymous Coward | more than 2 years ago | (#38305272)

The criticism of Dr. Wolfe-Simon has largely focused on the publicity surrounding the paper. The paper itself has problems but in and of themselves these would not reflect too badly on Dr. Wolfe-Simon, because the conclusions as stated in the paper are not too extreme and are supported by the evidence in the paper, such as it is.

However, she and her lab orchestrated a rather extreme degree of publicity for the paper, even though it was likely unwarranted based on the quality of the results, with much of it focusing on what a great scientist she was and how groundbreaking these findings were. Considering that the findings are widely disputed and possibly false, which is sort of the opposite of good and groundbreaking science, this rubbed a lot of people the wrong way.

Re:Well, she got the job. (3, Insightful)

Anonymous Coward | more than 2 years ago | (#38305680)

Same AC here.

I should elaborate: Sometimes a result that is disputed and possibly false ends up becoming good and groundbreaking science. However, this will only be the case after it has been confirmed independently and the disputed issues addressed. Publicizing it immediately, before that process occurs, as though this uncertain and doubtful piece of science is the gospel truth, is irresponsible.

Re:Well, she got the job. (1)

ColdWetDog (752185) | more than 2 years ago | (#38310342)

The BIG problem was getting the PR people involved. They started hyping it as if it were the discovery of the century. A paper with 'weird' results is fine - even if it turns out wrong. A paper with a dozen PR flacks hyping an entirely new paradigm in molecular biology not so much.

Re:Well, she got the job. (1)

TheGoodNamesWereGone (1844118) | more than 2 years ago | (#38313854)

I'm not a geneticist, nor a professional scientist; just a layman & space enthusiast following the story. It seems to me she's trying to cast herself as a poor female being attacked by the male 'establishment', even though some of her most vocal critics are women. The scientific method ought to be the only criteria of judgment here. Has anyone duplicated her results?

Re:Well, she got the job. (0)

Anonymous Coward | more than 2 years ago | (#38306326)

The data in the Science paper are misrepresented in the text of the Science article and the authors' response to technical comments. There is obvious contamination of the arsenate with phosphate. The paper has no merit whatsoever and should never have been published. Responsibility for this fiasco is widespread.

Wolfe-Simon (-1)

Anonymous Coward | more than 2 years ago | (#38304100)

Ah. The joys of a hyphenated last name.

Moronic headlines strike again. (1)

gurps_npc (621217) | more than 2 years ago | (#38306558)

If you actually sequence the genome, then you know if their is Arsenic in it. You look at what you sequences and see if it says anything but "ATCG", because all of those letters code for nucleotides containing phosphates.

You see those letters code for very specific chemicals Adenine, Cytosine, Guanine and Thymine, none of which have Arsenic.

When you change the nucleotides, you get something BESIDES ATCG. A prime example of this is RNA, a similar chemical that has no Thymine. Instead it uses Uracil which replaces Thymine (they both bind to Adenine). Uracil is basically Thymine with a CH3 replacing a single one of the Hydrogen molecules.

If you take out the Phosphorus, and put in Arsenic, you don't have A or T or C or G (or U).

Techincially whey they posted the genome sequence, as they used only A,T,C and G, they are claiming they found no arsenic.

Of course, I am sure that they are claiming that the A,T,C and G letters refer either to actual A,T,C and G OR to similar chemicals that have the Phosphorous replaced with Arsenic. But the DNA sequencing machines we use were designed to just identify real ATCG - their hypothesis is unsupported and untested.

To conclude - they ran the bacteria through standard genome sequencing and got a result that portrayed it without Arsenic. But they appear to think that their test results are wrong and the genome actually has arsenic in it - without any new evidence presented here.

Re:Moronic headlines strike again. (0)

Anonymous Coward | more than 2 years ago | (#38306774)

...this from a guy who thinks Adenine [wikipedia.org] , Cytosine [wikipedia.org] , Guanine [wikipedia.org] , and Thymine [wikipedia.org] contain phosphorous...

Re:Moronic headlines strike again. (1)

ClintJCL (264898) | more than 2 years ago | (#38307022)

His comment was still better than yours.

Re:Moronic headlines strike again. (0)

Anonymous Coward | more than 2 years ago | (#38307652)

indeed,

for the non-molecular biologists and chemists: adenine, cytosine, guanine and thymine often refer not just to the nucleotides, but also to the complete DNA or RNA base with that nucleotide. In that case, the nucleotide is covalently bound to a phosporous-(desoxy)ribose scaffold.

Re:Moronic headlines strike again. (1)

Anonymous Coward | more than 2 years ago | (#38316784)

If you use the word "adenine" to refer to the entire combination of adenine bound to the phosphorous-containing backbone, it makes absolutely no sense to claim that it's "something BESIDES" adenine just because a phosphorous atom in the backbone (not really even part of the adenine itself) has been replaced with arsenic. It's still adenine bound to a scaffold; the scaffold is different, but the adenine isn't.

So OP's point was completely invalid. No matter how pedantic you care to be, it makes just as much sense to call adenine+arsenic-containing scaffold "adenine" as it does to call adenine+phosphorous-containing scaffold "adenine".

Re:Moronic headlines strike again. (0)

Anonymous Coward | more than 2 years ago | (#38307130)

I Am Not A Molecular Biologist, but at least he knows the difference between a nucleobase and a nucleotide.

Re:Moronic headlines strike again. (1)

Anonymous Coward | more than 2 years ago | (#38307514)

This is simply not true (otherwise known as bull cookie)

The authors claim that some of the posphor in the ACTG bases may have been substituted by arsenic. All currently available genome sequencers "read" bases by either PCR based (Sanger, Illumina, Roche, Pac-bio or Ion-torrent) or ligation based (Solid) techniques. These techniques do not discriminate on the phosphor group.

In addition even if the arsenic in the DNA would interfere with the sequence, genome sequencing is not single molecule sequencing; So if the arsenic groups are randomly distributed over the genome, the phospor based nucleotides can still be easily read.

signed,

somebody who actually has experience with the technology ( we sequence ~300 gigabases a week)

Re:Moronic headlines strike again. (1)

gurps_npc (621217) | more than 2 years ago | (#38357646)

Your comment indicates a lack of reading comprehension skills. And a lack of intelligence.

Let me ask you a simple question:

Someone gives you a written Portuguese book.

You have a Spanish translation program.

Would you then run it through the Spanish translation program and claim you have 'translated it"?

NO OF COURSE NOT, ONLY A MORON WOULD DO THIS.

I totally agree that if you use PCR (which I have experience in - minimal, but recent), or a ligation based system (of which I have read), on an arsenic based life form then it would not work. But if you do that, and claim to have 'sequenced' it, you are a MORON. Just as if you you claimed to have translated a Portuguese book with a Spanish translation program.

Chemicals are real, solid things with real solid definitions. The idea that some total idiot would use a standard PCR or ligation based sequencing technique on a potentially arsenic based life form and then claim to have SEQUENCED the DNA is idiotic.

Everything I wrote is correct. They did NOT sequence the DNA. They ran either a PCR or ligation based protocal on the DNA sample. It came up with results that, if the theory about arsenic is correct, are false.

They were incredibly inaccurate - in the headline, the article, and the study.

Lets say their really is arsenic in that life form. It will almost certainly affect the shape of the molecule, affect RBS, affect the amino acids created, etc. etc. etc.

From that point on, you (and everyone else that does sequencing) will need to create a new protocol with differentiate from arsenic bases from phosphate bases. Sequencing will undergo a major change and NEW names will be given to the new arsenic bases and new letters will be assigned.

Again, the writers of this headline, article all did a horrible job of communication what was done. Moronic headline strikes again., signed someone that is not an idiot and knows chemicals with even a single molecule difference are not given the same name.

Well I might have no clue but .. (1)

roguegramma (982660) | more than 2 years ago | (#38307518)

Well, I might have no clue how you sequence a gene or genome today, but I would guess the procedure would involve using traditional rna in a non-arsenic environment to multiply the dna before analysing it.

This process would of course not preserve the arsenic.
To get better tools, you would have to look at how the adapted lifeform reads and processes its dna, and how the cells factories actually translate the messenger rna, as this might be different.
See
http://en.wikipedia.org/wiki/Genetic_Code#Variations_to_the_standard_genetic_code [wikipedia.org]

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