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Genome of Controversial Arsenic Bacterium Sequenced
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."
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.
-- (this is a sig) My Computer Programming Forumhttp://www.programers.co.nr/
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"
Self proclaimed typo king, and inventor of the bear destroying coffee table (patent not pending).
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.
http://slashdot.org/submission/1062723/Cheap-mobile-data-plan?art_pos=2
Indeed. How much of Human DNA is actually useful? How mUch is just aking up space?
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.
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.
Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.
Good for her.
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...
"Convictions are more dangerous enemies of truth than lies."
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.
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
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.
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."
The Kruger Dunning explains most post on
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
whois gawk date unzip strip find touch finger mount join nice man top fsck grep eject more yes exit umount sleep dump
http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
"The space elevator will be built about 50 years after everyone stops laughing." - Arthur C. Clarke ~1980
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.
Give me Classic Slashdot or give me death!
Enhance!
http://www.sciencedaily.com/releases/2011/10/111025122615.htm
Why ESI specifically? Couldn't you use MALDI or any other ionization method? (Just curious...)
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.
excitingthingstodo.blogspot.com
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.
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
Hey don't blame me, IANAB
Wrong.
Here's a nice talk for you: http://www.youtube.com/watch?feature=player_embedded&v=DRsN7w7iW08
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.
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.
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.