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Fugu May Be Key To Human Genome
sulli writes ; "If it doesn't kill you first, it may get you a Nobel Prize. The fugu (puffer fish), best known for being a delicacy in Japan despite being poisonous if improperly prepared, has a very short genome (400M base pairs) compared to that of humans (3.5B base pairs). Says a sushi fan at DOE: "[W]henever researchers have gone into the fugu and looked for human genes, by and large they've found them." Info from a related project in the UK is here."
DNA polymerase, the enzyme which replicates DNA, isn't capable of getting all the way to the end of the chromosome. As a result, when you duplicate the DNA during cell division the copy you end up with is shorter than the original. This has obvious problems if you replicate enough. The solution is to code for an enzyme called telomerase which is capable of adding extra DNA to the end of a chromosome to get it back to the original length. This DNA doesn't code for anything (in most organisms it's made up of highly repetative sequences), and is only there to make sure you don't end up with shorter chromosomes than you started with.
Interestingly, Drosophila Melanogaster doesn't do this - rather than have an enzyme that adds DNA, transposable elements (short sections of DNA that are capable of moving themselves from place to place in the genome. Very cool.) jump in from further down the chromosome and replace the removed bits directly. AFAIK, it's the only organism known to do this - even yeast has a setup similar to the one we use.
The Minimal Genome Project tried to answer this question by disrupting genes in M. genitalium until they had an organism with a minimum number of genes that was still viable.
Just because the gene is there does not mean it is active. Remember that every cell in your body contains the exact same genetic information. It's just that different parts of the genes are active in different cells.
The cells in your heart, hand, brain, muscle and liver are completely different in their functionality, despite being created from the same DNA.
What you (and for some reason the author of the article) fail to realize is that there is not a continuous mapping between the size of genetic data and biological complexity. Quite often evolution occurs not by increased complexity, but by shedding un-needed functionality. Some primates have tails as well as more functional feet than humans do. Certainly that requires more data. So in that case, part of the evolution towards becoming human involved the discarding or deactivation of those active genes.
We may still have that data somewhere in our DNA, it's just not switched on.
-... ---
("Fugu me!!!", "My expert hands are busy!!" and other great quotes).
And now back to my pointless existance.
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The puffer fish does seem awfully human. Most genes code for biochemistry, not for structures that you'd notice by eye. Vertebrates are all really extremely similar at the genetic level. We're not even that different from mushrooms in terms of the whole genetic tree of life. (We're much closer to mushrooms than to green plants!) Yeah, a bunch of the human genome has to do with the brain, but even there puffer fish aren't that different from certain members of the U.S. Supreme Court.
I think genes that are common among all animals are probably of the least interest - they are sort of like the "int main()" of the human genome, in that every program (here, a biological program) must have them.
I'm sure there's room for a variety of approaches. Some people may want to study the mouse genome because it's so similar to the human one. Some people may want to study the genes that humans have in common with yeast. It all depends on what you're trying to find out. Yeast doesn't get cystic fibrosis, but it might have some of the same cell-metabolism genes we do. If you can get the info you want from a "simple" organism, it may be easier.
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70% of all dna shared by most animals anyway? I mean, even between a human and say, a yeast....
is it really surprising that a puffer fish has a lot of the same genetic material?
Thalia
most fugu that you get in Japan is farm raised and is not poisonous. It is also heavily government regulated, so there is absolutely no risk. This also has an affect on the flavor, the nonpoisonous fugu is bland and rather ordinary tasting. However, it is still possible to find the poisonous variety, though it can cost upwards of 1000USD for a plate.
The articles linked said that 50 people in Japan die from fugu, not the 1 or 2 that you claim. Still pretty safe.
:-)
As for regular sushi, it doesn't kill anyone. Sushi is very safe to eat, and it's extremely yummy. If I find a person who won't eat sushi, and has never tried it, then I feel very sorry for them. But what can I do if someone wants to die a virgin?
If tits were wings it'd be flying around.
Here is a link to the classic Simpsons episode, One Fish, Two Fish, Blowfish, Blue Fish. Homer eats poisonous puffer fish and he thinks he has only 24 hours to live.
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Oscarfish.com: tropical fish with attitude. Way t
I'm sorry, by posting this transcript, you have violated the Intellectual Property rights of the Simpson's owners. They'll be hauling you into court any day now.
[W]henever researchers have gone into the fugu and looked for human genes, by and large they've found them.
But only if they look in the right Plaice
Just remember... you're not really studying the mice. They're conducting incredibly subtle experiments on YOU.
End of lesson. You may press the button.
Liver, gonads, intestines and skin. (You could have read the provided FDA link, you know.)
There are fugu restaurants in Japan, where the thrill of risking death by eating even a slightly tainted sliver of meat is the whole point of the experience.
Yup. In fact, the more expensive the fugu part, the closer it is to the poisonous organs (and the greater the risk of dying!). Connoisseurs say you actually get a buzz from fugu with a tiny bit of poison in it...
You must be a licensed fugu chef to work at such a restaurant, but there are a number of "black market" fugu stands around, too.
This, on the other hand, is bunk. Any restaurant that tries to sell fugu without a licence would instantly get slammed by Japan's Health Ministry, as would any "stall" that tried to sell any type of raw fish. However, you're free to go fish your own fugu and serve it up to your family, and this is in fact the reason behind most of Japan's fugu deaths.
Michael T. Itamura refers the interested reader to the August 1984 issue of National Geographic. Stories and photographs of the leopard puffer. (Even a story about a famed Kabuki actor who ate the liver of the puffer and paid for it with his life).
Matsugoro Bando... XIV? Can't remember. Anyway, he wasn't quite stupid enough to eat an actual poison organ, but he did bribe a chef to give him a piece usually deemed inedible due to its proximity.
Incidentally, I'll be going to eat a fugu dinner next week...
Cheers,
-j.
Apparently that was one of the reasons for the great debate obver the ethics of exterminating the virus.
'There is a Light that never goes out.'
(...biologist)
But I have to say I'm suprised at the number of people posting who think "puffer fish are so different from humans"
Let me remind you of a fair number of similarities...bilateral symmetry, two eyes, fins vs. arms, spine, oxygen/co2 exchange is somewhat similar as I recall.
I've always thought most animals are quite similar. Not as much as say, bonobos and humans, which are some 97% genetically identical, if memory serves, but most animals share a number of basic traits that are probably nearly identical in the genome coding.
plus i've heard a lot of a given animals genetic makeup is dormant garbage left over from ages of evolution. In that case, there could well be a puffer hidden in all of us (and not via the sushi method)
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true - however, i believe most of these "human" patents are done in such a way that the owners already have a spanning reach in this area. i.e. they can claim patents now not only on the "human" genes, etc. but those of the fugazi or whatever the hell it's called again (puffer fish).
anyone wanna hear my rant on why intellectual property is bad again?????? anyone????
FluX
After 16 years, MTV has finally completed its deevolution into the shiny things network
"It is seldom that liberty of any kind is lost all at once." -David Hume
Actually, couldn't you do an encoding in 2 bits?
1 bit - A/T (set), C/G (unset)
1 bit - first base + strand (set), first base - strand (unset)
Thus,
5' ATCGATCG 3'
3' TAGCTAGC 5'
becomes:
1110010011100100
('course, you have to make an assumption as to which strand is +, and what the "order" of a base pair is (A/T or T/A?)...)
Interesting...
Let's try not to let fact interfere with our speculation here, OK?
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In The Beginning
In the beginning there was the computer. And God said:
%Let there be light!
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#Warning system error in sector E95. Man and woman not in Garden.edn.
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- if you love something, set it free; if it doesn't come back, hunt it down and kill it
Anyone else notice that it looks like more the "more evolved" specicies have less base pairs?
Is this just the result of my pre-Coperican biases? Or some observational bias that they wouldn't have printed numbers for small spieces?
Does anyone know if this pattern I've inferred holds true with a larger database of species?
Only about an average of 1 or 2 people per year die in Japan from eating improperly prepared fugu, and all of these are from those black market places. More than that number of Japanese people probably die just from the fact that they're eating raw fish all the time :)
"The question of whether a computer can think is no more interesting than that of whether a submarine can swim" -EWD
More info on Homer's close brush with death can be obtained from the transcript of this episode of The Simpsons.
What would be really cool would be to work in some industrial strength error correction code into the copying mechanism (grey codes for example).
DNA replication is already good to 1 error in 10**9 bases duplicated. Assuming I haven't screwed my numbers up completely, that's about 3 single base pair errors per complete duplication of the genome. That's pretty damn good. What's more of a problem is DNA repair, which is somewhat less efficient (not just because it makes mistakes, but also because sometimes information has been completely lost). Some sort of checksumming would be nice, but it's not something you can retrofit without changing the entire biology of the cell.
Note that this wouldn't necessarily be a good thing - reducing mutation is probably good for the survival of individuals, but not necessarily for the long-term good of the species. Mind you, by the time we've reached sufficiently advanced technology to be able to cope with a project that size we'd probably be able to "enhance" genes somewhat more accurately than random changes.
does anyone know whether representation plays into gene interpretation? Ie the physical folding of the protein interacting with how the data it holds is interpreted (visualise paper tape which holds not only printed data, but is also knotted in such a way to expose some letters and obscure others).
I assume you mean DNA rather than protein? If so, yup. In its default state, DNA is tightly wound around a protein scaffold and can't be transcribed into RNA. Whether or not the DNA is in this inaccessible form depends to some extent on the sequence of the non-coding DNA around it amongst a variety of other things.
Thats the analogy my biology teacher used I personally think that its a crappy analogy, but i cant really think of anything better.
It's also not terribly accurate. Some of the non-coding DNA is involved in controlling gene activity, but large chunks really do seem to be, well, junk. Removing small chunks of non-coding DNA is unlikely to be enough of an advantage to give you a significantly better survival chance, and removing large chunks is difficult without also removing coding genes.
Sushi is the safest when the fish is fresh. I mean fresh. The longer a piece of fish sits around, the more likely it is to pick up something from the environment that will contaminate it. As for freezing, eeewwww. Sushi is also best when it is fresh. The freezing would destroy the consistancy of the seafood, which is one of the crucial parts to a good meal.
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It seems to me if we are finding human genes inside puffer fishes, it may be due to their diet :)
The average length of a human coding sequence in the DNA databases is approximately 1.2 Kbp and sensible estimates of the total number of genes in the human genome lie between 50 and 100,000. A gene number of 70,000 would give a total coding sequence of 85 Megabases, less than 3% of our genome. Herein lies one of the major problems. A 3% return on investment, even when genes are identifiable, is rather poor, especially when sequencing is an expensive business. As if that's not enough, a large percentage of highly re-iterated dispersed repeats serve to exacerbate the problem. The average length of a human coding sequence in the DNA databases is approximately 1.2 Kbp and sensible estimates of the total number of genes in the human genome lie between 50 and 100,000. A gene number of 70,000 would give a total coding sequence of 85 Megabases, less than 3% of our genome. Herein lies one of the major problems. A 3% return on investment, even when genes are identifiable, is rather poor, especially when sequencing is an expensive business. As if that's not enough, a large percentage of highly re-iterated dispersed repeats serve to exacerbate the problem. Consequently other more direct approaches are being used, mostly to identify coding sequences within large genomic regions of DNA, and it is only by using a combination of these more elegant strategies that 'gene hunters' are able to operate economically. Some of these methods compare human sequences with sequences from other organisms, using the premise that conserved sequences have some function. An extension of this, particularly amongst mammals but also with chicken, is to identify conserved linkage groups, and this may have particular value in positional cloning projects. Conserved linkage, or conserved synteny, can in fact be used to great advantage in comparative genomics, particularly if a genome is smaller and easier to work with than the human genome.
When an article states that a fish has the same genes as humans, the meaning of 'the same' is best compared to: A rabbit has all 'the same' organs and limbs as a human: liver, heart ,lungs, skin, eyes, arms, feet etc.
Patenting genes is not about patenting a sequence of base pairs. A bit of DNA on its own just isn't useful. The interesting bit, is the protein the gene codes for. I'd be very much surprised if the fugu had any genes identical to their human equivalent.
This is not a Fugazi
I think a more likely reason that "by and large, when we've looked for human genes in the puffer, we've found them" is that we currently know about only a few of the important genes in the genome - we've just scratched the surface. Perhaps now we should try to find genes in the human genome that are NOT in the puffer, and then see what THEY do. I think genes that are common among all animals are probably of the least interest - they are sort of like the "int main()" of the human genome, in that every program (here, a biological program) must have them.
It is fugu, a blow fish, that has the deadly nerve toxin in one of the internal organs (either the liver of gall bladder, I forget which). There are fugu restaurants in Japan, where the thrill of risking death by eating even a slightly tainted sliver of meat is the whole point of the experience.
You must be a licensed fugu chef to work at such a restaurant, but there are a number of "black market" fugu stands around, too.
However, fugu usually kills you within 15 minutes, not 24 hours. It starts with a tingling in the fingers, and works its way up your arms and legs, until you are completely paralyzed, and you die when it reaches your heart.
I'd guess that the fugu chef, and the doctor, were having a little fun at Homer's expense.
Spage Yee {sy}: This fish is poisonous because its innards contain tetratodoxin (TTX) which is a neurotoxin, which blocks either the sodium or potassium (one or the other it's been a while since I studied neurobiology) channels in your nervous system.
Michael T. Itamura refers the interested reader to the August 1984 issue of National Geographic. Stories and photographs of the leopard puffer. (Even a story about a famed Kabuki actor who ate the liver of the puffer and paid for it with his life). Quite interesting.
***
I'm actually watching tonight's episode (6:00p.m. where I live), 5F11, where the model UN gets stuck on the island - and Bart goes snorkeling to retrieve a cooler of food. There's a puffer fish waiting for him in the sunken school bus.
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Oscarfish.com: tropical fish with attitude. Way t
Well,I am not sure how useful this would be as far as locating disease causes and all is concerned, since humans are mammals and fish are aquatic creatures and I am sure that means a LOT of differences in the genes. Still, I think it might be a good idea to do it. Just curious here...anything like a complete genome for any organism, even this, means a LOT of information to be stored. I wonder how database applications would cope with this kind of info. I read something about special research going on for information storage techniques for genomic databases, but as far as I remember, they addressed the needs for the genome of one particular organism only. It would be a nice reserach problem to see if it possible to correlate the data from various organisms for similar genes and see what yields, both in terms of information science and biology.
Did you hear about the mathematician who named his dog Cauchy because it left a residue at every pole?
Seriously though...
If the fugu has nearly all of the genes humans do, could this be a backdoor around patents related to the human genome?
The idea that a compact genome could be used to look for genes (or at least exons) in the human genome has already been put into practice. If you go to http://kicy.genoscope.cns.fr/cgi-bin/exofish_kicy. cgi you will get a short introduction on the topic as well as have access to the interface allowing you to look for exons in a sequence that you input.
EXOFISH (Exon Finding by Sequence Homology) uses DNA from another fish which is a cousin of Fugu (Tetraodon nigroviridis) in order to find highly conserved regions between it and human sequences. A method was developed to find these evolutionary conserved regions (ecores) efficiently as it is believed that they represent exons. More info here.
I am not a geneticist
What I would like to know is:
Is it feasible to determine which genes are common to all life forms currently living on the planet.The answer may lead some insight into the question of what is the minimum requirement for life.
The answer is probably 42.
134340: I am not a number. I am a free planet!
Dr. Hibbert: You have twenty-four hours to live.
Homer: Twenty-four hours!
Dr. Hibbert: Well, twenty-two. I'm sorry I kept you waiting so long.
Dr. Hibbert: Well, if there's one consolation, it's that you will feel no pain at all until some time tomorrow evening, when your heart suddenly explodes.
Dr. Hibbert: Now, a little death anxiety is normal. You can expect to go through five stages. The first is denial.
Homer: No way! Because I'm not dying!
Dr. Hibbert: The second is anger.
Homer: Why you little!
Dr. Hibbert: After that comes fear.
Homer: What's after fear? What's after fear?
Dr. Hibbert: Bargaining.
Homer: Doc, you gotta get me out of this! I'll make it worth your while!
Dr. Hibbert: Finally, acceptance.
Homer: Well, we all gotta go sometime.
Dr. Hibbert: Mr. Simpson, your progress astounds me.
400 million base pairs.
;)
1 base pair == 2 bits of digital information in binary.
800 million bits of information == 100 million bytes.
Devide by 1024*1024 == 95 Mbytes.
Make you realize how shitty human coders are in comparison..
To truly understand biology you need a model organism that is accessible experimentally. A good model system should have the following traits:
(1) Genetically tractable: basically this means that you can reliably perform matings and score marker genes for mapping.
(2) Easy to culture: can grow large numbers of the organism in a relatively short time for relatively little money.
(3) Easy to manipulate: have the ability to generate both random and targeted mutations, have vectors by which to insert transgenes.
(4) Easy to observe: simple organisms that have transluscent body walls are the best.
Fugu doesn't have ANY of these advantages except the small genome, so probably the most use that will come out of it will be as a reference organism. Experimentally, the best model organisms biologists have are:
(1) mice: best characterized mammalian model. you can do targeted mutations and insert transgenes, but random mutagenisis is hard. Histology and embryology is pretty well established, but mice like most mammals are very complex and often studies raise more questions than answer them. Genome sequence note quite complete yet, but getting there. :)
(2) fruit flies: Drosophila melanogaster is a great model system. The genome is relatively small (about 10^8 base pairs of DNA, and estimated 15,000 genes), but it has all the relavent organs and systems as mammals, and many genes function in the same way. Genome sequence has been completed.
(3) nematodes: Caenorhabditis elegans is also a great model system. Genome size is approx. the same as flies. Has the added advantage of having its entire cell lineage mapped. It only has 1000 or so cells, so it makes a super model organism for studying differentiation. Genome sequence is also complete. Disadvantages is due to divergence from the mammalian branch, it does some things oddly, so not quite as similiar to humans as flies are.
(4) yeast: the bug you use to brew beer, Saccharomyces cerevisiae. Single cell eukaryote, in fact the first eukaryote to have its genome completely sequenced. Great organism to work on really basic things like DNA replication and repair, and basic cell biology, but obviously not great if you are interested in Alzheimer's disease or hypertension. OTOH good for studying some kinds of cancers. You can grow a TON of yeast in the lab easily
(5) bacteria: Escherichia coli is ever simpler that yeast because it is a prokaryote, it has no nucleus. But it is good for stufying really basic mechanisms such as protein folding, translation, etc etc. You can grow 10 TONS of E. coli in the lab easily
Also, some ppl study Xenopus lavis (African bullfrogs), Danio rio (zebrafish), chickens, rats, among others, but by and large the major model organisms that are studied in a way relavent to medicine are flies, worms, and mice, and yeast and bacteria to a lesser extent. Often different investigators will collaborate with each other in a cross-species manner, and compare results between organisms to look for common themes in common problems.
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