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."

Comments

Contrary to popular belief.....

[RJ11]

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.

IANAB

[small_dick]

(...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)

The beginning

[H*rus]

Let me tell you how it all started:

In The Beginning
In the beginning there was the computer. And God said:
%Let there be light!
#Enter user id.
%God
#Enter password.
%Omniscient
#Password incorrect. Try again.
%Omnipotent
#Password incorrect. Try again.
%Technocrat
#And God logged on at 12:01:00 AM, Sunday, March 1.
%Let there be light!
#Unrecognizable command. Try again.
%Create light
#Done
%Run heaven and earth
#And God created Day and Night. And God saw there were 0 errors.
#And God logged off at 12:02:00 AM, Sunday, March 1.
#Approx. funds remaining: $92.50.

#And God logged on at 12:01:00 AM, Monday, March 2.
%Let there be firmament in the midst of water and light
#Unrecognizable command. Try again.
%Create firmament
#Done.
%Run firmament
#And God divided the waters. And God saw there were 0 errors.
#And God logged off at 12:02:00 AM, Monday, March 2.
#Approx. funds remaining: $84.60.

#And God logged on at 12:01:00 AM, Tuesday, March 3.
%Let the waters under heaven be gathered together unto one place and let the dry land appear and
#Too many characters in specification string. Try again.
%Create dry_land
#Done.
%Run firmament
#And God divided the waters. And God saw there were 0 errors.
#And God logged off at 12:02:00 AM, Tuesday, March 3.
#Approx. funds remaining: $65.00.

#And God logged on at 12:01:00 AM, Wednesday, March 4.
%Create lights in the firmament to divide the day from the night
#Unspecified type. Try again.
%Create sun_moon_stars
#Done
%Run sun_moon_stars
#And God created the heavens. And God saw there were 0 errors.
#And God logged off at 12:02:00 AM, Wednesday, March 4.
#Approx. funds remaining: $54.00.

#And God logged on at 12:01:00 AM, Thursday, March 5.
%Create fish
#Done
%Create fowl
#Done
%Run fish, fowl
#And God created the great sea monsters and every living creature that creepeth wherewith the waters swarmed after its kind and every winged fowl after its kind. And God saw there were 0 errors.
#And God logged off at 12:02:00 AM, Thursday, March 5.
#Approx. funds remaining: $45.00.

#And God logged on at 12:01:00 AM, Friday, March 6.
%Create cattle
#Done
%Create creepy_things
#Done
%Now let us make man in our image
#Unspecified type. Try again.
%Create man
#Done
%Be fruitful and multiply and replenish the earth and subdue it and have dominion over the fish of the sea and over the fowl of the air and over every living thing that creepeth upon the earth
#Too many command operands. Try again.
%Run multiplication
#Execution terminated. 6 errors.
%Insert breath
#Done
%Run multiplication
#Execution terminated. 5 errors.
%Move man to Garden of Eden
#File Garden of Eden does not exist.
%Create Garden.edn
#Done
%Move man to Garden.edn
#Done
%Run multiplication
#Execution terminated. 4 errors.
%Copy woman from man
#Done
%Run multiplication
#Execution terminated. 3 errors.
%Insert woman into man
#Illegal parameters. Try again.
%Insert man into woman
#Done
%Run multiplication
#Execution terminated. 2 errors.
%Create desire
#Done
%Run multiplication
#And God saw man and woman being fruitful and multiplying in Garden.edn
#Warning: No time limit on this run. 1 errors.
%Create freewill
#Done
%Run freewill
#And God saw man and woman being fruitful and multiplying in Garden.edn
#Warning: No time limit on this run. 1 errors.
%Undo desire
#Desire cannot be undone once freewill is created.
%Destroy freewill
#Freewill is an inaccessible file and cannot be destroyed.
#Enter replacement, cancel, or ask for help.
%Help
#Desire cannot be undone once freewill is created.
#Freewill is an inaccessible file and cannot be destroyed.
#Enter replacement, cancel, or ask for help.
%Create tree_of_knowledge
#And God saw man and woman being fruitful and multiplying in Garden.edn
#Warning: No time limit on this run. 1 errors.
%Create good, evil
#Done
%Activate evil
#And God saw he had created shame.
#Warning system error in sector E95. Man and woman not in Garden.edn.
#1 errors.
%Scan Garden.edn for man, woman
#Search failed.
%Delete shame
#Shame cannot be deleted once evil has been activated.
%Destroy freewill
#Freewill is an inaccessible file and cannot be destroyed.
#Enter replacement, cancel, or ask for help.
%Stop
#Unrecognizable command. Try again
%Break
%Break
%Break
#ATTENTION ALL USERS *** ATTENTION ALL USERS: COMPUTER GOING DOWN FOR REGULAR DAY OF MAINTENANCE AND REST IN FIVE MINUTES. PLEASE LOG OFF.
%Create new world
#You have exceeded your allocated file space. You must destroy old files before new ones can be created.
%Destroy earth
#Destroy earth: Please confirm.
%Destroy earth confirmed
#COMPUTER DOWN *** COMPUTER DOWN. SERVICES WILL RESUME SUNDAY, MARCH 8 AT 6:00 AM. YOU MUST SIGN OFF NOW.
#And God logged off at 11:59:59 PM, Friday, March 6.
#Approx. funds remaining: $0.00.

Re:Consider this

[Jonathan the Nerd]

We may still have that data somewhere in our DNA, it's just not switched on.

It'd be interesting if we found out what those genes do and how to activate them. Someone could even make a movie about it. They could have characters whose unusual genes allow them to move things mentally, heal quickly, shoot lasers out of their eyes, control the weather, manipulate magnetic fields, etc. I know I'd go see it.

# of Base Pairs vs Evolvedness/Complexity

[astrophysics]

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?

Re:Consider this

[Dannon]

Just what we need. A Marvel Mutant with spines all over and the ability to puff up his body. Didn't I see this guy on The Tick?

---

Open Source Genome

[sparcv9]

Of the 3.4 billion chemical building blocks that make up the human DNA strand, scientists believe only 3 to 5 percent represent actual instructions that make some people tall, some blue-eyed and some prone to heart disease.

/* ... the rest is comments and a copy of the GPL */

More about the puffer...

[Oscarfish]

...ripped from the link I posted just a couple of minutes ago.

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.

Homer eats the fugu...

[doorbot.com]

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.

no one single organism is the key

[myc]

Fugu is useful because of it's small genome size, but genomic information only tells you so much. Imagine not understanding computer code, and someone hands you the source code for the entire Red Hat distro; it's not very useful insofar as understanding how your computer works, unless you understand what the code means.

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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Santa Claus: "Ho ho ho!"

Re:IANAG

[myc]

You wrote:

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.

IAAG. This question is more philisophical than scientific. Define life first. You can generate self-replicating molecules using themselves as templates using RNA only, under specific in vitro conditions. Is that life? Generally speaking, organisms (i.e., one or more cell, not viruses) adapt to an environmental niche that they occupy and retain what genes they need to survive in that niche. Since each niche is a different microenvironment, all organisms have different genes (evolutionary adaptation).

However, to answer your question somewhat more directly I recall that mycoplasma has the currently known smallest genome of any organism, with 580074 base pairs of DNA, and 483 genes. See The Mycoplasma genetalium Genome Database for more info.


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Santa Claus: "Ho ho ho!"