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Honeybee Genome Sequenced

kdawson posted more than 7 years ago | from the plan-bee dept.

67

mapkinase writes to let us know about articles in Nature on the completed sequencing of the honeybee genome. From the first article: "Two other insects have already been sequenced: the malaria-carrying mosquito Anopheles gambiae, and one of science's great model organisms, the fruitfly Drosophila melanogaster. Like these, the bee is much easier to manipulate and study than, say, the monkey. But unlike the mosquito and the fruitfly, the bee's social behavior is of special interest." Another article in the same issue clarifies why this sequencing is important: "The genome is helping to reveal some of those [such as the bees' dance language and the division of labor in the hive] mechanisms. For instance, there are 65 spots in the genome that seem to code for short RNA molecules called microRNAs (miRNAs), molecular switches that can turn genes on or off. The researchers found that miRNA activity differs between bees doing different jobs."

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I have a question (0)

Anonymous Coward | more than 7 years ago | (#16623786)

So which micro RNA codes for BeeBeards?

I chime in! (0)

BeeBeard (999187) | more than 7 years ago | (#16626584)

What's all this buzzing about? I will say on the record that my DNA has not been collected in any way to further their research. I've got just the one WeeBeard (that I know of...heh heh). But, off the record, there was that one time in Tijuana when I woke up in a dumpster behind a roach-infested laundromat, surrounded by empty boxes of Tide, and with an unexplainable soreness in my groin. That was some night! The last thing I remember before I blacked out was some odd fellow running away from me. He was carrying some kind of jar filled with milky fluid right before he disappeared into a white, windowless van. I think he might have muttered something about an "army of giant, unstoppable, bearded killer bees." Oh well, it's probably nothing. See ya!

miRNA? (2, Interesting)

Iron (III) Chloride (922186) | more than 7 years ago | (#16623894)

Interesting that miRNA could be turned off and on. These play a role in helping dicer form the RISC, so I wonder what this may lead to, not only in terms of info on honeybee's social behavior, but RNAi.

Re:miRNA? (3, Interesting)

Tatarize (682683) | more than 7 years ago | (#16623990)

It's neat to find, but it had to be there. Each bee has the same core DNA. The drones and queen and each sub variety of bee all use the same DNA. For the geeks in the audience who aren't bio-geeks as well.

Make Wings;
Make Thorax;
Make Head;
Size = 10;
if (Bee == Queen){//miRNA
        Size = 30;
        Behavior = "Go around laying eggs";
}
else {
        Size = 10;
        Behavior = "Go around gathering honey";
}

Give or take. miRNA goes around turning off certain gene stuff. I'm too lazy to RTFA, but I'd like to know the relationship between miRNA and royal jelly.

Re:miRNA? (3, Informative)

MikShapi (681808) | more than 7 years ago | (#16625256)

Not exactly. More like:

Make Wings;
Make Thorax;
Make Head;
Size = 10;
if (GrowthStoppingHormonePresent == false){
                Size+=20;
                if (OtherQueenPresent == true){kill it;}
                Spray Growth Stopping Hormone On All Bees Around You;
}
else
{
                Behavior = "Go around gathering honey";
}

Re:miRNA? (0)

Anonymous Coward | more than 7 years ago | (#16628260)

I hope the sequencing is more efficient than to set Size = 10 when it's going to be overwritten in either case!

Re:miRNA? (1)

Tatarize (682683) | more than 7 years ago | (#16629142)

Come now, a good optimized compiler could catch it.

And we're talking biology, so there's no coder. It can do stuff in the most brilliant way possible or in a way so stupid a third grader might wince. Evolution isn't smart, but it solves problems.

----------------------

Class Bee : Public arthropod {
        public:
                Dance(location flowerLocation); //odd way to communicate
                Lay(Object egg);
                Kill(*Object t) { while (state == alive && t->state == alive) Sting(t); }
                Sting(*Object t) { Stinger.Sting(*t); if (Bee != Queen) Die(); } //why?
                Die() { state = dead; }
        private:
                Part Wings;
                Part Thorax;
                Part Head;
                Part Stinger;
                type Bee;
                int size;
                behavior Behavior;
                existence state;
}
Bee::Bee {
        state = alive;
        size = 10;
        if (Bee == Queen){
                Behavior = "Go around laying eggs";
        }
        else {
                StopGrowthHormone();//calls miRNA routine
                Behavior = "Go around gathering honey";
        }
        If (exists(GrowthHormone)) {
                size += 20;
        }
}

Re:miRNA? (1)

rootEToTheIPi (937469) | more than 7 years ago | (#16624444)

Interesting that miRNA could be turned off and on.
I didn't RTFA, but the summary says:
molecular switches that can turn genes on or off

Honey bee genome sequenced? (1)

stunt_penguin (906223) | more than 7 years ago | (#16623914)

How long before we can expect genetically milk and honey-producing cows? (or, indeed, cow overlords)

C'mon I want this to put on my cereal!

Re:Honey bee genome sequenced? (1)

Kryptonian Jor-El (970056) | more than 7 years ago | (#16623936)

I, for one, look forward to our Bee Overlords

Re:Honey bee genome sequenced? (1)

stunt_penguin (906223) | more than 7 years ago | (#16623938)

/genetically modified

Re:Honey bee genome sequenced? (1, Funny)

Anonymous Coward | more than 7 years ago | (#16623984)

And you didn't even get first post :)

Re:Honey bee genome sequenced? (4, Funny)

kfg (145172) | more than 7 years ago | (#16624418)

Gee thanks, now I'm going to spend the rest of the day imagining cows flitting from flower to flower gathering pollen.

KFG

Re:Honey bee genome sequenced? (1)

bussdriver (620565) | more than 7 years ago | (#16624754)

How long before we can expect obedient human worker drones?

Re:Honey bee genome sequenced? (1)

Blighten (992637) | more than 7 years ago | (#16627276)

I prefer good'o fashioned human-grown milk [evilchili.com]

WARNING link contains nudity!!!!!!!!!!!

Re:Honey bee genome sequenced? (1)

hiervision (1019736) | more than 7 years ago | (#16629270)

I'm so against this type of science. The altering of genetic material is imminent in the research. Has anyone read Deus Machine? I'm not about to compare realities to fiction, but why tamper with the perfection of nature when we do not fully understand it. myflyfamily.com [myflyfamily.com]

How cool. (5, Funny)

DrunkenTerror (561616) | more than 7 years ago | (#16623928)

I bet this creates quite a buzz among genome researchers.

Re:How cool. (4, Funny)

Renfield Spiffioso (982789) | more than 7 years ago | (#16624502)

Yes, they'll have plenty of information to comb through.

Re:How cool. (0)

Anonymous Coward | more than 7 years ago | (#16624642)

BC says;

What are they going to discover about what is turned OFF or ON in the gay community?

In DRUG ADDICTS?

in mental illness?

Politicians?

Dictators or other despots?

socialists, communists,etc?

Re:How cool. (1)

duguk (589689) | more than 7 years ago | (#16625424)

Seems like a bit of a troll, but I'll bite because he's got a point here.

> What are they going to discover about what is turned OFF or ON in the gay community?
Violence? :D

> In DRUG ADDICTS?
Now thats a problem with addiction, but the problem occurs from something else. Difficult subject but whatever is the cause -- society? Is to blame.

> in mental illness?
Lack of stupidity? Depression is a sane reaction to the insane environment. [Taken from this very good comment [slashdot.org] ]

> Politicians?
Heh, more stupidity :)

> Dictators or other despots? socialists, communists,etc?
I think that's an opinion/envoirmental influence.



I am a gay addict ;) (I love my coffee... amongst other things!)

Monkeyboi

Re:How cool. (1)

Anne_Nonymous (313852) | more than 7 years ago | (#16625016)

Sweet!

first thing (0)

Anonymous Coward | more than 7 years ago | (#16623944)

The first thing they should do is figure out how to resequnce bee's dna to make them live longer. Worker bee lives anywhere from 1 to 4 months, depending on the season and how much work it's doing.

And in related news... (0)

Anonymous Coward | more than 7 years ago | (#16623950)

Scientists have proven that the honeybee genome can't fly either. (However, Transcendental Meditation [factnet.org] has offered to teach it to fly by butt-bouncing.)

Now they just need to sequence the Applebee (0)

Anonymous Coward | more than 7 years ago | (#16623962)

It's probably 99% identical to whitebread.

softICE, anyone? (3, Interesting)

Connie_Lingus (317691) | more than 7 years ago | (#16623972)

Is it just me, or does the whole DNA/Genome decoding process sound like rather complex dis-assembly project? Every living thing on this planet is nothing but a quad-nary based executable with VERY VERY good error-correction duplication.

Re:softICE, anyone? (3, Interesting)

Nigel Stepp (446) | more than 7 years ago | (#16624112)

Oh, it's much worse than that. Imagine if the opcode for ADD, say, would add to BX if it were after a JMP, but to AX if it were after a MOV.

Many of the features of biology are context dependent, which makes predicative analysis quite difficult.

Re:softICE, anyone? (1)

TheRaven64 (641858) | more than 7 years ago | (#16624178)

So you're saying that living creatures are written in x86 machine code?

Re:softICE, anyone? (1)

Nigel Stepp (446) | more than 7 years ago | (#16624200)

Quite the opposite :)

Re:softICE, anyone? (0)

Anonymous Coward | more than 7 years ago | (#16624344)

So now you're saying that x86 machine code is written in living creatures?

Re:softICE, anyone? (3, Funny)

Stealth Potato (619366) | more than 7 years ago | (#16624614)

Considering the number of live sacrifices I had to make to ensure the success of my last x86 project, yes, I'd say that sounds reasonable.

Re:softICE, anyone? (0)

Anonymous Coward | more than 7 years ago | (#16624564)

Only in Soviet Russia.

Re:softICE, anyone? (0)

Anonymous Coward | more than 7 years ago | (#16625590)

So you're saying that living creatures are written in x86 machine code?

Close, but the fact is, most organisms are really written in cleverly obfuscated Perl.

Re:softICE, anyone? (1)

Plutonite (999141) | more than 7 years ago | (#16624176)

Or you could spend 5 years getting an advanced degree in micro-biology and find out that there's a little more to it than that, eh ;)

Re:softICE, anyone? (2, Interesting)

Dark_MadMax666 (907288) | more than 7 years ago | (#16624440)

Very RY VERY good error-correction duplication

Uhh. ohhh. quite the opposite. Error correction is very bad (by IT standards at least) -that is how actually things evolve (since there is no mechanism for modification except mutation - which is an error). On average every single cell in human body has at least one error. Granted absolute majority of them are insignificant (since they happen on non functioning parts of code for this cell) .

  Living organism are quite a freaking mess from engineer's point of view. -Heck that's what you get if you launch a very shoddy evolutionary algorithm and run it for a couple of hundred millions of years.

Re:softICE, anyone? (1)

anubi (640541) | more than 7 years ago | (#16626774)

Yes, but what I find so astounding is that we will run for about 70 years without reboot.

In damn near all programming work I have ever done, the slightest error usually resulted in an immediate terminal fault or worse, a BSOD.

When I consider that my entire biological OS - everything that coded me for what I am - consists of about 1 gigabyte of code ( considering human DNA consists of 3 billion base pair; 3 base pair to a codon; codon roughly equivalent to byte ), I can hardly consider my coding shoddy. I consider it far more likely that we are at this point quite ignorant on the subtleties of DNA coding.

I don't see any more "bang for the buck" as I see in biology.

If I spent the rest of my life in front of a DNA sequencer, I doubt I could code to get the chemistry of a single cell to work, much less an entire organism.

I can't harp too much on this, but the elegance of this whole thing sure makes me wonder how it came to be.

Re:softICE, anyone? (1)

Dark_MadMax666 (907288) | more than 7 years ago | (#16627072)

Yes, but what I find so astounding is that we will run for about 70 years without reboot.

  Ermm.. you can't boast 5 nines of uptime either. And it doesn't take 20 years just to boot up and do anything remotely useful.


In damn near all programming work I have ever done, the slightest error usually resulted in an immediate terminal fault or worse, a BSOD.
I don't see any more "bang for the buck" as I see in biology.
If I spent the rest of my life in front of a DNA sequencer, I doubt I could code to get the chemistry of a single cell to work, much less an entire organism
I can't harp too much on this, but the elegance of this whole thing sure makes me wonder how it came to be


  You seem to fail to take into account hundreds of millions (or even billions -depending from which point you count) years it took to come to this . I fail to see any elegance in the resulting mess. But I can understand it - evolution is not an engineer its a random number generator .

Re:softICE, anyone? (1)

anubi (640541) | more than 7 years ago | (#16638110)

By any chance, are you working in genomics?

For me, DNA is like being given a 1 gigabyte ROM containing the complete OS of an unknown system. I am not given the instruction set of the machine...just the raw source. Its up to me to diddle the code- see what the machine does, and from this, deduce how the machine works.

Quite a puzzle.

I envy the guys that are in the middle of this. But I do not envy them the "pressure to show progress" when dealing with such an unknown.

Re:softICE, anyone? (1)

mikael (484) | more than 7 years ago | (#16624472)

Everything DNA related, shares a common encoding scheme. The following web page [uni-hamburg.de] explains the basic of amino acid encoding. DNA consists of four nucleotides A, T, C and G. For proteins, triplets of these are used to specify any one of 24 amino acids used. But this could simply be the DNA equivalent of Logo or VHDL (a programming language used to specify silicon chip circuits).

For some organs of the body to grow into complex shapes, some cells have to be pre-programmed to die at the correct time in order for folding to take place. So this has to be encoded in the DNA.

DNA could also be used as the tape of a Turing Machine [wikipedia.org] storing permanent state information (such as which genes are active in a honey bee).

Re:softICE, anyone? (2, Informative)

valis (947) | more than 7 years ago | (#16625422)

> Everything DNA related, shares a common encoding scheme

Not so sure about that. The encoding of amino acids in genes is quite well defined (though there are exceptions, such as selenocysteine which is produced when a signal in the 3' UTR changes the meaning of a stop codon).

And protein coding sequences only make up about 1.5% of the genome for humans. Other things in DNA are much less clear, everything in biology is stochastic. Many functional elements are directly involved in protein-DNA interactions where structure is more important than specific sequence. And not everything DNA related is in the genetic code. Positions of histones, DNA methylation, and other signals might be important.

honeybees are very cool (4, Interesting)

myc (105406) | more than 7 years ago | (#16624006)

besides their social behavior, there is a lot known about how the navigation system of honeybees works (i.e., how they find the hive after foraging). Understanding honeybee genetics could have an impact on understanding and designing autonomous systems for robotics.

Re:honeybees are very cool (2, Insightful)

w33t (978574) | more than 7 years ago | (#16624432)

Indeed, design of future machines, if it follows Kurtzweil's GNR (Genetics, Nanotech, Robotics) predictions, could very well be genetically modified at nano scale, creations endowed with artificial intelligence.

I could see the use of a self-replicating macromolecule (if not DNA, then like it) to code for proteins or some other material.

Genome sequencing seems akin to early (and current) physicists work at discovering and defining the periodic table of elements.

Re:honeybees are very cool (1)

kfg (145172) | more than 7 years ago | (#16624520)

Knowing what behaviors/qualities a gene effects is a very far cry from knowing how a complete organism goes about its business. Remember, this is poke it and see what happens reverse engineering of a very complex system.

How's WINE coming along these days? I know it's hard to believe but the Windows API isn't nearly as complex as the genetics of a bee.

Knowing how an organism goes about its business can be a far cry from how a robot should go about its business.

Do you really want robots spiraling in toward every lamp post?

KFG

Re:honeybees are very cool (4, Informative)

edschurr (999028) | more than 7 years ago | (#16627124)

Another cool thing about them is that two genes exist in some groups of honey bee which helps them fight a disease that affects larvae. The first gene causes* them to remove the wax covering the diseased larvae, and the second causes* them to toss the larvae out of the nest to die. Groups of honey bees that only have the first gene will remove the wax and leave it at that. However, it's apparantly more complex than two genes causing behaviour because some honey bees do it without those genes.

Well, that's how I remember it from The Selfish Gene by Dawkins.

* perhaps not completely

Let me guess. . . (0)

Anonymous Coward | more than 7 years ago | (#16624048)

Patent pending on the honeybee genome now, despite somewhere between thousands and billions of years' worth of prior art?

so when can we download it? (0)

Anonymous Coward | more than 7 years ago | (#16624066)

honeybee.dna.torrent link plz

Re:so when can we download it? (1, Funny)

Anonymous Coward | more than 7 years ago | (#16624154)

Careful! I've heard that bad things happen if you play Region 5 bees (Africa) with Region 2 (Europe) players imported to Region 1.

Re:so when can we download it? (1)

TheDreadSlashdotterD (966361) | more than 7 years ago | (#16626118)

Can you really call them Region 2 bees when they become Region 5 bees once exposed to each other?

Re:so when can we download it? (1)

noigmn (929935) | more than 7 years ago | (#16627232)

Yes.

They are only Region 5 bees if they marry a region 5 bee or wait 3 years for citizenship.

Reuters Error (5, Funny)

saviorsloth (467974) | more than 7 years ago | (#16624070)

Reuters' original online article about this misidentified the queen bee as Queen Elizabeth, stating that Britain's monarch was capable of laying "up to 2,000 eggs a day"
they've corrected it, but you can see the original article here:
http://www.regrettheerror.com/2006/10/reuters_typo _te.html [regrettheerror.com]

Purpose? (0)

Anonymous Coward | more than 7 years ago | (#16624134)

I can understand sequencing the human genome, but why the honeybee?
It's an insect and therefore, can't possibly be as close to humans genetically as say, a monkey.
Am I missing something here?

Re:Purpose? (2, Informative)

valis (947) | more than 7 years ago | (#16624518)

> Am I missing something here?

Yes. There is only so much you can do in a lab to humans. Or for that matter monkeys or mice. However PETA doesn't seem to realize that bees and flys are animals so...

More seriously, we work with model organisms because they are much easier to work with. You can do experiments that would either cost much much more or simply be impossible in a mammal model. Depending on what you are interested in there are lots of popular model organisms: nematodes, flys, bees, zebrafish, xenopus, mouse, rat, macaque... all useful for investigating different aspects of biology, and all relevant to human health at some level.

Pretty cool, but (2, Funny)

QuantumFTL (197300) | more than 7 years ago | (#16624194)

I understand this is pretty cool, but what could all the buzz bee about?

What about variations? (1)

DoofusOfDeath (636671) | more than 7 years ago | (#16624360)

This always confused me with the human genome project: For the most part, two different people will have somewhat different genes.

So when they sequence the human genome, how do they handle the variations? Does everyone in the project work from the same person's DNA?

Re:What about variations? (3, Informative)

valis (947) | more than 7 years ago | (#16624468)

The human genome projects worked from DNA samples pooled from a number of individuals, which were then assembled into a consensus "human genome". However the original sequenced reads can be aligned back to the reference to find differences (such as SNPs -- single nucleotide polymorphisms).

Substantial effort is underway to resequence the human genome in different individuals from different populations. The International Hapmap Project (http://www.hapmap.org/) is among the most high profile.

Re:What about variations? (3, Informative)

CharlesEGrant (465919) | more than 7 years ago | (#16626274)

So when they sequence the human genome, how do they handle the variations?

For the purposes of creating the reference sequence they essentially ignored them. In the public human genome project the DNA from a handful of individuals was used. The Celera project used mostly the DNA of one individual, Craig Venter, the head of Celera. This does make the reference sequence arbitrary, but so was the block of platinum that was used to define the kilogram. The idea is that you measure differences from the standard.

The rule of thumb is that the sequence of any two individualss differ in about 1 base in 1000. This ignores complications like that fact that women have of two copies of the X chromosome and men have 1 X and 1 Y chromosome, and that whole sections of sequence can sometimes get shifted from one chromosome to another. As the other responder pointed out the variations are a major focus of research, particularly Single Nucleotide Polymorphisms (SNPs) [nih.gov] where 90% of the population have an 'A' in a particulary position and 10% have a 'G'.

Re:What about variations? (1)

Rosonowski (250492) | more than 7 years ago | (#16627238)

I thought the kilogram was also defined as the (and I'm probably wrong on these figures) mass of a volume of water 1cmx1cm at ocean level? Kind of arbitrary as well, but it's at least tied in.

Re:What about variations? (2, Informative)

CharlesEGrant (465919) | more than 7 years ago | (#16627566)

The definition of the kilogram [nist.gov] was originally made in terms of a particular volume of water, but was later changed to the weight of a particluar ingot of irridium-platinum.

Re:What about variations? (1)

cr0sh (43134) | more than 7 years ago | (#16644041)

Actually, the "cubic centimeter of water" definition is that of a gram of water, not a kilogram - however, I am pretty sure that definition is inaccurate, and most likely came about to give a "layman's" visual to teach Americans about the metric system. The metric system's "standards" (ie, physical representative objects of quantity) are based on objects with much greater accuracy (and even then, they are only a representation, which can and does change over time as our knowledge increases, and as better representative materials and systems of manufacture become available).

Re:What about variations? (1)

Rosonowski (250492) | more than 7 years ago | (#16650259)

Yeah, I knew that, I just slipped on the order of magnitude. Thanks anyway.

Direct application: cheap honey (1)

lheal (86013) | more than 7 years ago | (#16624608)

There have been three developments in apiculture in the last 30 years or so that have driven down the availability of honey, thus driving up the price.

First, DDT got banned [salem-news.com] . Ever hear the Joni Mitchell song that goes, "Hey farmer farmer, take away the DDT now. Give me spots on apples, but leave me the birds and the bees, please." Unfortunately, the opposite happened: without DDT, honeybee competitors thrived, and stronger pesticides that actually did harm the bee were introduced.

The next problem was the spread of African or "killer" bees, which came to us via South America. These bees are basically the same as the European ones we've historically had, except for one trait: if they perceive hive attack, they don't stop attacking once the immediate threat is past, but follow the attacker until it is taught a lesson. They're somewhat more agressive in other ways, too, but it's been some years since I dealt with that.

Lastly, and possibly related to DDT removal, is a tracheal mite [ohio-state.edu] , Acarapis woodi, that kills off entire colonies. I don't think they've found any bees with defenses against the mites, nor against varroa jacobsoni, another deadly mite.

These threats have basically wiped out the cottage beekeeping industry. It got to be expensive, and no fun.

But if genetic alterations can be engineered to make the "attack until dead" gene recessive, the mite problem would be tolerable, even for hobbyists. The mites can be warded off -- that's a solvable problem, but having the hive attack you isn't. It's unlikely that genetics or DDT could do much to counter the mites directly, but you never know.

Re:Direct application: cheap honey (1)

cr0sh (43134) | more than 7 years ago | (#16643913)

Lastly, and possibly related to DDT removal, is a tracheal mite, Acarapis woodi, that kills off entire colonies. I don't think they've found any bees with defenses against the mites, nor against varroa jacobsoni, another deadly mite.


I could have sworn that the africanized honeybees were immune to the mites? I must be wrong...

Ever hear the Joni Mitchell song that goes, "Hey farmer farmer, take away the DDT now. Give me spots on apples, but leave me the birds and the bees, please."

BTW - the song is called Big Yellow Taxi [lyricsfreak.com] ...

oblig (1)

chowdy (992689) | more than 7 years ago | (#16625152)

many bees died to bring us this information

Re:oblig (1)

f8l_0e (775982) | more than 7 years ago | (#16626164)

I believe it might be illegal to have a post containing a Star Wars quote, also containing a sig with a ST:TNG quote.

Sequenced ... really ? (1)

Rain Knight (1019662) | more than 7 years ago | (#16626588)

Every time I read about DNA being sequenced I wonder if this means 3 or 4 dimensions. Is it known already what switches one gene on or off during a lifespan ? Where are the time or trigger informations stored ? ... just wondering and really am no expert ...

Re:Sequenced ... really ? (0)

Anonymous Coward | more than 7 years ago | (#16629136)

There's a very large and extensive amount of work that has been done on precisely those kinds of questions. In fact, billions of dollars are poured yearly into them.

One place to start (probably a bit advanced) is NCBI - which houses GenBank, the biggest DNA database on Earth -- http://www.ncbi.nlm.nih.gov/ [nih.gov] they have a ton of great resources and even whole textbooks which can be freely read on the subject.

There a massive amount that is still unknown, but also a suprisingly large amount which is quite well known, about how genes work.

Honey... (1)

node.four (992023) | more than 7 years ago | (#16631598)

mmm, as long as i get to eat honey life is sweet.
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