Scientists sequenced the genome of the honeybee.

http://www.sciencenews.org/articles/20061028/fob1.asp

In this article the reporter writes "Among the novelties of the honeybee,
Apis mellifera, are its 170 genes for odor receptors."

Now, how do they know that?

Back in the dark ages when I was in school, if we had time off from burning
witches at the stake we were taught that DNA was a double helix strand with
codes for stops and starts and that was about what was known at the time.
This was in the 'one gene, one protein' system of thought. Nowadays I
understand genetic expression depends on when a gene or genetic sequence is
switched on or off etc. (All very mind boggling to me)

But if this is the first time a species' genome has been looked at and if
there are only 5 other insects that have had their genome cracked, much less
studied, then 'How do they know?"

K Barrett

K Barrett wrote:
Scientists sequenced the genome of the honeybee.

http://www.sciencenews.org/articles/20061028/fob1.asp

In this article the reporter writes "Among the novelties of the honeybee,
Apis mellifera, are its 170 genes for odor receptors."

(snip)

But if this is the first time a species' genome has been looked at and if
there are only 5 other insects that have had their genome cracked, much less
studied, then 'How do they know?"

By comparison with known odor receptor genes in fruit flies, Drosophila
melanogaster. It doesn't actually matter how many insects have had
their genomes sequenced. What matters is that fruitflies have been
sequenced, AND their genes have been mutated to see what they do.

wrote:
K Barrett wrote:
Scientists sequenced the genome of the honeybee.

http://www.sciencenews.org/articles/20061028/fob1.asp

In this article the reporter writes "Among the novelties of the honeybee,
Apis mellifera, are its 170 genes for odor receptors."

(snip)

But if this is the first time a species' genome has been looked at and if
there are only 5 other insects that have had their genome cracked, much less
studied, then 'How do they know?"

By comparison with known odor receptor genes in fruit flies, Drosophila
melanogaster. It doesn't actually matter how many insects have had
their genomes sequenced. What matters is that fruitflies have been
sequenced, AND their genes have been mutated to see what they do.


Yep. We bioinformatics geeks do this all the time. It doesn't much
matter that we haven't figured out all the honeybee genes, it does
matter that we know a lot about related genes in other organisms.

The 170 genes were probably mostly predicted computationally. We know
what coding DNA looks like from experience with other organisms. We
assume that it is similar in 'unknown' organisms. It is a computational
model (probably several different ones) that of course isn't perfect.
Perhaps some of those 170 genes aren't real, or slightly mis-predicted.
But we might have missed a few, too.

--
Rob's Rules: http://littlefrogfarm.com
1) There is always room for one more orchid
2) There is always room for two more orchids
2a) See rule 1
3) When one has insufficient credit to obtain more
orchids, obtain more credit

Thank you both for answering.

K


"Rob" wrote in message
...
wrote:
K Barrett wrote:
Scientists sequenced the genome of the honeybee.

http://www.sciencenews.org/articles/20061028/fob1.asp

In this article the reporter writes "Among the novelties of the
honeybee,
Apis mellifera, are its 170 genes for odor receptors."

(snip)

But if this is the first time a species' genome has been looked at and
if
there are only 5 other insects that have had their genome cracked, much
less
studied, then 'How do they know?"

By comparison with known odor receptor genes in fruit flies, Drosophila
melanogaster. It doesn't actually matter how many insects have had
their genomes sequenced. What matters is that fruitflies have been
sequenced, AND their genes have been mutated to see what they do.


Yep. We bioinformatics geeks do this all the time. It doesn't much
matter that we haven't figured out all the honeybee genes, it does matter
that we know a lot about related genes in other organisms.

The 170 genes were probably mostly predicted computationally. We know
what coding DNA looks like from experience with other organisms. We
assume that it is similar in 'unknown' organisms. It is a computational
model (probably several different ones) that of course isn't perfect.
Perhaps some of those 170 genes aren't real, or slightly mis-predicted.
But we might have missed a few, too.

--
Rob's Rules: http://littlefrogfarm.com
1) There is always room for one more orchid
2) There is always room for two more orchids
2a) See rule 1
3) When one has insufficient credit to obtain more
orchids, obtain more credit

Well it's simple Kathy, I was kicked out of science class for turning on
the Bunson Burners ( in a 3rd world class in Africa)

Anyway it's all in the genes. If you don't gnome the mutant then leave it
to the odor receptors!

HaH!
Cheers Wendy


email Address Invalid

K Barrett wrote:
Thank you both for answering.

K


"Rob" wrote in message
...
wrote:
K Barrett wrote:
Scientists sequenced the genome of the honeybee.

http://www.sciencenews.org/articles/20061028/fob1.asp

In this article the reporter writes "Among the novelties of the
honeybee,
Apis mellifera, are its 170 genes for odor receptors."

(snip)

But if this is the first time a species' genome has been looked at
and if
there are only 5 other insects that have had their genome cracked,
much less
studied, then 'How do they know?"

By comparison with known odor receptor genes in fruit flies,
Drosophila melanogaster. It doesn't actually matter how many
insects have had their genomes sequenced. What matters is that
fruitflies have been sequenced, AND their genes have been mutated
to see what they do.

Yep. We bioinformatics geeks do this all the time. It doesn't much
matter that we haven't figured out all the honeybee genes, it does
matter that we know a lot about related genes in other organisms.

The 170 genes were probably mostly predicted computationally. We
know what coding DNA looks like from experience with other
organisms. We assume that it is similar in 'unknown' organisms. It
is a computational model (probably several different ones) that of
course isn't perfect. Perhaps some of those 170 genes aren't real,
or slightly mis-predicted. But we might have missed a few, too.

--
Rob's Rules: http://littlefrogfarm.com
1) There is always room for one more orchid
2) There is always room for two more orchids
2a) See rule 1
3) When one has insufficient credit to obtain more
orchids, obtain more credit

Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

K

"wendy7" wrote in message
...
Well it's simple Kathy, I was kicked out of science class for turning on
the Bunson Burners ( in a 3rd world class in Africa)

Anyway it's all in the genes. If you don't gnome the mutant then leave it
to the odor receptors!

HaH!
Cheers Wendy


email Address Invalid

K Barrett wrote:
Thank you both for answering.

K


"Rob" wrote in message
...
wrote:
K Barrett wrote:
Scientists sequenced the genome of the honeybee.

http://www.sciencenews.org/articles/20061028/fob1.asp

In this article the reporter writes "Among the novelties of the
honeybee,
Apis mellifera, are its 170 genes for odor receptors."

(snip)

But if this is the first time a species' genome has been looked at
and if
there are only 5 other insects that have had their genome cracked,
much less
studied, then 'How do they know?"

By comparison with known odor receptor genes in fruit flies,
Drosophila melanogaster. It doesn't actually matter how many
insects have had their genomes sequenced. What matters is that
fruitflies have been sequenced, AND their genes have been mutated
to see what they do.

Yep. We bioinformatics geeks do this all the time. It doesn't much
matter that we haven't figured out all the honeybee genes, it does
matter that we know a lot about related genes in other organisms.

The 170 genes were probably mostly predicted computationally. We
know what coding DNA looks like from experience with other
organisms. We assume that it is similar in 'unknown' organisms. It
is a computational model (probably several different ones) that of
course isn't perfect. Perhaps some of those 170 genes aren't real,
or slightly mis-predicted. But we might have missed a few, too.

--
Rob's Rules: http://littlefrogfarm.com
1) There is always room for one more orchid
2) There is always room for two more orchids
2a) See rule 1
3) When one has insufficient credit to obtain more
orchids, obtain more credit

K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

I saw a TV show on my new 60" HD TV about a census of marine micro organisms
that is currently underway.

They are using cutting edge genetic sequencing tools to count new micro
organisms in sea water. They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes something
a computer program can use to count the number of unique organisms that were
in the sea water sample BEFORE they were chopped to bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species at the microscopic level are
lots of gene groups with interesting mutations on gene groups which they
already know are used by these organisms to do things like turn light into
energy, break down oily carbon compounds, enhance immunity to cold, etc.

It is just scary what bags of genes called 'humans' can infer about
themselves based on what is literally a sampling of their gene pool.



wrote in message
oups.com...
K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

Was that on the Sorceror II? J Craig Ventner's effort? He was the fellow
that beat the government's Human Genome Project to sequence the human
genome. He also was one of the folks I was thinking about when I asked my
question. A few years ago he was on 'Science Friday' (NPR) talking about
how he scoops up plankton, sequences the DNA, and has found over 800 genes
that deal with handling light. Again, I wondered 'how does he know?' Plus,
he's got one hell of a web page:
http://www.sorcerer2expedition.org/v.../HTML/main.htm

Jealousy overwhelms me.

K Barrett

"al" wrote in message news:i_x2h.5189$Z66.2452@trnddc07...
I saw a TV show on my new 60" HD TV about a census of marine micro
organisms that is currently underway.

They are using cutting edge genetic sequencing tools to count new micro
organisms in sea water. They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes
something a computer program can use to count the number of unique
organisms that were in the sea water sample BEFORE they were chopped to
bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species at the microscopic level
are lots of gene groups with interesting mutations on gene groups which
they already know are used by these organisms to do things like turn light
into energy, break down oily carbon compounds, enhance immunity to cold,
etc.

It is just scary what bags of genes called 'humans' can infer about
themselves based on what is literally a sampling of their gene pool.



wrote in message
oups.com...
K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past,
raising the question(s) how do they know and what then is human?

I don't mean to beat this to death, because Nick and Rob have already
answered, but boy. If you wanted to start writing thrillers with conspiracy
theories you wouldnt have to go much further than a DNA lab.

K Barrett

"al" wrote in message news:i_x2h.5189$Z66.2452@trnddc07...
I saw a TV show on my new 60" HD TV about a census of marine micro
organisms that is currently underway.

They are using cutting edge genetic sequencing tools to count new micro
organisms in sea water. They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes
something a computer program can use to count the number of unique
organisms that were in the sea water sample BEFORE they were chopped to
bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species at the microscopic level
are lots of gene groups with interesting mutations on gene groups which
they already know are used by these organisms to do things like turn light
into energy, break down oily carbon compounds, enhance immunity to cold,
etc.

It is just scary what bags of genes called 'humans' can infer about
themselves based on what is literally a sampling of their gene pool.



wrote in message
oups.com...
K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

K Barrett wrote:
Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past,
raising the question(s) how do they know and what then is human?

In many cases, old viral sequence has features that scream "virus"
(long terminal repeats, etc) or can be identified by homology to
current, active viruses. But sometimes, it's not obvious that there is
a bright line dividing "human" and "virus." Viruses can pick up human
sequences. The reverse can also happen: sometimes, the evolutionary
history of a human gene includes insertion of viral elements. For
instance, the salivary amylase gene appears to have been generated when
a retroviral sequence inserted into the promoter region of an ancestral
pancreatic amylase gene. The retroviral sequence is what causes the
amylase gene to be expressed in salivary glands. So, in this case, the
sequence of a virus has become human.

Thanks again! This is great. Like having my own little continuing
education class.

Science really has exploded since I was in school. Recently I googled
Robert J. Griesbach USDA in order to read if he had any papers published on
microfungus (a question from a different thread here and more orchid
related) and came up with a list of abstracts for his papers, someof which
dealt with color (blue) in phalaenopsis. One google search on terms led to
another and another and I came away impressed at how some very minute
research leads to greater knowledge.

Anyway,

Thanks again for filling me in. I appreciate it.

K Barrett
wrote in message
oups.com...
K Barrett wrote:
Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past,
raising the question(s) how do they know and what then is human?

In many cases, old viral sequence has features that scream "virus"
(long terminal repeats, etc) or can be identified by homology to
current, active viruses. But sometimes, it's not obvious that there is
a bright line dividing "human" and "virus." Viruses can pick up human
sequences. The reverse can also happen: sometimes, the evolutionary
history of a human gene includes insertion of viral elements. For
instance, the salivary amylase gene appears to have been generated when
a retroviral sequence inserted into the promoter region of an ancestral
pancreatic amylase gene. The retroviral sequence is what causes the
amylase gene to be expressed in salivary glands. So, in this case, the
sequence of a virus has become human.

Yes, the Sorcerer II expedition. Very VERY Amazing.

"K Barrett" wrote in message
. ..
Was that on the Sorceror II? J Craig Ventner's effort? He was the fellow
that beat the government's Human Genome Project to sequence the human
genome. He also was one of the folks I was thinking about when I asked my
question. A few years ago he was on 'Science Friday' (NPR) talking about
how he scoops up plankton, sequences the DNA, and has found over 800 genes
that deal with handling light. Again, I wondered 'how does he know?'
Plus, he's got one hell of a web page:
http://www.sorcerer2expedition.org/v.../HTML/main.htm

Jealousy overwhelms me.

K Barrett

K Barrett wrote:
Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past....


Yes, I remember reading about this several years ago. In the years that
have passed since then, I have often wondered what I would look like and
what I would feel like if there was a way to magically get rid of all
the useless crap in my DNA and leave only the pure me.

Steve

al wrote:

...............They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes something
a computer program can use to count the number of unique organisms that were
in the sea water sample BEFORE they were chopped to bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species.........................

Well no wonder! It sounds to me like they are MAKING new species.

Steve