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Old 02-06-2004, 02:04 PM
Dicky
 
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Default DNA of Plants

I am going to make some researches on DNA of paphiopedilums. First, i need
to ask if there were horticulturists who can do an Artifical variety of
Paphs successfully before. Second, Where can i find the DNA of each Paphs?

--
---

Visit this website to get more information about gardening and buy flowers
securely!
http://www.dickyhorticulture.freehomepage.com



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Old 02-06-2004, 09:04 PM
TQPL
 
Posts: n/a
Default DNA of Plants

Hi Dicky,

Can you re-write you question differently so I can
understand it?
Are you trying to breed Paphiopedilums?
Are you looking for genetics of Paphiopedilums?
Are you trying to raise Paphipedilums
artificially....seedlings?

Research on Pahiopedilum DNA is limited..
Some people may have done DNA fingerprinting to
study origins, but I do not think you
will find results on the www.

With regards
Alan



"Dicky" wrote in
message ...
I am going to make some researches on DNA of

paphiopedilums. First, i need
to ask if there were horticulturists who can do

an Artifical variety of
Paphs successfully before. Second, Where can i

find the DNA of each Paphs?

--
---

Visit this website to get more information about

gardening and buy flowers
securely!
http://www.dickyhorticulture.freehomepage.com




  #3   Report Post  
Old 02-06-2004, 10:06 PM
Rob Halgren
 
Posts: n/a
Default DNA of Plants

TQPL wrote:

Hi Dicky,

Can you re-write you question differently so I can
understand it?
Are you trying to breed Paphiopedilums?
Are you looking for genetics of Paphiopedilums?
Are you trying to raise Paphipedilums
artificially....seedlings?



I was a little unclear myself.

Research on Paphiopedilum DNA is limited..
Some people may have done DNA fingerprinting to
study origins, but I do not think you
will find results on the www.



No taxonomic analyses that I could find, but there are some DNA
sequences published. Mainly 5.8S rRNA and ITS2 sequences, so somebody
is working on it. You could take these sequences and run some
phylogenetic analyses. Of course you would have to learn how to do that
properly (it is quite easy to do it improperly). I'd suggest PAUP as a
good software package to use for this.

http://www.ncbi.nlm.nih.gov/entrez/q...aphioped ilum

Now, if you are looking for other things (full genomic sequence, or
even just specific gene sequences), you are out of luck. None of that
has been done (or if it has, it hasn't been published). We aren't quite
to the point of making it trivial to sequence a genome, it still takes a
while and a lot of money. Less time and less money than a couple years
ago (or a couple months ago). I think that Paphiopedilum as a genus is
probably similar enough at the genomic level that you would only really
have to sequence one species, at least as a reference set. Pick a
species, any species...

There is a program from the JGI (US Department of Energy Joint
Genomes Institute) that will fund genome sequencing, if you can convince
them that your organism is interesting enough and that you can handle
the data analysis. At least I assume they are still soliciting
proposals. If there is enough interest in this, I can provide the data
analysis if somebody wants to provide the rationale and paperwork. I'm
supporting a proposal to look at a fungus (death angel mushroom,
actually), but orchids would be more fun.

Rob (why yes, I am a bioinformatician...)

--
Rob's Rules: http://www.msu.edu/~halgren
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 purchase
more orchids, obtain more credit
  #4   Report Post  
Old 03-06-2004, 11:07 AM
Dicky
 
Posts: n/a
Default DNA of Plants

I am meaning that i want to make a Variety Paphs by human technology, for
example how to turn Paph.hangianum from yellow to blue...etc.
And i would like to know the method in making some paphs into Alba/Album
form, i.e bellatulum -- bellatulum fma. album , philippinense --
philippinense fma. album.. thank you ^^
"Rob Halgren"
...
TQPL wrote:

Hi Dicky,

Can you re-write you question differently so I can
understand it?
Are you trying to breed Paphiopedilums?
Are you looking for genetics of Paphiopedilums?
Are you trying to raise Paphipedilums
artificially....seedlings?



I was a little unclear myself.

Research on Paphiopedilum DNA is limited..
Some people may have done DNA fingerprinting to
study origins, but I do not think you
will find results on the www.



No taxonomic analyses that I could find, but there are some DNA
sequences published. Mainly 5.8S rRNA and ITS2 sequences, so somebody
is working on it. You could take these sequences and run some
phylogenetic analyses. Of course you would have to learn how to do that
properly (it is quite easy to do it improperly). I'd suggest PAUP as a
good software package to use for this.


http://www.ncbi.nlm.nih.gov/entrez/q...cleotide&term=
paphiopedilum

Now, if you are looking for other things (full genomic sequence, or
even just specific gene sequences), you are out of luck. None of that
has been done (or if it has, it hasn't been published). We aren't quite
to the point of making it trivial to sequence a genome, it still takes a
while and a lot of money. Less time and less money than a couple years
ago (or a couple months ago). I think that Paphiopedilum as a genus is
probably similar enough at the genomic level that you would only really
have to sequence one species, at least as a reference set. Pick a
species, any species...

There is a program from the JGI (US Department of Energy Joint
Genomes Institute) that will fund genome sequencing, if you can convince
them that your organism is interesting enough and that you can handle
the data analysis. At least I assume they are still soliciting
proposals. If there is enough interest in this, I can provide the data
analysis if somebody wants to provide the rationale and paperwork. I'm
supporting a proposal to look at a fungus (death angel mushroom,
actually), but orchids would be more fun.

Rob (why yes, I am a bioinformatician...)

--
Rob's Rules: http://www.msu.edu/~halgren
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 purchase
more orchids, obtain more credit



  #5   Report Post  
Old 03-06-2004, 11:07 AM
Dicky
 
Posts: n/a
Default DNA of Plants

In addition, If i want to study in this type of research, what universities
can i enter? And what is the subject for that, Horticulture? Biochem? ....
etc. Also, should i learn Genetics?
"Dicky" 级糶秎ン穝籇
...
I am meaning that i want to make a Variety Paphs by human technology, for
example how to turn Paph.hangianum from yellow to blue...etc.
And i would like to know the method in making some paphs into Alba/Album
form, i.e bellatulum -- bellatulum fma. album , philippinense --
philippinense fma. album.. thank you ^^
"Rob Halgren"
...
TQPL wrote:

Hi Dicky,

Can you re-write you question differently so I can
understand it?
Are you trying to breed Paphiopedilums?
Are you looking for genetics of Paphiopedilums?
Are you trying to raise Paphipedilums
artificially....seedlings?



I was a little unclear myself.

Research on Paphiopedilum DNA is limited..
Some people may have done DNA fingerprinting to
study origins, but I do not think you
will find results on the www.



No taxonomic analyses that I could find, but there are some DNA
sequences published. Mainly 5.8S rRNA and ITS2 sequences, so somebody
is working on it. You could take these sequences and run some
phylogenetic analyses. Of course you would have to learn how to do that
properly (it is quite easy to do it improperly). I'd suggest PAUP as a
good software package to use for this.



http://www.ncbi.nlm.nih.gov/entrez/q...cleotide&term=
paphiopedilum

Now, if you are looking for other things (full genomic sequence, or
even just specific gene sequences), you are out of luck. None of that
has been done (or if it has, it hasn't been published). We aren't quite
to the point of making it trivial to sequence a genome, it still takes a
while and a lot of money. Less time and less money than a couple years
ago (or a couple months ago). I think that Paphiopedilum as a genus is
probably similar enough at the genomic level that you would only really
have to sequence one species, at least as a reference set. Pick a
species, any species...

There is a program from the JGI (US Department of Energy Joint
Genomes Institute) that will fund genome sequencing, if you can convince
them that your organism is interesting enough and that you can handle
the data analysis. At least I assume they are still soliciting
proposals. If there is enough interest in this, I can provide the data
analysis if somebody wants to provide the rationale and paperwork. I'm
supporting a proposal to look at a fungus (death angel mushroom,
actually), but orchids would be more fun.

Rob (why yes, I am a bioinformatician...)

--
Rob's Rules: http://www.msu.edu/~halgren
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 purchase
more orchids, obtain more credit







  #6   Report Post  
Old 03-06-2004, 11:08 AM
Dicky
 
Posts: n/a
Default DNA of Plants

Thanks for Rob's reply. The data is very useful. ^^
"Dicky" 级糶秎ン穝籇
...
In addition, If i want to study in this type of research, what

universities
can i enter? And what is the subject for that, Horticulture? Biochem? ....
etc. Also, should i learn Genetics?
"Dicky" 级糶秎ン穝籇
...
I am meaning that i want to make a Variety Paphs by human technology,

for
example how to turn Paph.hangianum from yellow to blue...etc.
And i would like to know the method in making some paphs into Alba/Album
form, i.e bellatulum -- bellatulum fma. album , philippinense --
philippinense fma. album.. thank you ^^
"Rob Halgren"
...
TQPL wrote:

Hi Dicky,

Can you re-write you question differently so I can
understand it?
Are you trying to breed Paphiopedilums?
Are you looking for genetics of Paphiopedilums?
Are you trying to raise Paphipedilums
artificially....seedlings?



I was a little unclear myself.

Research on Paphiopedilum DNA is limited..
Some people may have done DNA fingerprinting to
study origins, but I do not think you
will find results on the www.



No taxonomic analyses that I could find, but there are some DNA
sequences published. Mainly 5.8S rRNA and ITS2 sequences, so somebody
is working on it. You could take these sequences and run some
phylogenetic analyses. Of course you would have to learn how to do

that
properly (it is quite easy to do it improperly). I'd suggest PAUP as

a
good software package to use for this.




http://www.ncbi.nlm.nih.gov/entrez/q...cleotide&term=
paphiopedilum

Now, if you are looking for other things (full genomic sequence,

or
even just specific gene sequences), you are out of luck. None of that
has been done (or if it has, it hasn't been published). We aren't

quite
to the point of making it trivial to sequence a genome, it still takes

a
while and a lot of money. Less time and less money than a couple

years
ago (or a couple months ago). I think that Paphiopedilum as a genus

is
probably similar enough at the genomic level that you would only

really
have to sequence one species, at least as a reference set. Pick a
species, any species...

There is a program from the JGI (US Department of Energy Joint
Genomes Institute) that will fund genome sequencing, if you can

convince
them that your organism is interesting enough and that you can handle
the data analysis. At least I assume they are still soliciting
proposals. If there is enough interest in this, I can provide the

data
analysis if somebody wants to provide the rationale and paperwork.

I'm
supporting a proposal to look at a fungus (death angel mushroom,
actually), but orchids would be more fun.

Rob (why yes, I am a bioinformatician...)

--
Rob's Rules: http://www.msu.edu/~halgren
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 purchase
more orchids, obtain more credit







  #7   Report Post  
Old 03-06-2004, 04:10 PM
Rob Halgren
 
Posts: n/a
Default DNA of Plants

Dicky wrote:

In addition, If i want to study in this type of research, what universities
can i enter? And what is the subject for that, Horticulture? Biochem? ....
etc. Also, should i learn Genetics?


If you are thinking about studying in the US, pick one of the big
state universities that specializes in agricultural research. Michigan
State, for example. The reason for this is that gene transformation in
plants often requires very expensive equipment (gold particle guns,
etc.), which may not be available at a smaller school. There are
several oriental institutions that have substantial orchid research
departments (in China, Taiwan, and Japan, for sure). I would study
biochemistry, genetics, and molecular biology. All three. You need all
that to even start with the project you propose. It isn't impossible,
in fact it is quite possible, but there are substantial barriers in the way.


1. The genes for pigment formation have not been sequenced in paphs (or
any orchid that I know of). You can get a good idea from other plants
(arabidopsis) where these pathways are reasonably well understood, but
you would still need to clone out the orchid genes.


2. You could make alba orchids fairly readily by disrupting pigment
synthesis. I'm not that familiar with the literature, but I don't know
of anybody who has done that yet. It has always been a little pet
project of mine, actually. Project in the sense that I have been
thinking about how to do it, not in that I've actually tried.


3. I did see a paper recently about introducing foreign DNA into ...
cymbidium? ... Problem was that it was a transient transfection -
meaning the DNA wasn't stably integrated into the target organism. You
really want your genetic manipulations to be permanent. I think that
has been demonstrated, I just haven't seen the paper.


4. The major barrier to doing this with paphiopedilum is that it is
very difficult to grow these cells in tissue culture. Otherwise we
would be able to 'clone' paphs, which just doesn't happen very easily.
Hence, paphs aren't the best system to learn how to do genetic
modifications in. I'd stick with phals or cymbidiums, at least to learn
the techniques.


Don't let any of that stop you from dreaming about doing it. It isn't
easy, and it isn't cheap. But it is interesting. You could make a very
good scientific career out of answering the kinds of questions you ask.

Rob

--
Rob's Rules: http://www.msu.edu/~halgren

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 purchase
more orchids, obtain more credit
  #8   Report Post  
Old 03-06-2004, 08:07 PM
TQPL
 
Posts: n/a
Default DNA of Plants

Hi Dicky,

Thanks for explaining your goals.
Rob is very optimistic and gives you some good
sound ideas.
Unfortunately I am not otpimistic for you.
As Rob said "the big problem is going to be the
Paph tc." Though even that is small...compared
to your aims.

I would go for bio-technology studies even though
GM has a bad press.
If you could in the future colour modify tobacco
( a comparative easy bio-engineering plant)
it might be a start.

Your work would have to be carried out in research
institutions and be licenced. You probably would
need to be part of a team or have a doctorate.

There are many more commercial orchids than Paphs
that might give more lucrative results.

However if you look around at horticulture,
changing flower colour has not been achieved
with any great success todate.
Many would consider there are easier plants
around to study than orchids for such goals.

The red rose turned into the blue of delphinium is
simply not with us in 2004.
There are multimillion pound projects searching
for solutions but they are not arriving
with results.

Then you have the problem....will the public
accept such plants. If not - they are
commercially dead. You cannot simply 'release'
modified plants.

Some people, including companies and institutions
would argue that there are more lucrative and
humanitarian avenues to follow,
such as medical drug production in plant crops.

Achieving albums, albas and other variants from
seedlings on flowering may be a much easier to
achieve goal for you in Paphiopedilums.

Good luck.
If you can achieve it you will become a
billionaire.

With regards
Alan.










"Rob Halgren" wrote in
message ...



4. The major barrier to doing this with

paphiopedilum is that it is
very difficult to grow these cells in tissue

culture. Otherwise we
would be able to 'clone' paphs, which just

doesn't happen very easily.
Hence, paphs aren't the best system to learn how

to do genetic
modifications in. I'd stick with phals or

cymbidiums, at least to learn
the techniques.


Don't let any of that stop you from dreaming

about doing it. It isn't
easy, and it isn't cheap. But it is

interesting. You could make a very
good scientific career out of answering the

kinds of questions you ask.

Rob

--
Rob's Rules:

http://www.msu.edu/~halgren

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

purchase
more orchids, obtain more credit









  #9   Report Post  
Old 05-06-2004, 02:03 PM
Dicky
 
Posts: n/a
Default DNA of Plants

Rob,
Are the weird code at the bottom of each page of the Nuleotide the DNA
arrangement?
"TQPL" 级糶秎ン穝籇
...
Hi Dicky,

Thanks for explaining your goals.
Rob is very optimistic and gives you some good
sound ideas.
Unfortunately I am not otpimistic for you.
As Rob said "the big problem is going to be the
Paph tc." Though even that is small...compared
to your aims.

I would go for bio-technology studies even though
GM has a bad press.
If you could in the future colour modify tobacco
( a comparative easy bio-engineering plant)
it might be a start.

Your work would have to be carried out in research
institutions and be licenced. You probably would
need to be part of a team or have a doctorate.

There are many more commercial orchids than Paphs
that might give more lucrative results.

However if you look around at horticulture,
changing flower colour has not been achieved
with any great success todate.
Many would consider there are easier plants
around to study than orchids for such goals.

The red rose turned into the blue of delphinium is
simply not with us in 2004.
There are multimillion pound projects searching
for solutions but they are not arriving
with results.

Then you have the problem....will the public
accept such plants. If not - they are
commercially dead. You cannot simply 'release'
modified plants.

Some people, including companies and institutions
would argue that there are more lucrative and
humanitarian avenues to follow,
such as medical drug production in plant crops.

Achieving albums, albas and other variants from
seedlings on flowering may be a much easier to
achieve goal for you in Paphiopedilums.

Good luck.
If you can achieve it you will become a
billionaire.

With regards
Alan.










"Rob Halgren" wrote in
message ...



4. The major barrier to doing this with

paphiopedilum is that it is
very difficult to grow these cells in tissue

culture. Otherwise we
would be able to 'clone' paphs, which just

doesn't happen very easily.
Hence, paphs aren't the best system to learn how

to do genetic
modifications in. I'd stick with phals or

cymbidiums, at least to learn
the techniques.


Don't let any of that stop you from dreaming

about doing it. It isn't
easy, and it isn't cheap. But it is

interesting. You could make a very
good scientific career out of answering the

kinds of questions you ask.

Rob

--
Rob's Rules:

http://www.msu.edu/~halgren

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

purchase
more orchids, obtain more credit











  #10   Report Post  
Old 06-06-2004, 01:07 AM
lo kim lin
 
Posts: n/a
Default DNA of Plants

Cribb has done research on this. He has a done this in order to establish an
overview of the genetic relationships and on the web you should be able to
find the tree like structure he produced from his findings. If found it once
so it should be there.

Good luck.

"Dicky" schreef in bericht
...
Rob,
Are the weird code at the bottom of each page of the Nuleotide the DNA
arrangement?
"TQPL" 级糶秎ン穝籇
...
Hi Dicky,

Thanks for explaining your goals.
Rob is very optimistic and gives you some good
sound ideas.
Unfortunately I am not otpimistic for you.
As Rob said "the big problem is going to be the
Paph tc." Though even that is small...compared
to your aims.

I would go for bio-technology studies even though
GM has a bad press.
If you could in the future colour modify tobacco
( a comparative easy bio-engineering plant)
it might be a start.

Your work would have to be carried out in research
institutions and be licenced. You probably would
need to be part of a team or have a doctorate.

There are many more commercial orchids than Paphs
that might give more lucrative results.

However if you look around at horticulture,
changing flower colour has not been achieved
with any great success todate.
Many would consider there are easier plants
around to study than orchids for such goals.

The red rose turned into the blue of delphinium is
simply not with us in 2004.
There are multimillion pound projects searching
for solutions but they are not arriving
with results.

Then you have the problem....will the public
accept such plants. If not - they are
commercially dead. You cannot simply 'release'
modified plants.

Some people, including companies and institutions
would argue that there are more lucrative and
humanitarian avenues to follow,
such as medical drug production in plant crops.

Achieving albums, albas and other variants from
seedlings on flowering may be a much easier to
achieve goal for you in Paphiopedilums.

Good luck.
If you can achieve it you will become a
billionaire.

With regards
Alan.










"Rob Halgren" wrote in
message ...



4. The major barrier to doing this with

paphiopedilum is that it is
very difficult to grow these cells in tissue

culture. Otherwise we
would be able to 'clone' paphs, which just

doesn't happen very easily.
Hence, paphs aren't the best system to learn how

to do genetic
modifications in. I'd stick with phals or

cymbidiums, at least to learn
the techniques.


Don't let any of that stop you from dreaming

about doing it. It isn't
easy, and it isn't cheap. But it is

interesting. You could make a very
good scientific career out of answering the

kinds of questions you ask.

Rob

--
Rob's Rules:

http://www.msu.edu/~halgren

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

purchase
more orchids, obtain more credit















  #11   Report Post  
Old 08-06-2004, 05:31 PM
Rob Halgren
 
Posts: n/a
Default DNA of Plants

Dicky wrote:

Rob,
Are the weird code at the bottom of each page of the Nuleotide the DNA
arrangement?


If it is some combination of (a t g c) then yes.

Rob

--
Rob's Rules: http://www.msu.edu/~halgren
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 purchase
more orchids, obtain more credit


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