The Feb issue of 'Orchids' has a nice article that's way over my head on the
genetic fingerprint for Phrag. kovachii.

Finally I can see the results of a so-called fingerprint and I can see how
the A,T,G and C's all match up - so I can see how they'd be valuable in
forensics.

Now.

How does one recognise and isolate one individual from another?

Is "CSI/Orchids" our next TV program?

K Barrett
(Yes, I'm amazed you have to explain this to me. I *love* reading forensic
murder mysteries, yet I know that the forensic DNA PCR tests that are used
in a court of law only check 9 or so places in order to determine within a
certain probability that the DNA in question comes from a certain
individual or not. However the article makes note that 'they' will be using
the genome of P. kovachii to forensically identify individuals - presumably
tracking them from known source materials - and tracking the use of this
'known source DNA' in hybrids. Surely making P. kovachii one of the best
(worst) known and tracked individuals on the planet! I tell you, its a
Shakespearian tale! - A tale told by an idiot, full of wind and fury,
signifying nothing...)

The basic idea is to use an enzyme (restriction enzyme) to cut the
organism's DNA strands at particular base sequence (ATGC...) regions.
The resulting pieces are placed on a gel and an electrical field is
applied to the gel causing the pieces to move across the gel at pacing
that varies with fragment size. After awhile, the various fragments
form separate bands that can be compared to other sample.

The possibility of having two digestion results that match that are
not in truth identical is low. Refinements of this technique, and
other evidence, bring the mismatch rate even lower.

Jim
============================================
James Aldridge - Fort Worth, Texas, USA
www.JamesAldridge.com -

In this instance they tested 4 separate plants of Phrag kovachii and the
resultant DNA sequences were all the same. Wouldn't there have been some
sort of difference in their DNA if they were individuals? I'm thinking they
tested 4 plants that were pieces of one original plant. Some Phrags will
make separate plantlets along one long rhizome, like besseae for example.
I'm wondering if all kovachiis aren't really from one plant, that they are
a clone - like what happens with sea anemones. (Sorry, that's what I have my
degree in, so that's what I fall back on)

K Barrett

"James Aldridge" wrote in message
...
The basic idea is to use an enzyme (restriction enzyme) to cut the
organism's DNA strands at particular base sequence (ATGC...) regions.
The resulting pieces are placed on a gel and an electrical field is
applied to the gel causing the pieces to move across the gel at pacing
that varies with fragment size. After awhile, the various fragments
form separate bands that can be compared to other sample.

The possibility of having two digestion results that match that are
not in truth identical is low. Refinements of this technique, and
other evidence, bring the mismatch rate even lower.

Jim
============================================
James Aldridge - Fort Worth, Texas, USA
www.JamesAldridge.com -

K Barrett wrote:

In this instance they tested 4 separate plants of Phrag kovachii and the
resultant DNA sequences were all the same. Wouldn't there have been some
sort of difference in their DNA if they were individuals?.................

If you can believe that more than 98% of human DNA is identical to
chimpanzee DNA, it makes it easier to believe that they would find zero
difference between four different (but probably closely related)
kovachii plants.
Keep in mind that I'm not talking about the DNA actually having zero
difference. I'm assuming that Jim is right about how the analysis was
done. Breaking up the DNA strands at certain points still allows for
some undetected differences in between the breaks.
When pictures of different kovachii plants started to hit the print and
the internet, there seemed to be some obvious differences between
plants. If someone could map the entire genome of these different
plants, then some little variations would be seen.

Steve

You have a degree in sea anemones? Or do you mean marine biology?
Just curious,
Murri

"K Barrett" wrote in message
...
In this instance they tested 4 separate plants of Phrag kovachii and the
resultant DNA sequences were all the same. Wouldn't there have been some
sort of difference in their DNA if they were individuals? I'm thinking
they
tested 4 plants that were pieces of one original plant. Some Phrags will
make separate plantlets along one long rhizome, like besseae for example.
I'm wondering if all kovachiis aren't really from one plant, that they
are
a clone - like what happens with sea anemones. (Sorry, that's what I have
my
degree in, so that's what I fall back on)

K Barrett

"James Aldridge" wrote in message
...
The basic idea is to use an enzyme (restriction enzyme) to cut the
organism's DNA strands at particular base sequence (ATGC...) regions.
The resulting pieces are placed on a gel and an electrical field is
applied to the gel causing the pieces to move across the gel at pacing
that varies with fragment size. After awhile, the various fragments
form separate bands that can be compared to other sample.

The possibility of having two digestion results that match that are
not in truth identical is low. Refinements of this technique, and
other evidence, bring the mismatch rate even lower.

Jim
============================================
James Aldridge - Fort Worth, Texas, USA
www.JamesAldridge.com -

Though I feel it would be more appropriate to comment in two weeks when
I receive my copy here at the end of the postal world, Ohio, if we must
jump the gun, I take my cue from your note to OGD quoting the article I
won't see for fourteen more days:

On page 135, second paragraph they write "The individual and combined
analyses demonstrate the distinctiveness of the molecular sequence data of
Phrag. kovachii. All four plants of Phrag. kovachii were identical for
each
sequence analysed."

I think the key phrase is: "for each sequence analyzed". Indicating to
me that only certain parts of its DNA were analyzed. I'm not entirely
sure, but think items ALL of whose DNA has been sequenced are pretty rare.

tennis maynard wrote:
Though I feel it would be more appropriate to comment in two weeks when
I receive my copy here at the end of the postal world, Ohio, if we must
jump the gun, I take my cue from your note to OGD quoting the article I
won't see for fourteen more days:

On page 135, second paragraph they write "The individual and combined
analyses demonstrate the distinctiveness of the molecular sequence data of
Phrag. kovachii. All four plants of Phrag. kovachii were identical for
each
sequence analysed."

I think the key phrase is: "for each sequence analyzed". Indicating to
me that only certain parts of its DNA were analyzed. I'm not entirely
sure, but think items ALL of whose DNA has been sequenced are pretty rare.

Why yes, I am a bioinformatician... This is what I do for a living. I
haven't seen the article on P. kovachii yet (and knowing how things
work, might not for a week). However, it is not at all unusual that
they might sequence four markers with identical sequence. Why?

They probably have selected genes that they know are well conserved.
While it is true that these genes will vary in sequence across long
evolutionary distances, they don't vary that much in the short term. In
fact, if they were really variable, we could never use those sequences
to determine the relationship between kovachii and other phragmipediums.

In a very abstract and simplified nutshell, it is the difference
between the marker sequences that gives an indication of how far apart
(in time) two species are. If you have only a few changes between the
species, you hypothesize that they are closely related. More changes
indicate that they may be more distantly related. However, you can't
have too many changes.

Why does P. kovachii look so different (even amongst themselves) if
they are identical at these four markers? Simple, these markers are
derived from genes that are required for survival (Cytochrome C,
ribosomal proteins, etc). The four examined don't reflect even a tiny
percentage of all the genes in the organism. Genes that have absolutely
required functions can't change that much (or they lose function).
Genes for flower size, color, and other things can (and do) vary quite a
bit, even in the same population. Quite a bit means (in humans, which
have been most studied for obvious reasons) 1 in every 100 bases or so.

Does that help?

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 obtain more
orchids, obtain more credit

LittlefrogFarm - Growing the plants Rob likes. )

*laughing at imagining Kathy with a degree solely in sea anemones*

*laughing again at how she would decorate the waiting room at her dentistry
practice today if she had a degree in sea anemones*

-Eric in SF
www.orchidphotos.org

"Lady Blacksword" wrote in message
...
You have a degree in sea anemones? Or do you mean marine biology?
Just curious,

"Rob Halgren" wrote in message
...
tennis maynard wrote:
Though I feel it would be more appropriate to comment in two weeks when
I receive my copy here at the end of the postal world, Ohio, if we must
jump the gun, I take my cue from your note to OGD quoting the article I
won't see for fourteen more days:

On page 135, second paragraph they write "The individual and combined
analyses demonstrate the distinctiveness of the molecular sequence data
of
Phrag. kovachii. All four plants of Phrag. kovachii were identical for
each
sequence analysed."

I think the key phrase is: "for each sequence analyzed". Indicating to
me that only certain parts of its DNA were analyzed. I'm not entirely
sure, but think items ALL of whose DNA has been sequenced are pretty
rare.

Why yes, I am a bioinformatician... This is what I do for a living. I
haven't seen the article on P. kovachii yet (and knowing how things
work, might not for a week). However, it is not at all unusual that
they might sequence four markers with identical sequence. Why?

They probably have selected genes that they know are well conserved.
While it is true that these genes will vary in sequence across long
evolutionary distances, they don't vary that much in the short term. In
fact, if they were really variable, we could never use those sequences
to determine the relationship between kovachii and other phragmipediums.

In a very abstract and simplified nutshell, it is the difference
between the marker sequences that gives an indication of how far apart
(in time) two species are. If you have only a few changes between the
species, you hypothesize that they are closely related. More changes
indicate that they may be more distantly related. However, you can't
have too many changes.

Why does P. kovachii look so different (even amongst themselves) if
they are identical at these four markers? Simple, these markers are
derived from genes that are required for survival (Cytochrome C,
ribosomal proteins, etc). The four examined don't reflect even a tiny
percentage of all the genes in the organism. Genes that have absolutely
required functions can't change that much (or they lose function).
Genes for flower size, color, and other things can (and do) vary quite a
bit, even in the same population. Quite a bit means (in humans, which
have been most studied for obvious reasons) 1 in every 100 bases or so.

Does that help?

Rob

You'll really like the article, Rob.

On page 134 Fig. 4 shows a portion of the ITS matrix (whatever that is).
Its 768 bases long. There are also gaps. (I understand the shotgun method
of sequencing DNA by necessity produces gaps.) But I'm not sure these are
the same sort of gaps.

The authors say that kovachii is separated from besseae by 29 bases, and
from schlimii by 48 (of the bases shown, they undoubtedly have more but
space allowed printing of only these 768).

Ok, I guess I'll have to defer discussion until everyone gets their copy of
'Orchids'.

K Barrett

Don't laugh! My land lady painted my office building's hallways with a
truly horrid red and blue sponge-paint technique that simply begs to have
little Nemo-like fish poking their heads from beneath it. Makes me (and the
architect next door) shudder whenever we venture out to get the mail. He
swears his clientele thinks it a reflection of his taste and that business
has dropped off since she did it last year. Personally, I think his lease
is up for negociation.... The degree was actually called "Aquatic Biology",
in that there was some limnology tossed in there, too. Nevertheless it was
all so long ago that it seems a dream now.

K

"Eric Hunt" wrote in message
...
*laughing at imagining Kathy with a degree solely in sea anemones*

*laughing again at how she would decorate the waiting room at her
dentistry
practice today if she had a degree in sea anemones*

-Eric in SF
www.orchidphotos.org

"Lady Blacksword" wrote in message
...
You have a degree in sea anemones? Or do you mean marine biology?
Just curious,

Eric Hunt wrote:
*laughing at imagining Kathy with a degree solely in sea anemones*

*laughing again at how she would decorate the waiting room at her dentistry
practice today if she had a degree in sea anemones*

Eric, you haven't seen her office, have you?

Steve
(just kidding, I haven't seen it either)

I can't wait to read this thing. What were they trying to learn from these
tests? What conclusions does it draw from these similarities? It is trying
to show it really is a species? That it is very recent evolved? That it is
not a hybrid? :-)
"K Barrett" wrote in message
...
"Rob Halgren" wrote in message
...
tennis maynard wrote:
Though I feel it would be more appropriate to comment in two weeks when
I receive my copy here at the end of the postal world, Ohio, if we must
jump the gun, I take my cue from your note to OGD quoting the article I
won't see for fourteen more days:

On page 135, second paragraph they write "The individual and combined
analyses demonstrate the distinctiveness of the molecular sequence data
of
Phrag. kovachii. All four plants of Phrag. kovachii were identical for
each
sequence analysed."

I think the key phrase is: "for each sequence analyzed". Indicating to
me that only certain parts of its DNA were analyzed. I'm not entirely
sure, but think items ALL of whose DNA has been sequenced are pretty
rare.

Why yes, I am a bioinformatician... This is what I do for a living. I
haven't seen the article on P. kovachii yet (and knowing how things
work, might not for a week). However, it is not at all unusual that
they might sequence four markers with identical sequence. Why?

They probably have selected genes that they know are well conserved.
While it is true that these genes will vary in sequence across long
evolutionary distances, they don't vary that much in the short term. In
fact, if they were really variable, we could never use those sequences
to determine the relationship between kovachii and other phragmipediums.

In a very abstract and simplified nutshell, it is the difference
between the marker sequences that gives an indication of how far apart
(in time) two species are. If you have only a few changes between the
species, you hypothesize that they are closely related. More changes
indicate that they may be more distantly related. However, you can't
have too many changes.

Why does P. kovachii look so different (even amongst themselves) if
they are identical at these four markers? Simple, these markers are
derived from genes that are required for survival (Cytochrome C,
ribosomal proteins, etc). The four examined don't reflect even a tiny
percentage of all the genes in the organism. Genes that have absolutely
required functions can't change that much (or they lose function).
Genes for flower size, color, and other things can (and do) vary quite a
bit, even in the same population. Quite a bit means (in humans, which
have been most studied for obvious reasons) 1 in every 100 bases or so.

Does that help?

Rob

You'll really like the article, Rob.

On page 134 Fig. 4 shows a portion of the ITS matrix (whatever that is).
Its 768 bases long. There are also gaps. (I understand the shotgun
method
of sequencing DNA by necessity produces gaps.) But I'm not sure these are
the same sort of gaps.

The authors say that kovachii is separated from besseae by 29 bases, and
from schlimii by 48 (of the bases shown, they undoubtedly have more but
space allowed printing of only these 768).

Ok, I guess I'll have to defer discussion until everyone gets their copy
of
'Orchids'.

K Barrett

They were doing a cladistic analysis. Interestingly, their analysis put it
in the same subsection as bessee and schlmii - micropetalum...
MICROpetalum...go figure! And as an aside they thought that they could
forensically identify plant tissue as well as trace future hybrids... I
guess Williams et al had written a similar article on Tolumnia vs Oncidium
in ' Orchids' 70:1056-1061 - which I haven't looked up yet.

K

"Al" wrote in message
...
I can't wait to read this thing. What were they trying to learn from
these
tests? What conclusions does it draw from these similarities? It is
trying
to show it really is a species? That it is very recent evolved? That it
is
not a hybrid? :-)
"K Barrett" wrote in message
...
"Rob Halgren" wrote in message
...
tennis maynard wrote:
Though I feel it would be more appropriate to comment in two weeks
when
I receive my copy here at the end of the postal world, Ohio, if we
must
jump the gun, I take my cue from your note to OGD quoting the article
I
won't see for fourteen more days:

On page 135, second paragraph they write "The individual and combined
analyses demonstrate the distinctiveness of the molecular sequence
data
of
Phrag. kovachii. All four plants of Phrag. kovachii were identical
for
each
sequence analysed."

I think the key phrase is: "for each sequence analyzed". Indicating
to
me that only certain parts of its DNA were analyzed. I'm not entirely
sure, but think items ALL of whose DNA has been sequenced are pretty
rare.

Why yes, I am a bioinformatician... This is what I do for a living. I
haven't seen the article on P. kovachii yet (and knowing how things
work, might not for a week). However, it is not at all unusual that
they might sequence four markers with identical sequence. Why?

They probably have selected genes that they know are well conserved.
While it is true that these genes will vary in sequence across long
evolutionary distances, they don't vary that much in the short term.
In
fact, if they were really variable, we could never use those
sequences
to determine the relationship between kovachii and other
phragmipediums.

In a very abstract and simplified nutshell, it is the difference
between the marker sequences that gives an indication of how far apart
(in time) two species are. If you have only a few changes between the
species, you hypothesize that they are closely related. More changes
indicate that they may be more distantly related. However, you can't
have too many changes.

Why does P. kovachii look so different (even amongst themselves) if
they are identical at these four markers? Simple, these markers are
derived from genes that are required for survival (Cytochrome C,
ribosomal proteins, etc). The four examined don't reflect even a tiny
percentage of all the genes in the organism. Genes that have
absolutely
required functions can't change that much (or they lose function).
Genes for flower size, color, and other things can (and do) vary quite
a
bit, even in the same population. Quite a bit means (in humans, which
have been most studied for obvious reasons) 1 in every 100 bases or so.

Does that help?

Rob

You'll really like the article, Rob.

On page 134 Fig. 4 shows a portion of the ITS matrix (whatever that is).
Its 768 bases long. There are also gaps. (I understand the shotgun
method
of sequencing DNA by necessity produces gaps.) But I'm not sure these
are
the same sort of gaps.

The authors say that kovachii is separated from besseae by 29 bases, and

from schlimii by 48 (of the bases shown, they undoubtedly have more but
space allowed printing of only these 768).

Ok, I guess I'll have to defer discussion until everyone gets their copy
of
'Orchids'.

K Barrett

"Steve" wrote in message
...
Eric Hunt wrote:
*laughing at imagining Kathy with a degree solely in sea anemones*

*laughing again at how she would decorate the waiting room at her
dentistry
practice today if she had a degree in sea anemones*

Eric, you haven't seen her office, have you?

Steve
(just kidding, I haven't seen it either)

I like to say that at least my career stayed in a moist environment.

K Barrett

On Mon, 31 Jan 2005 13:39:24 -0800, "K Barrett"
wrote:


I like to say that at least my career stayed in a moist environment.

K Barrett

Almost as bad as your landlady's paint.


I was ready to ask if the DNA analysis was their attempt to say
they would have evidence for prosecution at a later date for
non-legal but it sounds like they are not trying to work that
angle.


SuE
http://orchids.legolas.org/gallery/albums.php