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Re: 25000 genes


zonneveld wrote:
RE:>>The number of genes in Arabidopsis has been determined at 25000 So
my guess for Hosta was pretty close!

Yes, now I can see how this is done.  Since Arabidopsis has 25,498
genes, give or take a couple, and one knows approximately how many base
pairs it takes to weigh a pg, then this extrapolation seems fairly
plausible, irrespective of gene density.  Very good, Herr Zonneveld.

There are some strange things about Arabidopsis that I do not
understand, as well as Hosta (go figure):

1) A. Thaliana has but five Chromosomes.   Diploid Hosta have 60.  Why
the odd number for Arabidopsis?  Are Hosta considered more ecologically
adaptive because of the larger number of Chromosomes, or would the
reverse of this logic be true (i.e. not so many pairs that need to be
matched during cell division).

2) The gene density per Chromosome varies from 3,825 to 6,543 in A.
Thaliana.  I presume that when you are doing a DNA Analysis with Flow
Cytometry, it really doesn't matter how many Chromosomes exist because
the resultant value for pg of DNA is derived from the ratio of the
relative flourescence intensity, a ratio which is applied against a
standard plant (and in your case, Agave americana for which known values
are established).

Does it seem likely that Arabidopsis should become a new standard, since
controls are the single most important consideration for cytometric
determinations?  Is there any move toward this in the scientific
community, and more particularly, have you considered using this plant
as a standard?  What is your thinking on the value of this plant as a
possible new standard?

3) Since knowing the sample AT/GC ratio is quite important when using
DAPI (DAPI produces reliable results only when comparing DNA contents of
samples with the same AT/GC ratio) many molecular biologists measure DNA
using both PI and DAPi, as you have done in your work published in
Euphytica (on ploidy chimeras).  What methods can be used to help
determine the AT/GC ratio in Hosta?  Is there a staining technique that
is used?  I imagine but I'm just curious.  Would this be of benefit?
Does it seem likely that the same or very similar AT/GC ratio is found
throughout the many different Hosta species, even though we have such a
wide divergence in plant morphology?

4) Reading you Table 2, I see that H. fortuneii 'Patriot 1' has 27.7 pg
DNA per nucleus in 2C Chromosomes and 55.9 pg DNA per nucleus in 4C
Chromosomes.   How do you go about splitting those types of cells up
when you are doing this analysis?   Are the 2C cells found in one layer
in the root and the 4C cells in another?   I imagine this is part of
your stock in trade, or is this something you are willing to share?  Are
you willing to explain how this type of measurement is done?  (The same
question applies to the leaf center measurement).  This is difficult for
me to comprehend without being there in the lab to ask the questions and
see how such is performed.  8<))

5) And one last more general question.  If H. 'Cheatin' Heart' has a
tetraploid L3 and a diploid L1, does this help explain why my slugs
start a major marjurita-induced dance party whenever I add more
specimens to the stock?  I don't suppose you know of a way to force the
4C cells up into the 2C tissues of the leaf--or a hypotheses of how one
might go about accomplishing this objective?

Thanks in advance for any help and/or answers.   I may have a few more
later 8<)) but please tell me if I am too much the pest or whether you
would prefer these be private emails.

Andrew Lietzow

P.S.  In case you are wondering, in college, when the class was already
10 minutes late in adjorning, I'm the geek that sat in the back with
raised hand when the Prof asked, "Now, are there any more questions"?


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