DNA sequencing has advanced by leaps and bounds since its first
inception. In fact, in the five years that I have been in the
business, the process has evolved from several labor intensive steps
to incorporate a radioisotope, running the reaction by-products
through a gel matrix in an electrical field, exposing the radioactive
gel to X-ray film, and hand reading the sequence from the exposed
film, to a single step reaction that incorporates a fluorescent dye.
The reaction is still run through a gel, however the signal is
analyzed and the sequence determined by a computer. Whereas 10-15
sequences of 300 basepairs per gel could be determined the old way,
now 96 sequences of 800 basepairs can be performed in a single run.
As much as the science has evolved, it is still unlikely and
unpractical that a machine would ever be designed to sequence whole
organinsms. The "state of the art" machine that we developed is the
size of a dishwasher and costs $200,000. The only customer for these
devices are public centers involved in the human genome project and
with hundreds of machines in operation, the most optimistic prediction
of completion of the DNA sequence of a single person is ther year
2003.
For the purpose of phylogenetic studies it is more practical to
compare mitochondrial DNA sequences. mtDNA is ubiquitously distributed
among eukaryotes, is conserved to span the full evolutionary spectrum,
and shares a common ancestor. Comparison of mtDNA sequences between
different organisms can infer relatedness. Also since DNA is hightly
conserved, any number of protein sequences can be used as a piece of
the puzzle to compare different species within a single genus. This
is a much more effective strategy than sequencing three billion base
paires.
Since DNA sequencing is performed by a modified bacterial enzyme,
there is a biological limit to the procedure. It is unlikely in its
present form that a sequencing reaction can produce a significantly
larger base pair read. New advances with the science will be with the
engineering of the machine itself (i.e. matrix, sample size), however,
this will not significantly speed up an effort as large as the human
genome project.
The difficulty in determining species with a "breadbox" DNA
sequencer is the homologous nature of DNA itself. Two animals as
phenotypically different as humans and chimpanzees have 98% the same
DNA sequence. Yet, it this 2% difference which allows us to bounce an
electronic signal off of a satellite in space to communicate with a
fellow list member on a different continent as opposed to sitting in a
tree picking lice off of each other.
Michael Reagin
Cleveland Heights, OH
______________________________ Reply Separator _________________________________
Subject: DNA question -Reply
Author: Conchologists of America List <[log in to unmask]> at
Internet-APBiotech-America
Date: 10/15/98 12:24 PM
Dear Paul and David;-
As you may have noted, I only have questions---not answers. It
appears to me, however, that DNA studies are a lot like Early TV or
ball-point pens. (remember the Parker 21, so named because that's
what it cost). Similarly, the computer I use is the grandson of one
that took up two walls and a cabinet a few years ago. I wonder if
more work on the process of DNA studies might not bring it into more
common usage and more practical pricing. I can envision a time when
you have a little box about TV size. It has a door where you slip in
a whole mollusk (with or without shell). The machine hums and clicks,
then spits out a nice 20 inch tape with all the information done in
numbers.
I know, and so do you, what this process would do for "new" Conus
species. Among the Epitiniidae, we'd like to find out whether our
notable look-a-likes, zelandica from NZ and blainei from Florida, are
the same or just accidently similar.
Your humble Question Man
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