[Coral-List] Porites Genome

craigdowns craigdowns at envirtue.com
Wed Sep 17 16:58:18 EDT 2003

Dear Coral List Serv,

Dr. Cheryl Woodley will be posting a letter soon concerning this issue,
but I thought I should give some comment back.

Almost two years ago, we began evaluating criteria for a coral 'lab
rat', an organism representative of scleractinians to be used as a model
for molecular genetics, cell biology, biochemistry, lipid chemistry,
sterol/polyphenol chemistry, environmental/physiological monitoring,
ecotoxicology, stress physiology, coral immunity, coral 'oncology',
coral endocrinology, and coral neurophysiology.  This quest was
formalized at the U.S. CDHC's January 2002 workshop and its subsequent
National Report.  Personally, I've been asking folks with diverse
backgrounds such as Eric Borneman and Phil Dusan to Barbara Brown and
Yossi Loya since 1999 to "nominate a coral species candidate and
justify."  Response has been slow coming. I'm a lab biologist - without
a lab rat for other labs to repeat my experiments or take the work
further, I'm at a standstill, as are other coral laboratory biologists.
Everyone who may be associated with field coral biology has suggested
'their' species as the 'best species'.  This is understandable.  Heck,
my vote was for Oculina varicosa.

As a lab rat, the most important criteria is accessibility.  Everyone in
the world should have relative ease in obtaining 'laboratory strains' of
coral.  These strains must be genetically identifiable, which means that
Strain 1 will come from a single colony from somewhere, and mass
cultured.  Someone or some entity must then have the facilities to rear
this coral in abundance and be able to distribute this coral to any lab
in the world that asks for it, whether it be a lab in Eilat, AIMS, or
Dalhousie University.  The coral must also SURVIVE the trip.  As someone
who ships and receives corals from all over the world, shipping with the
least expense possible of coral that will recover and grow in the lab is
an essential reality to consider.  Spending $800 (includes tariffs,
custom fees, CITES fees, etc..) for a shipment of 150 grams of coral
from Miami to India gets old after awhile if your corals arrive dead.
Most folks have seen the phoenix effect with Porites, few species
besides Gonistrea or Pavona have the resilience of Porites.

Also, the point is not to sequence the genome from a Caribbean coral
species, or a Pacific one.  This has been mentioned several times, I
believe the point is being missed and Cheryl will expound upon that
issue further.

Another issue is: can many of the tools of molecular, cellular, and
physiological biology be applied to that species?  As someone who has
had considerable experience in this area, I can say that Acroporas are
ruled out.  Next time you run a western on an Acropora sample, and assay
for a protein that is cysteine or histidine rich, the really
high-molecular weight banding patterns you see are the result of the
very rich sulfo-glyolipid composition of Acroporids (ask Carolyn Smith).
As the field of Natural Products Research can attest, evidence argues
that these compounds come from the dino, dino 'clades' that are found
abundantly in fast growing corals, such as Acropora.  These compounds
like to adduct with proteins, which makes protein biochemistry in these
species difficult.  Besides this, Acropora are rich in some very active
polyphenols (all symboint corals have these to a lesser or greater
degree, depends on your dino), resulting in extensive maillard product
formation.  This can be seen when you isolate DNA from a number of coral
species and you DNA pellet is tan or brown.  To correct for this, you
add PVPP or borate, but you know that the PVPP isn't that great as a
Maillard scavenger and borate comes with its own problems.  Some folks
have mentioned mRNAsi and perhaps microarrays, these nuances have
significant affect on the outcome of your results when using these
techniques.  All of this is unfortunate, becase as many have pointed
out, Acroporids grow extremely fast, and this characteristic would be a
tremendous boon.

I've worked and published with Montastrea.  Its important ecologically
in the Caribbean and in the Gulf of Mexico.  Draw back is its continuous
mucus production when stressed (and I've stressed Montastrea from
everything from atrazine to oil).  And since a lot of folks are getting
into the stress biology of corals, this is a draw back.  More so, the
amount of polysaccharide production inhibitors and polysaccharide
degrading enzymes you have to add to Montastrea (or Gonistrea) for coral
cell culture will make you bankrupt.  Coral cell culture is a next big
step in coral laboratory biology, and the lab rat has to be a good
species to which apply these techniques.  Acroporids aren't bad, Gary
has had tremendous success with Pocillipora, Cheryl Woodley has had
success with Oculina, and I with Porites and Occulina.  You can put
Montipora in this category of high mucus content - funny, few elected
for this species.  When we tried to heat stress Montipora on Heron
Island to do some bleaching experiments, it was impossible to work with.

Actually, to just argue for a lab rat, Oculina varicosa (or any of its
sibling species) would win, hand down.  Grows fairly quickly, gets
disease, beautiful cell culture, and its not an obligate symbiont,
something that is extremely advantageous when wanting to do in vivo
experiments and not having the presence of the to dino interfere, such
as during physiology investigations.  Oculina on protein gels/westerns
or running it on a GC-MS for lipid analysis, beautiful! Unfortunately,
its not a major tropical reef builder, and it doesn't handle shipping
very well.

So from a lab technique perspective, again, Porites exhibits the least
amount of technique artifact (Oculina less so), and can be shipped using
a wet paper towel, plastic breather bag, and blue ice with highest
success of survival after shipping.

To move into the realm of physiological ecology, environmental
assessment, Acroporids and Porites are found in abundance worldwide,
though Porites can be found in cooler climes than Acropora (just got to
Bermuda or western Costa Rica).  Problem with Acropora is that for the
most part, they are not resilient species, and are the first to crash
during an environmental event, whether that event be an unusually high
SST or an oil spill.  So if you're looking at a system to gauge its
recovery (process), then you need a species that will be around after
the environmental event (Jessica diesel spill in Galapogos, or Okinawa
after 1998 El Nino).

Objective and potential applications.  This seems to be an issue, but I
can't understand why.  The sequenced genome is a platform, a platform to
extend basic research into areas of coral biology where it has been so
difficult to conduct in the past, or a platform to develop new
technologies to allow us to see further (is this coral immunocompetent
or endocrine modulated?  How will you assay for this?  We need the genes
that contribute to these systems to better explore their individual and
combined behavior).  Cnidarians have the most priminite nervous system.
How are their neuropeptides different from ours, and why?  Corals also
get hyperplasias whose tissues (and their composition) are radically
different from 'normal' polyps.  Can our understanding of cancer in
mammals be aided by our understanding and the future discoveries of how
corals get 'cancer'?  These basic science questions can be greatly aided
by knowing the sequence of the coral genome.  Look at the magnitude of
success genomics has brought to human biology, yeast biology, drosophila
biology, C. elegans biology, etc..

The technologies that can be developed from a sequence coral genome are.
well you're only limited by your imagination and determination.  Here is
an example: some anti-foulant components in boat paint may be having an
adverse affect on corals.  Some of these components are cyanobacteria
biocides, or just general biocides.  Corals (all the way up to us) have
as part of our innate immunity the production of anti-microbial,
anti-fungal, anti-botanical compounds.  Some of these are polyphenols,
while others are polypeptides.  If you can elucidate the biochemical
pathway or obtain the gene(s) to the proprotein that creates these
anti-microbial, anti-fungal, anti-botanical compounds from coral, its
possible that you could encapsulate these polypetides into a
nano-structure (capsule) to be added to the paint instead of using
something like TBT.  You would be using the coral's own anti-foulant
chemistry on your boat - and since corals make it, there is a lower
probability of toxic side affects on the corals themselves (but that
would have to be determined experimentally).

I hope this help in understanding the position we've taken (Cheryl's
letter will reinforce points I had to gloss over).  

I also want to point out that the deadline is fast approaching for
letters of endorsement and look forward to receiving them.



Craig A. Downs
EnVirtue Biotechnologies, Inc.
35 W. Piccadilly Street
Winchester, Virginia 22601   U.S.A.

Phone: 540-723-0597
Fax: 540-723-0598

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