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02/07/2007

A Relative Sequenced

Greetings from sunny, warm Marco Island in Florida. Actually,
everything is relative, isn’t it? When I started this column at
around noon on Monday, the day after Super Bowl Sunday, the
temperature outside was 59 degrees Fahrenheit and it was
“breezy”. When the local TV weather people say “breezy”, the
wind is howling outside and the wind chill factor definitely
comes into play. As for the sun, there were three days during
which sunshine was virtually nonexistent and in the week we’ve
been here I’ve only managed three of my early morning walks on
the beach.

However, one reason we like Marco Island is that it’s generally
warmer and often escapes stormy weather north of here in
Florida. This certainly was the case last week and we are
especially grateful to have missed those deadly tornadoes up in
Central Florida. On the day of the tornadoes our weather was
indeed sunny and warm. It’s ironic that one of the places hit
hard by the tornadoes was The Villages, a retirement community
that advertises heavily on the New York TV stations we watch
back in New Jersey.

Longtime readers know that I look forward to my early morning
walks on Marco’s impressive beach. My first walk here this year
was illuminated by a full moon but a cloudbank precluded my
ideal of a moonset combined with a sunrise. This morning, after
a 3-day weather-induced hiatus, I resumed my walking and was
happy to see that three walkers I’ve traded greetings with over
many years are back. Another fellow, a tall gaunt runner, has
also returned but this fellow has never waved or said a word of
greeting in at least ten years that we’ve passed each other.

So far, I’ve been surprised at the lack of any but the smallest
shells on the beach. While I haven’t seen any interesting shells
on the beach, as in most Marco condos, there are containers of
shells collected by the owners. As I write this I’m looking at one
such collection topped by the shells of two sea urchins, a segue
into the subject I had planned since last November to write about
when I came to Marco - the purple sea urchin.

I decided that the purple sea urchin would be a suitable subject
here on Marco when I found a special section on it in the
November 10, 2006 issue of Science. The section contained
several papers on the urchin, a perspective, a news report and a
colorful poster suitable for wall hanging. Why all the fuss about
the sea urchin? It dates back to a day in December of 1997,
when a male purple sea urchin gave up some of its sperm to an
international group of over 200 researchers from 78 institutions
in the U.S., Canada and Europe. The group, known as the Sea
Urchin Genome Sequencing Consortium, took that sperm and
sequenced the genome of the purple sea urchin. Thus the sea
urchin joins the human, chimpanzee and other animals whose
genomes have now been decoded or are being decoded.

What’s so interesting about the sea urchin? It was back in the
1870s that H. Fol and G. Hertwig took advantage of the fact that
the sea urchin’s eggs are transparent. It was in a sea urchin egg
that these researchers for the first time observed the fusion of the
nucleus of a sperm with the nucleus of the egg. In 1902,
Theodor Boveri showed that only if each cell in a sea urchin
embryo had a full set of chromosomes would the embryo
develop normally into a normal adult. Ever since those early
days, scientists have used the transparent and easily manipulated
sea urchin egg to study embryonic development and the effects
of introducing different types of DNA into the egg.

Aside from the relatively easy access to the egg and its contents,
the sea urchin has another important feature. It’s a deuterostome.
I admit that, before reading the Science articles, I didn’t have the
foggiest idea what a deuterostome is and was shocked to learn
that you and I are deuterostomes! (I regret that I never took
biology in college and my only significant memory of biology in
high school is dissecting a frog.) To more or less complete the
classification scheme, you and I are vertebrates, a subset of
chordates, which in turn are a subset of deuterostomes. Another
class of deuterostomes includes the echinoderms, which includes
such critters as the starfish and the sea urchin. If you have
trouble following this, the bottom line is that the sea urchin is
related to us humans more closely than you might think.

If a sea urchin doesn’t get eaten or otherwise done in, its lifespan
can be similar to our own. The purple sea urchin that donated its
sperm may live about 30 years while another type of sea urchin
can live a hundred years! Surprisingly, to me at least, the sea
urchin is more closely related to you and me than it is to sea
dwellers such as clams or crabs. The fruit fly, the subject of vast
numbers of studies that have helped shed light on human
maladies or characteristics, is not even a deuterostome. It’s a
protostome, another major class of animal life that also includes
the mollusks.

It was roughly 540 million years ago that we and the sea urchin
last shared a common ancestor and the deuterostome group
began to branch out into different forms of life. One of the
fascinating things about the achievement of the sequencing of the
sea urchin genome is that we can now compare the genes in the
sea urchin with the genes in our human genome. This means we
can see which genes have been preserved by both us and the sea
urchin over these millions of years and we can see which genes
are new or have been dropped by either human or urchin. One
thing already is clear – we both have a similar numbers of genes.
The purple sea urchin has roughly 23,300 genes while the last I
heard the human gene count was also in the low 20 thousands.

One of the surprising things to emerge from the sea urchin
genome studies concerns the fact that the sea urchin has no eyes,
no nose, no antennae and doesn’t even have a centralized brain to
handle visual or odor cues. Yet it has nearly a thousand genes
that code for proteins that we vertebrates use to sense odors or
light. You may recall that some time ago I wrote about a
possible evolutionary route for forming an eye and I mentioned a
protein called “opsin”. Opsin is a key molecule in sensing light.
The researchers have found genes for opsin in the tips of the sea
urchin’s tube feet and in tiny pincers below the spines. Urchins
do respond to light. Are they “seeing” with their feet?

Perhaps equally surprising is the immune system of the sea
urchin. Its immune system is amazingly wealthy in genes that
are associated with various diseases in humans. Some of the
genes found in the sea urchin are involved in humans in the
production of antibodies to combat various pathogens. The sea
urchin has these genes even though it doesn’t produce antibodies.
The sea urchin genome also contains genes that help cells stick
together. One such gene in humans helps in our mammalian
brain development. Yet the sea urchin doesn’t have the brain!
The implications are that we vertebrates have taken genes that
existed long before we came along and have taken those genes
and adapted them to our own uses. Evolution is real!

A report on the work by Elizabeth Pennisi in Science quotes
immunologist Chris Amemiya as calling it “mind-boggling to
think of all the many inferences one can make with the genome
sequence [of the sea urchin] in hand.” If I find any urchins on
the beach I’ll treat them with greater respect!

Allen F. Bortrum



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-02/07/2007-      
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Dr. Bortrum

02/07/2007

A Relative Sequenced

Greetings from sunny, warm Marco Island in Florida. Actually,
everything is relative, isn’t it? When I started this column at
around noon on Monday, the day after Super Bowl Sunday, the
temperature outside was 59 degrees Fahrenheit and it was
“breezy”. When the local TV weather people say “breezy”, the
wind is howling outside and the wind chill factor definitely
comes into play. As for the sun, there were three days during
which sunshine was virtually nonexistent and in the week we’ve
been here I’ve only managed three of my early morning walks on
the beach.

However, one reason we like Marco Island is that it’s generally
warmer and often escapes stormy weather north of here in
Florida. This certainly was the case last week and we are
especially grateful to have missed those deadly tornadoes up in
Central Florida. On the day of the tornadoes our weather was
indeed sunny and warm. It’s ironic that one of the places hit
hard by the tornadoes was The Villages, a retirement community
that advertises heavily on the New York TV stations we watch
back in New Jersey.

Longtime readers know that I look forward to my early morning
walks on Marco’s impressive beach. My first walk here this year
was illuminated by a full moon but a cloudbank precluded my
ideal of a moonset combined with a sunrise. This morning, after
a 3-day weather-induced hiatus, I resumed my walking and was
happy to see that three walkers I’ve traded greetings with over
many years are back. Another fellow, a tall gaunt runner, has
also returned but this fellow has never waved or said a word of
greeting in at least ten years that we’ve passed each other.

So far, I’ve been surprised at the lack of any but the smallest
shells on the beach. While I haven’t seen any interesting shells
on the beach, as in most Marco condos, there are containers of
shells collected by the owners. As I write this I’m looking at one
such collection topped by the shells of two sea urchins, a segue
into the subject I had planned since last November to write about
when I came to Marco - the purple sea urchin.

I decided that the purple sea urchin would be a suitable subject
here on Marco when I found a special section on it in the
November 10, 2006 issue of Science. The section contained
several papers on the urchin, a perspective, a news report and a
colorful poster suitable for wall hanging. Why all the fuss about
the sea urchin? It dates back to a day in December of 1997,
when a male purple sea urchin gave up some of its sperm to an
international group of over 200 researchers from 78 institutions
in the U.S., Canada and Europe. The group, known as the Sea
Urchin Genome Sequencing Consortium, took that sperm and
sequenced the genome of the purple sea urchin. Thus the sea
urchin joins the human, chimpanzee and other animals whose
genomes have now been decoded or are being decoded.

What’s so interesting about the sea urchin? It was back in the
1870s that H. Fol and G. Hertwig took advantage of the fact that
the sea urchin’s eggs are transparent. It was in a sea urchin egg
that these researchers for the first time observed the fusion of the
nucleus of a sperm with the nucleus of the egg. In 1902,
Theodor Boveri showed that only if each cell in a sea urchin
embryo had a full set of chromosomes would the embryo
develop normally into a normal adult. Ever since those early
days, scientists have used the transparent and easily manipulated
sea urchin egg to study embryonic development and the effects
of introducing different types of DNA into the egg.

Aside from the relatively easy access to the egg and its contents,
the sea urchin has another important feature. It’s a deuterostome.
I admit that, before reading the Science articles, I didn’t have the
foggiest idea what a deuterostome is and was shocked to learn
that you and I are deuterostomes! (I regret that I never took
biology in college and my only significant memory of biology in
high school is dissecting a frog.) To more or less complete the
classification scheme, you and I are vertebrates, a subset of
chordates, which in turn are a subset of deuterostomes. Another
class of deuterostomes includes the echinoderms, which includes
such critters as the starfish and the sea urchin. If you have
trouble following this, the bottom line is that the sea urchin is
related to us humans more closely than you might think.

If a sea urchin doesn’t get eaten or otherwise done in, its lifespan
can be similar to our own. The purple sea urchin that donated its
sperm may live about 30 years while another type of sea urchin
can live a hundred years! Surprisingly, to me at least, the sea
urchin is more closely related to you and me than it is to sea
dwellers such as clams or crabs. The fruit fly, the subject of vast
numbers of studies that have helped shed light on human
maladies or characteristics, is not even a deuterostome. It’s a
protostome, another major class of animal life that also includes
the mollusks.

It was roughly 540 million years ago that we and the sea urchin
last shared a common ancestor and the deuterostome group
began to branch out into different forms of life. One of the
fascinating things about the achievement of the sequencing of the
sea urchin genome is that we can now compare the genes in the
sea urchin with the genes in our human genome. This means we
can see which genes have been preserved by both us and the sea
urchin over these millions of years and we can see which genes
are new or have been dropped by either human or urchin. One
thing already is clear – we both have a similar numbers of genes.
The purple sea urchin has roughly 23,300 genes while the last I
heard the human gene count was also in the low 20 thousands.

One of the surprising things to emerge from the sea urchin
genome studies concerns the fact that the sea urchin has no eyes,
no nose, no antennae and doesn’t even have a centralized brain to
handle visual or odor cues. Yet it has nearly a thousand genes
that code for proteins that we vertebrates use to sense odors or
light. You may recall that some time ago I wrote about a
possible evolutionary route for forming an eye and I mentioned a
protein called “opsin”. Opsin is a key molecule in sensing light.
The researchers have found genes for opsin in the tips of the sea
urchin’s tube feet and in tiny pincers below the spines. Urchins
do respond to light. Are they “seeing” with their feet?

Perhaps equally surprising is the immune system of the sea
urchin. Its immune system is amazingly wealthy in genes that
are associated with various diseases in humans. Some of the
genes found in the sea urchin are involved in humans in the
production of antibodies to combat various pathogens. The sea
urchin has these genes even though it doesn’t produce antibodies.
The sea urchin genome also contains genes that help cells stick
together. One such gene in humans helps in our mammalian
brain development. Yet the sea urchin doesn’t have the brain!
The implications are that we vertebrates have taken genes that
existed long before we came along and have taken those genes
and adapted them to our own uses. Evolution is real!

A report on the work by Elizabeth Pennisi in Science quotes
immunologist Chris Amemiya as calling it “mind-boggling to
think of all the many inferences one can make with the genome
sequence [of the sea urchin] in hand.” If I find any urchins on
the beach I’ll treat them with greater respect!

Allen F. Bortrum