Puffer Fish

Fugu rubripes

‘The human body's genetic make-up is surprisingly similar to that of the puffer fish.’ BBC News

“For the bits that count it's extraordinary how similar we are…When we compare stretches of the human genome with the Fugu rubripes genome, only small pieces look alike. These are the genes.” Dr Greg Elgar, Medical Research Council Human Genome Mapping Resource Centre, UK

‘Sequencing of pufferfish genome will help scientists understand human disease - A poisonous fish, eaten as a delicacy in Japan, may hold the key to decoding the human genome, said MRC researchers in Cambridge today. An international consortium of scientists from Cambridge, California and Singapore have finished the first draft of the genome of the pufferfish (fugu rubripes).Although a lot of the human genome has been sequenced, much of it remains a mystery because of the difficulty in identifying genes, and the key DNA sequences needed to control them amongst a sea of intervening DNA. The pufferfish is only the second vertebrate animal genome to be sequenced and, like the mouse, has approximately the same number of genes as a human. Therefore, a particular gene in the fish may decide where fins are placed and what they look like, while a very similar gene sequence may be present in humans, but acts slightly differently to produce a leg. The great advantage of the pufferfish genome is that it is a staggering eight times more compact than the human. Four hundred and fifty million years of evolution have conserved vital gene sequences, without accumulating large stretches of DNA between them. Therefore, when compared to the human sequence, important regions are quickly highlighted. This allows scientists to identify genes and will have direct application to understanding and treating human disease. The Fugu genome project started in Cambridge in the early 1990s under Professor Sydney Brenner, supported by the MRC, and is now led by the International Fugu Genome Consortium. This group represents the largest international genome-sequencing project since the Human Genome Project. The consortium includes the MRC UK Human Genome Mapping Resource Centre (MRC UK HGMP-RC), US Department of Energy’s Joint Genome Institute (JGI) and the Singapore Biomedical Research Council’s Institute for Molecular and Cell Biology (IMCB). Further collaborators include the Cambridge University Department of Oncology, the Institute for Systems Biology in Seattle, Celera Genomics of Rockville and Myriad Genetics Inc, Utah. Dr Greg Elgar from the MRC UK HGMP-RC, is currently completing a map of the genome. His group compares the information from the pufferfish and human genomes as a way of increasing scientists’ knowledge of genes and disease. He said: "Finishing the draft sequence of the pufferfish genome is the culmination of a decade of research and we’re very excited about the implications this has for human disease. This information will have enormous benefits to scientists working on the human genome and will certainly be instrumental in the fight against genetic disease”.’ Medical Research Council, UK

‘Comparison of whole-genome shotgun sequence from the pufferfish T. nigroviridis with the human genome can be used to estimate the density of exons (detected as conserved sequences between fish and human).’ International Human Genome Sequencing Consortium

While some countries were joining together

to start a fishy war that would kill people -

other countries were joining together to study

a fish that would save people; and some were

even doing both. Thus marking the craziest

species on the plant - worse than lemmings,

or drunk giraffes; black widow and preying

mantis wives - that will send money to save

children, but also bombs that make them curl

up as instinctively, as uselessly as a hedgehog.

‘The human body's genetic make-up is surprisingly similar to that of the puffer fish, Fugu rubripes, of Japanese culinary fame. That is one of the conclusions of a year-long international effort to sequence the fish's genome. The fish's DNA has proved easier to map than that of the human body and scientists believe there will be medical applications for their new knowledge. “This information will have enormous benefits to scientists working on the human genome and will certainly be instrumental in the fight against genetic disease," said Dr Elgar of the UK Medical Research Council's Human Genome Mapping Resource Centre. The sequencing effort, which took a day under a year to complete, is part of the efforts scientists are making to understand and apply the information derived from decoding the human body's own programme for reproducing itself and staying alive. One of the best ways of doing this is to compare humans with other organisms…Throughout evolution, the DNA of all organisms has been subject to random mutations. Mutations which give their host some kind of benefit have survived, while harmful mutations have ultimately killed off their hosts and any offspring. Many of these useful mutations took place early on in Earth history and are common to organisms as diverse as yeast, fruit flies, humans and the puffer fish. "They have to be there because each one of them does an essential task like develop a leg or fin or haemoglobin," said Dr Elgar.’ Ivan Noble, BBC News Online

‘The fish in the stone/ knows to fail/ is to do the living a favour.’ Rita Dove, The Fish in the Stone

On finding out humans and puffer fish are closely related

In the strange light of day, revealed

beyond unwoven miles of skin, bone,

hair, fingers – beyond matter, human-

printed molecules, such skill with air;

preserved in the Genome - I am fish.

I swam in night’s black bowl,

illuminated; a host of fireflies -

gold, bee-hiving round my head;

glow-worms in my open palm -

peacock iridescence in my hair,

and I dared not look behind me,

where swan wings might vanish -

Moon had found their white fossil-

roots under skin, shoulder-blades -

hunting skeletal clues in luminous

owls - they had opened like flowers -

easily as a hand, muscular; would fall

like petals in winter, like a dead moth

crumbling into silver dust, an ancient

wedding dress shedding wormy fibres.

And night air was navy - thick

as water; stars floated like lilies

you could gather up like blooms -

smelling of new snow, old roses;

kindling hands into red anemones.

Salmon that had kept on leaping

against river-gravity slipped silver,

in and out of this liquid darkness -

slippery shooting stars, streaking,

showing the wet soul of rainbows.

I dived with cormorants,

folding my white wings

like an angel being born;

among dark angels I fell,

water touching me thin

as air in my coral garden.

I was colours, swimming -

phosphorescent blue in blue,

led by the telepathic mercury

herring shoals with one bright

muscle movement to a ruined sea,

where mad fish cried like mothers

among despoiled coral and spawn,

farm-fish tears only God could see;

I reached out my arm for comfort -

growing fins, scales, mermaid tail,

blood chilling down as milk, wine;

remembering I knew the quiet cold

water-home - sea, salt of my blood -

my water-skin; first sticky molecules

coagulating from sun chemistry,

original formula – bursting forth

to my time of puffer fish - raging

my spines, hurrying up Evolution

to stand on shore - do something -

awaken Man, my relatives preserved -

to preserve fish-kin - using whatever

natural selection has made possible.

The voice - such blessings of voice,

raised in protection of native ocean.

‘Puffer fish Zool. Any of several fish, found mainly near tropical reefs, that are able to inflate their spine-covered bodies to become amost spherical, in response to attacks by predators. The internal organs of many species are highly poisonous, but when correctly prepared the fish is regarded as a delicacy in Japan.’ Chambers Encylopaedic English Dictionary

Re-awakened Puffer Fish Gene

I found out at a cocktail party,

he’d done me one more wrong -

blood-curtain! Genetic implosion!

You should have seen the look

on that bugger’s face as thorny

spines split, ripped from my back

where metaphorical swan wings

had been - hedgehogged silver

as swords! Big lips blubbered -

lush, puckering, smacky, sucker-

kiss; his Kermit eyeballs bulging,

wee man returned to green frog -

when I inflated, whoosh, all at once,

like Harry’s awful Aunty Marge -

almost spherical, under pressure;

button-pushed, gross, unstoppable -

the first prong of mighty cold breast

smote his shivering wine to splinters,

trembled his precarious mini-nibbles –

miniature vol-au-vents taking flight!

Japanese crackers banging in fright!

Mussels, oysters, snapped tight shut!

Chicken skewers running squawking,

flapping! And some vulture others -

both faces astonished, gawking -

stinking, slinking, smiling hyenas,

ran for cover, scattering canapés -

caviar filling the air like gunshot!

The chocolate-dipped strawberries

burst into bombs - bloody red seed-

shrapnel peppering guests - smoked

salmon leapt hot from white plates;

come back from the raw, to escape -

Evolution was coming to play; suddenly

I was in touch with my inner puffer fish,

bile and bubble in my gurgling stomach –

will she blow? Spontaneously combust;

alchemy of tears, unfairness, injustice -

perfumed revenge; they could smell me

like the fish I am - going off, overdue -

mouldered, seething, festered, fucked

off, twitchy rabbits sniffing unstuffed

fox; fear, guilt, bursting like bullet-poppies,

Remembrance petals fluttering down - as I

explained in a precise mixture of English -

Greek, Latin, Gaelic, Parseltongue, (adapted

from the silent ‘Fish’), that from now on, as a

delicacy, I needed treated with extreme care -

having realised I, too, have highly poisonous

insides, given the right circumstances; pushed

far enough to tap Evolution’s deadly memory.

On finding out one bears a stunning ressemblance to a Puffer Fish

It’s all getting a bit weird…

Being the same as a mouse I could just about take,

Something cute and furry, warm-blooded at least,

But a poisonous fish with a funny name the Japanese like seared…

Even the worm – fly - and now fish -

Everyone is better for finding out about us, than us -

Great lumps of bacteria, viruses, junk,

More like walking warts, less advanced than something grown in a dish -

Being made in a day from a lump of clay,

Is beginning to sound much less far-fetched -

In fact, far more preferable - if not downright desireable,

Than being so closely related to a foreign delicacy.

‘In a separate development, scientists have sequenced a second pufferfish genome. The near-complete sequence of the spotted green pufferfish, Tetraodon nigroviridis, was also published in the journal Nature. Scientists had previously sequenced the genome of the poisonous Japanese pufferfish Takifugu rubripes. Tetraodon's 21 chromosomes, which together contain more than 300 million letters of DNA, tell a twisting evolutionary tale, and even shed light on our own genetic make-up. By matching the genes on the pufferfish chromosomes to related genes on human chromosomes, the authors were able to peer into the genome of our shared ancestor - a primitive bony fish that lived hundreds of millions of years ago. Tetraodon's genome is interesting because it is about one sixth the size of ours, even though it has a similar number of genes. This means it has less of the "shady" DNA that hides in the gaps between genes - the very stuff that scientists are puzzling over in the human genome. Quite why the pufferfish can do without it, while humans and other mammals apparently cannot, is something of a mystery. "The pufferfish has managed to get rid of the so-called junk - all of the gaps between the fragments are shorter," explained Dr Hubbard. "This kind of implies - since you get a perfectly reasonable fish out of it - that you can delete a lot of it." BBC, 2004

Suspended in sea, I remember the fish

I was; just strung from water into bone,

glued with light from volatile molecules.

Propulsion was discovered by this hand -

turning something I could not see - but feel

in clearness, understanding grand principles,

motion, from the skeleton of stars to earth

potions alchemising sunlight into flowers.

In my fin, future, lay the clue to my nature;

one day I would see myself remembering -

this still moment of suspension - immature

light on my back, wing-roots, fertile fossils;