Eye Evolution, Pax6 And Blind Cave Fishes

[kyrani99]

[quote="Calilasseia";p="44759"]I obtained my data direct from the Swiss-Prot database. Go here and have fun searching lots of genomes.

EDIT: Here is the BLAST search I performed on the first 60 base pairs from my above sequence.

When you perform the BLAST search and click on the identifier P26367 in the list, you're taken to this page containing information about the human Pax6 gene. Under "Protein attributes", it says:

Sequence length: 422 AA

That's 422 amino acids. You'll find my sequence matches precisely. Click on this link and you're taken to the protein sequence. Let's compare my list:

MQNSHSGVNQLGGVFVNGRP
LPDSTRQKIVELAHSGARPC
DISRILQVSNGCVSKILGRY
YETGSIRPRAIGGSKPRVAT
PEVVSKIAQYKRECPSIFAW
EIRDRLLSEGVCTNDNIPSV
SSINRVLRNLASEKQQMGAD
GMYDKLRMLNGQTGSWGTRP
GWYPGTSVPGQPTQDGCQQQ
EGGGENTNSISSNGEDSDEA
QMRLQLKRKLQRNRTSFTQE
QIEALEKEFERTHYPDVFAR
ERLAAKIDLPEARIQVWFSN
RRAKWRREEKLRNQRRQASN
TPSHIPISSSFSTSVYQPIP
QPTTPVSSFTSGSMLGLTDT
ALTNTYSALPPMPSFTMANN
LPMQPPVPSQTSSYSCMLPT
SPSVNGRSYDTYTPPHMQTH
MNSQPMGTSGTTSTGLISPG
VSVPVQVPGSEPDMSQYWPR
LQ Ochre

with theirs:

MQNSHSGVNQLGGVFVNGRP
LPDSTRQKIVELAHSGARPC
DISRILQVSN GCVSKILGRY
YETGSIRPRAIGGSKPRVAT
PEVVSKIAQYKRECPSIFAW
EIRDRLLSEGVCTNDNIPSV
SSINRVLRNLASEKQQMGAD
GMYDKLRMLNGQTGSWGTRP
GWYPGTSVPGQPTQDGCQQQ
EGGGENTNSISSNGEDSDEA
QMRLQLKRKLQRNRTSFTQE
QIEALEKEFERTHYPDVFAR
ERLAAKIDLPEARIQVWFSN
RRAKWRREEKLRNQRRQASN
TPSHIPISSSFSTSVYQPIP
QPTTPVSSFTSGSMLGRTDT
ALTNTYSALPPMPSFTMANN
LPMQPPVPSQTSSYSCMLPT
SPSVNGRSYDTYTPPHMQTH
MNSQPMGTSGTTSTGLISPG
VSVPVQVPGSEPDMSQYWPR
LQ

They don't bother with the stop codon, but I think you'll all find that the sequences are an exact match.

You honestly think I wouldn't have gone to the trouble of searching actual protein and genome databases to obtain my information? Oh ye of little faith! [/quote]
There is one difference. Is it important?
The seventh row up from the bottom.
Your list........ QPTTPVSSFTSGSMLGLTDT
with theirs..... QPTTPVSSFTSGSMLGRTDT

[kyrani99]

[quote="Calilasseia";p="37503"]

From the latter paper about Hedgehog signalling, I provide the abstract:

[quote="Yamamoto et al, 2004";p="37503"]Hedgehog (Hh) proteins are responsible for critical signalling events during development but their evolutionary roles remain to be determined. Here we show that hh gene expression at the embryonic midline controls eye degeneration in blind cavefish. We use the teleost Astyanax mexicanus, a single species with an eyed surface-dwelling form (surface fish) and many blind cave forms (cavefish), to study the evolution of eye degeneration. Small eye primordia are formed during cavefish embryogenesis, which later arrest in development, degenerate and sink into the orbits. Eye degeneration is caused by apoptosis of the embryonic lens, and transplanting a surface fish embryonic lens into a cavefish optic cup can restore a complete eye. Here we show that sonic hedgehog (shh) and tiggy-winkle hedgehog (twhh) gene expression is expanded along the anterior embryonic midline in several different cavefish populations. The expansion of hh signalling results in hyperactivation of downstream genes, lens apoptosis and arrested eye growth and development. These features can be mimicked in surface fish by twhh and/or shh overexpression, supporting the role of hh signalling in the evolution of cavefish eye regression.[/quote]

So it transpires that if you transplant an embryonic lens taken from a surface-dwelling Astyanax mexicanus with normal eyes into the optic cup of an embryonic blind cavefish, normal eye development resumes. Interesting is it not? And, by manipulating the shh and twhh gene expression in surface-dwelling eyed fishes during embryonic development, the scientists were able to reproduce the eye apoptosis seen in the cave dwelling fishes.
[/quote]

Does this mean that the same genes are there and that the difference is that the blind fish destroys the lens after it is formed to become eyeless? Does this possibly happen to allow more low level light into the eye of the cave fish so that they may detect light? That they have some sight, though blurred or is it totally dark in the cave?

[DavidMcC]

[quote="kyrani99";p="2466362"][quote="Calilasseia";p="37503"]

From the latter paper about Hedgehog signalling, I provide the abstract:

[quote="Yamamoto et al, 2004";p="37503"]Hedgehog (Hh) proteins are responsible for critical signalling events during development but their evolutionary roles remain to be determined. Here we show that hh gene expression at the embryonic midline controls eye degeneration in blind cavefish. We use the teleost Astyanax mexicanus, a single species with an eyed surface-dwelling form (surface fish) and many blind cave forms (cavefish), to study the evolution of eye degeneration. Small eye primordia are formed during cavefish embryogenesis, which later arrest in development, degenerate and sink into the orbits. Eye degeneration is caused by apoptosis of the embryonic lens, and transplanting a surface fish embryonic lens into a cavefish optic cup can restore a complete eye. Here we show that sonic hedgehog (shh) and tiggy-winkle hedgehog (twhh) gene expression is expanded along the anterior embryonic midline in several different cavefish populations. The expansion of hh signalling results in hyperactivation of downstream genes, lens apoptosis and arrested eye growth and development. These features can be mimicked in surface fish by twhh and/or shh overexpression, supporting the role of hh signalling in the evolution of cavefish eye regression.[/quote]

So it transpires that if you transplant an embryonic lens taken from a surface-dwelling Astyanax mexicanus with normal eyes into the optic cup of an embryonic blind cavefish, normal eye development resumes. Interesting is it not? And, by manipulating the shh and twhh gene expression in surface-dwelling eyed fishes during embryonic development, the scientists were able to reproduce the eye apoptosis seen in the cave dwelling fishes.
[/quote]

Does this mean that the same genes are there and that the difference is that the blind fish destroys the lens after it is formed to become eyeless? Does this possibly happen to allow more low level light into the eye of the cave fish so that they may detect light? That they have some sight, though blurred or is it totally dark in the cave?[/quote]
What I think it means is the the expression of the genetic structure determining whether eye development is sustained for long enough to form a useful eye is localised to the eye itself.
In other words, there is difference between the genetic structure of the blind and sighted cave fish. It is not clear how useful the eye is when created this way, because sight requires some kind of visual cortex in the brain, and this might well not develop properly after the implant, though it is not impossible that there would be some adaptive development of the brain to what is there, triggered by signals form the eye.

[Rumraket]

It's a shame the forum update seems to have broken so many old posts.