Biology student with a curiosity about cephalopod neuroscience.

Discussion in 'Introduce Yourself' started by neurobadger, Apr 19, 2010.

  1. neurobadger

    neurobadger Vampyroteuthis Registered

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    Hi, folks.

    I'm an undergraduate biology student. I've been to this website a number of times, but was tempted to join it because I found a few posts on the octopus genome and didn't find any information on the internet about it.

    Sequencing the genome of some representative species of octopus - perhaps Enteroctopus dofleini or Octopus vulgaris - and afterward mapping the various genes to each sequenced chromosome would help to elucidate, among other things, nature's pattern for the nervous system, since it's convergently evolved within both cephalopods and vertebrates, and I have heard that the octopus's intelligence varies anywhere from a housecat to a 3-year-old human. My primary interest, actually, is in neurogenetics and developmental neurobiology of cognition, particularly as relates to intelligence.

    Has any progress been made since the last post on it? The transcriptome is complete for Octopus, according to the post, and this is huge, of course, but there's no indication of the pre-RNA newly transcribed gene products, as well as the junk DNA (you can extrapolate certain sequences of DNA from the RNA products, of course, but you have to order it).
     
  2. Architeuthoceras

    Architeuthoceras Architeuthis Staff Member Moderator

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    :welcome: to TONMO neurobadger!

    If only cephalopod intelligence could fossilize, maybe I could help... I'm sure someone will chime in.
     
  3. DWhatley

    DWhatley Cthulhu Staff Member Moderator

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    WAIT, Kevin aren't youi and I living proof of fossilized intelligence (I am the older:old::old:)?
     
  4. Architeuthoceras

    Architeuthoceras Architeuthis Staff Member Moderator

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    Who you callin intelgent ? :sly:
     
  5. neurobadger

    neurobadger Vampyroteuthis Registered

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    'Fossilize'. Nice. :P

    Actually, I found out the 'octopus' transcriptome was nothing more than the transcriptome of Arabidopsis, which is a plant.

    However, Sydney Brenner at the Okinawa Institute of Science and Technology is going to study the octopus genome.
     
  6. lance

    lance Wonderpus Registered

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    welcome to TONMO

    lance
     
  7. monty

    monty Colossal Squid Staff Member Supporter

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    :welcome: to TONMO! I tried to find information on Sydney Brenner's project a year or two ago, and found that there was very little information. If you have an update, please post!

    I'm really hoping people do some more developmental studies of cephs, too. I've recently gotten excited about developmental gene regulatory networks, but I'm not aware of anyone who has done more than HOX gene expression in cephalopods.
     
  8. robyn

    robyn Vampyroteuthis Supporter

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    I'm not sure who is claiming the octopus genome that is actually Arabidopsis, however neuronal transcriptomes of various cephalopods are being compiled and annotated primarily by Leonid Moroz, who is in Florida. To my knowledge there have been no attempts to sequence the entire genome, so you might have some trouble tracking down pre-RNA products and 'junk DNA' as you mention in your first post. Try a pubmed search for Leonid's name - he has a number of abstracts on cephalopod transcriptomes, I think, but I don't believe the work has been published yet.
    Also there are a few groups currently working on development of the cephalopod CNS and neurotransmitter expression etc. during development. Try searching for papers by Shuichi Shigeno, or by Andreas Wanninger and Tim Wollesen.
     
  9. fleb

    fleb Larval Mass Registered

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    Hi there !

    New to this forum (hello everybody!), I'm a PhD in developmental biology, looking for a post doc and interested as well in neural development of cephalopoda.
    So thanks for the scientist names you cited, it may actually help me :)

    Idon't think as well any cephalopoda genome is sequenced yet.
    Weirdly I couldn't find any information on the one that Sydney Brenner claim he will study (according to its lab page at the okinawa university) No information are available on the DOE Joint Genome institute (which he claims is its partner) neither on the GOLD (Genome online Database) website. Which make me doubt any serious project is currently on the way.

    To the people you already cited studying cephalopoda neuroscience, you can also add "Heinz Gert de Couet" which is working in Hawaii, and "Laure Bonnaud" which is working on Cuttlefish (Sepia officinalis) embryos in Paris. It is to note that Laure bonnaud as an ongoing project of sequencing of a large EST database (cDNAs made from reverse transcription of total mRNAs harvested at various developmental stages) for this animal in collaboration with the sequencing platform of the Genoscope, but it is not to date a public project
    (http://www.genoscope.cns.fr/spip/ESTs-library-of-Sepia-officinalis.html)

    As far as I've looked, Immunostainings and insitu Hybridisations works pretty well on some species but major problem concerning cephalopoda as a competitive model for neuroscience/neural development is the lack of gain/loss of activity tools as well as serious public database for DNA sequence (either EST or genomic). Basically all the publications so far are only descriptive, and do not have functionnal data.

    So it may be a bit early now for cephalopoda as a serious and competitive experimental model, but hey ! I have the feeling it won't last for long

    Does anyone has clues concerning attempts to block a gene function (RNAi, morpholinos or whatever) by injection s in cephalopoda eggs ???

    Cheers ! (waving one of my tentacle)
     
  10. monty

    monty Colossal Squid Staff Member Supporter

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    :welcome: fleb. I think Martindale's lab in Hawaii may have done some gene function studies in developing Euprymna scolopes but I may be remembering wrong...
     
  11. neurobadger

    neurobadger Vampyroteuthis Registered

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    Total mRNAs? Is this the pre-spliceosome mRNA?

    I've heard of issues with the methodology.
     
  12. fleb

    fleb Larval Mass Registered

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    Hi neurobadger

    "total mRNA" was maybe a misleading term.

    I'm not such an expert in that field but basicaly ESTs are usally made from polyAdenilated mRNAs.

    First you have to obtain total RNA (this should include pre mRNAs - not spliced, not polyadenilated and not 5' capped - as well as mRNAs - which are them spliced, polyA+ and capped - I suppose as well that "total RNA" may include as well small nuclear RNA and other non coding small RNAs if the purification method you use does not exclude such small molecules)

    Second, using oligodT (TTTTTTTT sequence) bound to beads for example, you can in a second round of purification isolate polyAdenilated mRNA that can be reverse transcribed to obtain cDNAs

    The cDNA you get at the end should reflect the total composition of mRNA (spliced, capped and polyAdenilated) in a given sample

    If you want to get pre-splicosome RNA I guess you could do the same protocol but just keep the supernatant when you precipitate your oligodT beads in the second round of purification

    or look directly if genome sequences are available difference you observe between a given DNA gene sequence (not spliced) and the corresponding EST (spliced)

    You can get additional informations on this page, which describes some commercial kits you can buy to purify RNA
    http://www.ambion.com/techlib/basics/rnaisol/index.html

    hope it helps
     
  13. neurobadger

    neurobadger Vampyroteuthis Registered

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    The pre-mRNA would better reflect the actual transcribed portion of the gene.

    Another good question to ask, I suspect, would be whether they've sequenced octopus proteins - have they taken a dead octopus, smashy smashied it, and found out what's in the proteins in it? There's going to be plenty of similar proteins to humans, but I know that there are minor differences in primary structure in some of these proteins .
     
  14. mucktopus

    mucktopus Haliphron Atlanticus Staff Member Moderator

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    A group in Berkeley started sequencing the genome of octopus in 2005, but I haven't heard the latest despite my attempts to contact them. I'll try again this summer.
     
  15. fleb

    fleb Larval Mass Registered

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    @ monty : thanks for the welcoming, I know someone which is working in martindale's lab, I'll try to ask him if they actualy do some functional analysis on Euprymna scolopes

    @ mucktopus : Would you have the name of the Principal Investigator of the Berkeley team you're talking about ???

    @ neurobadger : indeed pre mRNA tells you precisely which portion of the gene is transcribed, but mature mRNA tells you precisely which sequence is translated into protein. it can as well gives you information about splicing variant for a given gene, which can be difficult to derive from a premRNA sequence.

    For the protein question, once again I'm not such an expert, but it seems to me that protein isolation and sequencing are very difficult task, because starting from a whole organisms you would have such a high number of prots that you could only randomly and partially sequence a few of them, second problem concern composition of the proteins you would extract. I bet doing so you would get so much muscular protein, and miss a lot of protein that are expressed in very small area of the animal. One way to overcome the second point would be to isolate from several animals small regions of interest, like for instance brain or skin or anything you want.
    Once again if you are interested of protein function, starting from DNA or RNA sequence is much more easy because you can deduce the whole protein sequence, and because DNA sequencing technology as improved a lot these last years, they're accurate and really fast.

    If you're interested in protein folding and structure, once again I would first get the DNA sequence then make a synthetic mRNA and express it in an heterologue system (i.e put an octopus mRNA into yeast or reticulocyte lysate, then host cell machinery will make you lot of octopus protein, but with the risk that host cells which are not octopus cells may fold and process your protein slightly differently).
    It is some of the way scientist get enouch purified protein (major limitation of these studies) to make cristallography and derive 3Dimentional structures.
    I guess as well informatic folding prediction might be derived directly from some protein sequences

    Aside from this, given the lack of knowledge about cephalopods, I bet youre method would get some results and I have to say that I would love to see your isolation methods working :)

    sorry for talking/writing so much :sleeping:
     

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