Hello from UC Berkeley

Discussion in 'Introduce Yourself' started by 000generic, Oct 11, 2012.

  1. 000generic

    000generic Cuttlefish Registered

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    Hi Tonmo!

    I'm a postdoc in the Rokhsar lab at UC Berkeley. We are in the process of sequencing the genomes of Octopus bimaculoides (California Two-Spot Octopus) and Idiosepius notoides (Southern Pygmy Squid). We are interested in the development of a new cephalopod model(s) for next-generation lifecycle imaging, using cutting-edge techniques such as MuVi-SPIM and optogenetics (links are to examples in the fields, not of our research). As part of our genome projects, we will begin characterizing early development, focusing on the body plan, nervous system, heart, chromatophores, and transparency. More fundamentally,
    we are interested in the closing of cephalopod lifecycles and the establishment of research breeding colonies, in particular, for one or more species exhibiting features amenable to imaging, transgenics, and non-invasive functional studies in development, behavior, and physiology. Which species to focus on remains to be seen. Our gold standards here are zebrafish, fly, and worm but without the maintenance of mutants. Suggestions or collaborations welcome! I am also interested in the development of anatomical and lifecycle ontologies for cephalopods, molluscs, and animals in general, as these tools, in combination with sequencing, imaging, and functional studies, will facilitate comparative insights into cephalopod biology and animal evolution.

    This intro is jargon-rich for those who may be interested but for the Tonmo community in general, what's of potential interest is that our research generates lots of images or videos that never make it to publication, as only one, not one hundred, is required. For our new work with cephalopods, I'll be posting many of these extras here. If any of the jargon or images interest you, please feel free to contact me. I've been lurking on Tonmo in various forms for nearly 10 years but only got my first cephalopod this summer. I'm excited to go public and am looking forward to becoming an active part of the community. Also, I'll be speaking at CIAC at the end of this month and would be happy to meet with others in person.

    Eric
     
  2. GPO87

    GPO87 Sepia elegans Staff Member Moderator

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    Welcome to Tonmo! I was looking at your photo's and they are great! :)
     
  3. 000generic

    000generic Cuttlefish Registered

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    Thanks GPO87! The octo babies make it easy.
     
  4. DeepBlueWonders

    DeepBlueWonders Vampyroteuthis Registered

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    :welcome:to Tonmo!
     
  5. Heather Braid

    Heather Braid O. vulgaris Supporter

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    Welcome to TONMO! You have some very cute pictures of baby octopus! The whole AUT squid taxonomy lab will be giving talks at CIAC - GPO87, main_board, Tintenfisch, and me. I'm looking forward to meeting you since it's always nice to meet someone that is interested in cephs, and especially in DNA :)
     
  6. robyn

    robyn Vampyroteuthis Supporter

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    Hi Eric,

    Your work sounds fascinating! I am a postdoc at UT Houston (where we study pain and nociception) and the MBL (where we work on these questions in Loligo) - I work with the Hanlon lab in the summers and we collaborate on behaviour and sensory physiology. I'm interested to hear some more about what sorts of things you're planning to do with nervous system development. Can you share some more details about your goals there? Are you mapping temporal expression profiles of certain genes? Or doing cell-fate mapping type stuff? Since I'm very interested in the sensory neurons in the CNS, I'm looking for ways to identify or track neurons of different types. We have an ongoing collaboration with Leonid Moroz, too (I assume he is known to your lab, since it sounds like you're in similar fields!), where we're looking for sensory-neuron specific markers, but i"d be curious to hear of any similar attempts from people with different objectives.

    I'm not a developmental biologist, (I'm trained in evolution, behaviour and neuroscience) so if you feel comfortable sharing some general areas of interest in 'moderately technical' :wink: terms, I would love to hear more. We have a number of people here interested in sensory physiology, so I suspect I'm not alone!

    Good luck with your research.

    Robyn.
     
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  7. DWhatley

    DWhatley Cthulhu Staff Member Moderator

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    Not being the least bit technical (unless you want to talk software) I will likely ask for clarification if I can't follow but will enjoy whatever you can post. My biggest interest is in your success closing the lifecycle over time (not just one generation success). Bimacs seem to be the most successful with initial hatchlings but I don't recall any posts of tank bred of any species other than O. mercatoris surviving. I hear tell this will change soon for another species though :sagrin:. I would like you to post details on feeding (both foods and sizes of foods relative to the hatchlings) as you progress with trying to raise them. I would also appreciate your posting any anomalies you see in the first tank bred.
     
  8. GPO87

    GPO87 Sepia elegans Staff Member Moderator

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    OMG Eric!

    I must have totally zoned out when I read the part about you being at CIAC! How cool! Looking forward to talking with you there!
     
  9. DWhatley

    DWhatley Cthulhu Staff Member Moderator

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    :roflmao: GPO87 When I saw he was going to be there I was going to PM you then saw your response and "ASS U ME"d that it registered but was surprised you did not say something :roll:
     
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  10. 000generic

    000generic Cuttlefish Registered

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    Thanks everyone! To touch on some of the questions asked:


    For the coming year we're focused mostly on genome sequencing, assembly, and building a genetic map for our two species of interest, and potentially working with other groups and their sequencing projects. But like I've mentioned, I'm also interested in identifying one or more species that would work well as next-gen research models, specifically selected for their compatibility with new imaging techniques and functional tools. Based on my still limited knowledge of cephalopod lifehistory diversity - and, more importantly, on conversations with others in the field, there are a few potential Octopus species, not including bimaculoides, some of which others are working to close the lifecycle of. The Idiosepius genus is promising but remains problematic, as the lifecycles of species in the genus remain unclosed. As far as I know, though attempts have been made, no one is currently working to close the lifecycle in any of the seven Idiosepius species. So, closing an Idiosepius lifecycle is definitely an area where we are interested in collaboration. There is the possibility, if funding comes through, that I can start working with Idiosepius in the lab (I have experience culturing embryos and larvae for a number of marine invertebrates though not closing a cephalopod lifecycle) but at the moment my position is not funded to do so.


    In the mean time, I'm getting my cephalopod sea legs with bimaculoides as a side project. And it may be that I end up sticking with bimaculoides, as it is strong on many fronts in terms of research. But my feeling this last year or so, as optogenetics and light-sheet microscopy have taken hold, is that the onset of cephalopod genomics offers a unique opportunity to establish a new research model selected specifically to leverage the power of cutting-edge genomic, imaging, and non-invasive transgenic toolkits. And in creating a new model, the idea is that it will complement, not replace, current cephalopod model systems. Its definitely the case that no one species is perfect for all questions or methods. For myself, I'm not tied to any one species at this point, and am definitely open to working with others on any species that looks to hold real potential to become a next-gen research model system. For maintaining bimaculoides in the lab, I'll keep you posted if I have any success beyond the early hatchling stages. I may be wrong but I think others have in fact closed the lifecycle at this point, technically speaking, but things are still a long ways off from any sort of breeding colonies, which may prove difficult in a lab environment given the tank size required for adults. My hope is that there will be a number of exciting updates on culturing cephs at CIAC.


    As for specific research questions, there are any number of candidate genes for major areas of interest in cephalopod biology, such as nervous system, eyes, heart/blood vascular system, camoflague, bouyancy, transparency etc. At the informatic level we'll try to cover all of these areas, as will others. In taking things to the bench, it will most likely involve an expression screen for gene sets in one or two areas and then using a few candidate genes of interest to establish a slew of techniques, hopefully in parallel coordination with other labs around the world working on the same or other species. CIAC is a great opportunity to begin coordinating these efforts. The amount of work necessary to develop research tools for a new species, or cephalopods in general, is substantial, as I've learned first hand in working at the bench as an army of one on the Lottia gigantea genome project. Similarly, over the long-term, the number of genes that will be characterized, at least ideally, in a given genome is in the tens of thousands - and that's just protein coding genes. Much more than any one lab can do, but knowledge gained by one can guide many. My hope is that cephalopod research in its post-genomic era will be an open one, an environment where advances in one lab or area are made readily and openly available to help advance other labs and areas - a model of vice versa in all directions. As genome-enabled tools are established, and continue to be established, we can all dive into the biology, be it on a shared model system, or a given species of interest.
     
  11. DWhatley

    DWhatley Cthulhu Staff Member Moderator

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    000generic,
    Is there a reason you need to raise them in the lab (ie do they have to be related for the gene work)? Mexico has developed a nursery program for O. maya that might be an unstudied animal, one with food value (so funding might be more forthcoming) and is large egged. It IS a larger animal and I am not sure of housing requirements or if you can work out something with the university attached to the nursery work since my total exposure is the little that I have found in the news:
    http://www.ingentaconnect.com/content/umrsmas/bullmar/1966/00000016/00000003/art00012
    http://www.fis.com/fis/worldnews/wo...&special=&monthyear=&day=&id=41181&ndb=1&df=0
    http://www.panoramaacuicola.com/noticias/2010/03/24/octopus_maya_farming_progresses_in_yucatan_.html
     
  12. 000generic

    000generic Cuttlefish Registered

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    I gave O.maya serious consideration (particularly since my family has a house in Campeche) and I would be very interested in producing a staging series, if there is not one already, but like you point out, the adults are medium large. Most of the research techniques I would like to develop/see developed require working with early stages of development. So breeding animals are required in the lab. And a medium-sized lab would need new embryos on a weekly basis, if possible year round. So a fair number of adults are needed, meaning small adults. But I haven't seen the animal in person, or the facilities that have been developed for it, so its possible it could work in a lab environment that is not overly space limited for culturing. But for many labs, the space requirements would make it a less than perfect choice I suspect.

    But O.maya is great for the reasons you suggest. I'm looking forward to hearing about current efforts with it at CIAC. Thanks for all the links!
     
  13. DWhatley

    DWhatley Cthulhu Staff Member Moderator

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    As a thought, if you have extra animals, is it outside of the University ethics requirements to offer them to the public? If you could charge a nominal fee (shipping is expensive, somewhere in the neighborhood of $75-100 for the required overnight) and could sell a few (the market is not large), this might help a little with financing (I know not of the world of grants and restrictions so don't laugh if this is way outside a reality check. There is also the time involved for packing and shipping that might not make the thought worth while). To date, there are no CB animals available so even captive born might make them attractive to keepers. I know you can't do this with bimacs but most other octos don't carry their restrictions.

    A warm water species would also reduce the costs of keeping them in both equipment needed and ability to home extras. Octopus briareus is not commercially harvested but is plentiful and large egged. I have personally raised two from hatchling but was not successful in raising any young from the mating of the two tank born from a WC female. I would expect a lab would have a better chance. However, these are again a larger species (smaller mantle size but longer arms).

    The other species I can think of that is relatively (note the relative) easy to raise is O. mercatoris. We have not seen many of them lately though. These are a dwarf species that can be housed together if obtained from the same initial housing (usually live rock) or born from the same hatching. We have had several member to successfully raise hatchlings from tank born pairs.

    Since you are at Berkeley, I assume you have talked to Roy about other potential species.
     
  14. 000generic

    000generic Cuttlefish Registered

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    O.briareus and O.mercatoris are both great suggestions. And Roy and his lab are an incredible resource here at Berkeley. I'd be happy to share extra animals, for species where its legal, but have no idea as to university or other requirements etc. Also, I'm literally just past my second month with my first clutch, so shipping extras to a select few outside research is still a ways down the road, but its an idea I'm open to if it would be straight forward.

    Sorry, but what does CB and WC stand for.
     
  15. DWhatley

    DWhatley Cthulhu Staff Member Moderator

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    LOL, and I am the old ... person that can't read text speak :grin:

    WC wild caught, CB captive bred

    I was thinking about much further down the road and didn't realize you had eggs that you were already watching.

    While looking for an article about the O. maya aquaculture facility I came across a fairly recent abstract discussing the study of 3 different first foods (link posted in the Article and Journal Links sticky in the Raising Octopus from Eggs forum). Only the abstract is free but you may have access through the university. The gist of the abstract confirms what we already think we know, brine shrimp and freshwater animals are not the best foods for hatchlings where much better survival was seen with the saltwater feed. I don't remember what else is in that list but you might look through it for ideas.
     

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