Hello from UC Berkeley

000generic

Cuttlefish
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Jul 20, 2011
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16
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
 
Joined
Feb 18, 2007
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76
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 :smile:
 

robyn

Vampyroteuthis
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Jan 19, 2007
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313
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.
 

DWhatley

Kraken
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Sep 4, 2006
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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.
 

GPO87

Sepia elegans
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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!
 

DWhatley

Kraken
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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:
 

000generic

Cuttlefish
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Jul 20, 2011
Messages
16
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.
 

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