BAM and the Molecular Ticker Tape

paceWith annotIn my little corner of cyberspace BAM is now generating no little controversy, so let’s review some of major points. The Brain Activity Map (BAM) project is a proposal to fund a massive collaborative effort between neuroscientists and others to characterize the dynamic activity of complete neural circuits, first in “simpler” animals, then mammals, perhaps primates, and finally humans. The proposal may have been behind president Obama’s praise for neuroscience in the state of the union address, but the outline of a proposal (that does seem to be in some flux) appeared in the New York Times last week. There are apparently many scientists involved in the project, but Harvard molecular biologist George Church and Columbia neuroscientist Rafael Yuste seem to be the ones taking calls from the media and bending the ears of presidential advisors. I recently talked to a scientist who was a post-doc in the Yuste Lab who helped develop some of the high throughput neural recording techniques that are at the center of the BAM proposal. These imaging and electrophysiology methods are already capable of monitoring the activity of about 1,500 cells in brain slices, and somewhat fewer in behaving animals. One of the main questions of the feasibility of the BAM project is whether these techniques can be scaled up to the proposed goals, which could include neural systems with 1,000,000 cells (still far below the size of a whole human brain). As Ian Stevenson has pointed out, cell-count advances in multicellular recording have proceeded at a very sub-Moore’s Law pace, doubling only every 7.4 years. There is good reason to believe that even with substantially better funding these techniques may quickly run into basic physical limits before given us the high throughput data we want from neural systems (see the figure for pace of progress curves for neural recording, computing and molecular biological techniques).

One scientist who is not willing to wait for the kind of complete data set he wants to understand the brain is Konrad Kording, head of the Bayesian Behavior Lab at the Rehabilitation Institute of Chicago (and co-author of the Stevenson paper). He has a surprisingly eclectic curiosity and a sharp sense of humor. He is senior author on a commentary paper in Nature (with Daniel Acuna and Stefano Allesina, 2012) which introduces a model for predicting a metric of a scientist’s future influence from his/her current productivity. I’m sure the web-based version they set up get many more hits than any of us would like to admit (What? Scientists egotistical? I’m shocked!). He’s also managed to get a LOLCats figure into one of his papers; clearly he’s not one for taking the conventional path. Since he calculated that he would be long dead before getting his hands on the data he needed by conventional methods (he was senior author on the Stevenson paper mentioned above), he started to think about how he might be able to use the rapidly advancing techniques of molecular biology to radically increase the throughput of neural recording.

I heard this story when I met with Kording in his 14th floor lab (with a great view of Lake Michigan). He recalled that the idea of using molecular techniques was sort of in the air when he began to think about it in 2011, but most scientists were skeptical that a practical approach could be found. Kording, however, presented a possible strategy in a whimsically titled paper, Of Toasters and Molecular Ticker Tapes (open access, by the way), where he suggests it could be possible to have individual cells (in genetically accessible animals such as mice) record their own activity in strands of DNA. This would, he explains, work by inserting template DNA strands along with the special versions of DNA polymerase into the cells. DNA polymerases are the molecular machines that are responsible for copying DNA (typically, when cells divide). This process is generally pretty reliable under normal conditions in the nucleus of cells, but with certain versions of the molecule in certain conditions, the copying process can be susceptible to error, and the error rate can be proportional to the amount of calcium ions in the cell. Calcium ions are one of the main types of electrically charged particles used by neurons process and transmit signals, and in many neurons the flow of calcium ions into the cell tends to be greatest when that cell is actively communicating with other neurons. In fact, as I mentioned last time, it is exactly this property that allows neuroscientists like Jason MacLean to read neural activity from calcium imaging. So if you could compare each strand of DNA created by DNA polymerase with the template strand, you could tell how active the neuron was by how many mistakes were made in the copy. Inside the neurons in the animal’s brain, many molecules of DNA polymerase would be busy copying the target DNA strand while the neuron goes about its normal business receiving, processing and passing on electrical signals. As Kording explains it, the scientist would need to provide a synchronizing signal of some sort, say with a prominent sensory signal or by inducing a seizure, then after the animal is put through its experimental paces, the DNA could be recovered from the brain tissue and sequenced using modern high throughput techniques. The error rate of each strand in comparison with the template strand would provide a readout of each cell’s activity, with multiple strands improving the precision of the measurement. By carefully processing the brain tissue in a fine 3D grid pattern, an activity map of the animal’s entire brain could be recreated.

According to Kording, there would be some limitations to the technique. DNA polymerase from E. coli can work up to speeds of 1,000 bases a second, which is comparable to current electronic recording methods. Still the dynamics of cellular calcium are slow compared to the finest temporal scales of neural signaling, so the exact timing of neural activity with this method would be a little blurry. Nonetheless, in a multi-institution collaboration, Kording (with his collegues Keith Tyo and Ed Boyden) helped researchers from George Church’s lab (Zamft, 2012, also open) to establish the basic feasibility of using DNA replication as a calcium sensor (at least in a test tube), but the polymerases are not yet sensitive enough to detect the levels of calcium you would find in a normally functioning neuron.

Moving one step further into the hypothetical, Kording is particularly excited about the possibility of combining the molecular ticker tape method with another transformative approach recently proposed by Anthony Zador (et al.). They suggest that some of the genetic machinery used by the immune system to generate combinatorial complexity could be used to create a unique genetic barcode for each neuron in an animal’s brain, and that a virus could be engineered to allow these barcodes to fused together in a way that would indicate which cells were linked into connected neural circuits. In principal, this would allow the connections between most of the cells in an animal’s brain to be identified. This connectome sequencing method could be combined with the molecular ticker tape method to produce a nearly comprehensive representation of the connectivity and activity of a single animal’s brain. Kording argues that such technologies are close enough to practical application that a coordinated research effort could produce dramatic returns in the proposed time frame of the BAM proposal.

In a previous post, I argued that analytical methods might not be up to the task of handling such data sets, but Kording disagrees. He points out that including connectivity data would actually make understanding the activity network feasible because it would limit the number of possible explanations for any given data set. Circuit models could be analyzed on a cell-by-cell basis in terms of the activity of only directly connected partners, reducing the complexity of the task dramatically. Without going too far into the math, this simplification is the difference between problems requiring planetary scale computers from ones that can be solved with contemporary clusters.

 

Correction (2/28/2013): In an earlier version, I mistakenly stated that the Zamft 2012 paper established the feasibility of DNA polymerase calcium sensors in cell culture. In fact, it was in vitro. Thanks to co-author Adam Marblestone (see comment below) for alerting me to the error.

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~ by nucamb on February 27, 2013.

15 Responses to “BAM and the Molecular Ticker Tape”

  1. Another great informative post. These sound like terrific early-stage technology ideas and prototypes. Here’s what I don’t get about what we’ve heard so far about a big $300M/yr, 10-15 year project. It seems like the main item on the agenda is technology development. Just like with DNA sequencing, different technologies can be developed in individual labs or small-scale collaborations until ready to be commercialized or otherwise deployed on a large scale. Indeed, this seems to be happening already. Once we have such technologies, there are lots of experiments to be done with them. It’s not clear than any of them are large, centralized, factory-style projects. What exactly is the rationale for a big project with a huge infusion of new funds? I just don’t see the parallel to the Human Genome Project.

    • I agree completely. These proposed methods for using DNA sequence to study connectivity and firing rate are super exciting and promising, but they are still very preliminary and/or hypothetical. This is exactly the stage at which research is supposed to be funded by R01s — so that individual labs can tackle these problems with maximal creativity. Right now these technologies need competition between a large number of labs, not production-level implementation by a select few.

      • Would the RO1 funding approach be enough to integrate the different technologies and provide for a data sharing infrastructure (like NCBI)?

    • I’m glad to have your input here, and it’s good to hear that you found the post informative. I’m also not sure this project requires such a large investment (especially if it would gut funding for other projects). It’s also hard to debate specifics when we have so little information. In what ways do you feel this project differs from the HGP? What sort of project do you think would be worth a big science investment (asking completely seriously)?

  2. I echo the thoughts of Leonid Krugylyak (even though I find his name hard for my American fingers to type. @leonddkruglyak ) . These may well be wonderful, transformative technologies, but without: a. pilot data. and b. an interesting hypothesis to test, it’s hard to justify trading in 3000 RO1s for this project. A second point is that there is often a disconnect between molecular biologist (or physicists) and neuroscientists. Non-neuroscients typically fail to recognize the scope of the problem, or even to define it particularly well. (I’m trying to avoid using the word “arrogance”).

    • jkubie, reasonable questions. Though as I’ve mentioned elsewhere ‘hypothesis driven’ is relative when trying to establish a new scientific infrastructure. But, yes, if it meant defunding 3000 other RO1s that would be a high bar for justification (certainly requiring more than just hand-waving about Parkinson’s). One point however, Konrad Kording at least is actually a systems neuroscientist, so in this case it’s hard to say that it is overreaching molecular biologists making hay in someone else’s field.

  3. Nice post!

    In the PLoS ONE paper from 2012, we actually haven’t even done it in cell culture yet, just in a test tube, and the calcium effects are indeed weak. We’re working on addressing both of those. The main point of the paper was just that we can use a deep sequencer in high-throughput, without any traditional biochemical assays, to screen for cation-dependent effects on polymerase mis-incorporation, to aid in the future development of engineered sensors, and also to characterize those effects in detail at single-nucleotide resolution. It’s about as early-stage as you can get.

    I’d agree that at this stage of development, relatively modest funding consistent with a small-group, early-stage collaborative effort would be appropriate. I agree with the sentiment here that in many, but not all, cases technology development proceeds best through exploring many ideas in parallel: taking many modest-sized risks.

    On the broader BAM project, while I have no knowledge of the plans, I’d suggest from what I’ve read online that there does not seem to be an intention to centralize the project around a handful of speculative proto-technologies, let alone a single speculative proto-technology. Technology development in general is a clear thrust, as it well should be, but it seems like that would encompass many different technologies at different stages of development, including totally new ideas like synthetic biology approaches as well as established ideas like calcium imaging + opto-genetics.

    I personally haven’t perceived a risk that one new technology will be greatly favored over others, at least until a particular set of techniques is really proven applicable to comprehensive analysis of any given model organism.

    Indeed, this would arguably be an improvement over the genome project, where a small set of techniques was applied at scale from the outset (if I understand correctly): whereas here a wide variety of technology development efforts would be identified and front-loaded before picking a single approach to try to scale up to a whole mammalian brain, say.

    Anyway, ticker-tape is at an early stage where we are planting little seeds to let it grow: it’s a potentially promising idea but we need to develop and de-risk it before scaling it up… and like most basic research it may evolve in totally unforeseen directions. Variation and selection! Then scale later.

    In contrast, other technologies like silicon probe arrays, calcium imaging or 2-photon opto-genetics may greatly benefit from scale-up and infrastructure right now, beyond that given by the typical individual-investigator incentives: I’m confident that that can happen on an as-needed basis. I feel that building some centralized infrastructure for these more established technologies would not only help with large-scale data-gathering goals like BAM, but also aid in more incremental efforts to do targeted experiments, test hypotheses and aid in formulating more precise scientific questions. Note that other efforts like the Allen Institute’s MindScope project are also embarking on scaling and centralizing certain promising-and-well-proven techniques to do a comprehensive, but also apparently somewhat theory-driven, analysis of mouse visual cortex. BAM and MindScope seem highly synergistic to me.

    • Thanks so much for participating in this discussion. Are you saying that at the moment modest funding is enough for the current state of the ticker tape concept? As to the BAM project, you seem to be saying that funding diverse groups with diverse approaches would help insure success and applicability. What about the price tag? Do you think this is a $3B scale project, and what would your answer be if money was drawn from other areas?

  4. >Are you saying that at the moment modest funding is enough for the current state of the ticker tape concept?

    Yes. We need a funding source that is willing to take a risk to do some initial prototyping of this concept at the scale of a couple of small-to-medium sized laboratories over several years. Large investments for scaling to a whole mouse brain (for instance) might come later, or might not, depending on how things look in early testing.

    Almost any technology would require a much-larger-than-typical-R01 funding infusion to scale to a whole mouse brain, right? But that investment should come only once any given technology has passed preliminary milestones.

    Importantly, other techniques like calcium imaging or 2-photon-holography have already proved their usefulness at a small scale: for these, I’d personally suggest more-than-modest funding and some non-traditional institutional models to push for a first BAM in at least one tiny model organism (say, C. elegans, to start) using opto-electronic technologies.

    Separately, to me, the point of exploring more speculative ideas like ticker-tapes would be: to have fundamentally new technologies vetted-and-available-for-potential-further-investment by the time C. elegans / Zebrafish get mapped, as I believe it is widely agreed that the next stage, namely an activity map for mammalian brain, will require radically new technology ideas, not just incremental development of presently-used techniques. Hopefully something much better than a DNA ticker-tape will come along by then and the amount of investment required to search that possibility-space may not really be all that large in the scheme of things.

    >Do you think this is a $3B scale project, and what would your answer be if money was drawn from other areas?

    This is a strictly personal opinion, but personally I do think that goal-oriented but broadly-based technology development efforts to enable radically-more-scalable and lower-cost experimental methodologies in neuroscience would be worth this price tag, ultimately making it possible for small labs and individuals to ask more powerful questions for much less total money. I think that is in fact a near-optimal use for funding at this point, since there is so much about the brain that we simply can’t observe and therefore can’t ask systematic questions about at present.

    But hopefully this will not subtract from other areas. Ideally, it’s a positive-sum situation, but if I was in the un-enviable position of making a choice, I would personally go for technology development over most other options any day of the week.

  5. […] for significant growth that could be catalyzed by coordination and funding. As mentioned in the previous posts, analytical techniques are being developed that can characterize activity from large networks using […]

  6. So Kording is the inventor of the ticker tape then? I thought I saw a patent for it at the end of one of the BAM papers by Church? Why is not Zador big part of BAM then, if , at least in my book, the barcode, while difficult should precede the ticker tape, if the tape is to track many many neurons?

  7. @John: I’d tend to agree that cell-barcoding (e.g., Zador) comes first, more or less as a pre-requisite for DNA storage as a means to map activities (or other molecular changes, like RNA expression over time). I think Zador and others are making real progress in this area! In-situ sequencing would be another option but less direct.

  8. And here’s a lecture from Google’s Tom Dean which discusses some of the history-of-ideas on this :-}

    http://cs.brown.edu/people/tld/note/blog/13/04/19/

  9. […] of single neurons. For our thought experiment let’s suppose that I had access to the proposed molecular ticker tape technology talked about for BRAINI. What kinds of questions could I […]

  10. […] absolutists on this question, animal rights activists would be sensible to support techniques (like those proposed by the BRAIN Initiative) that would allow collection of huge amounts of data from individual animals in one […]

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