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Next-gen Connectomics

10/23/2012
Jesse Jenkins

Can DNA barcoding help to increase throughput and decrease the cost of tracing the neural connections?


Neurobiologists have proposed a new method to map the neuronal connections within a mouse cortex using next-generation sequencing. The technique promises to increase the speed and throughput with which researchers can map the connectome while decreasing the cost of connectomics.

Using a DNA barcoding approach, each neuron would be labeled with a unique sequence of DNA. Then, these unique DNA identifiers from synaptically connected neurons are associated with each other using the pseudorabies virus that carries genetic material across different synapses. In the end, these barcodes from synaptically connected neurons would be joined to create a single DNA strand that would be analyzed using next-generation sequencing to gather a synaptic wiring diagram of the cortex. Source: PLoS Biology





In a paper published by PLoS Biology (1), the researchers from Cold Spring Harbor Laboratory (CSHL) in Cold Spring Harbor, NY, report that their DNA barcoding method—called barcoding of individual neuronal connections (BOINC)—can trace connectivity at the level of synaptic contacts between pairs of individual neurons.

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“Basically, if we succeed, the potential impact on neuroscience is similar to the impact of knowing the human or animal genome in biological research,” said study author Anthony Zador, a professor of biology and program chair in neuroscience at CSHL.

Presently, several major connectomics efforts are under way to trace neural connectivity on the cellular level such as the BrainSTORM Consortium. To trace neuron connectivity at this resolution, labs have relied on electron microscopy (EM) and other imaging techniques that involve cutting the cortex into thin slices, imaging each slice individually, and then analyzing terabytes of imaging data to trace the neural connections. Overall, this approach is costly and slow.

“Basically, they are hoping to piece together a larger volume of tissue, but I don’t think that at this point anyone envisions that it is going to offer the kind of throughput that we can imagine with this technique,” explained Zador.

Using a DNA barcoding approach, each neuron would be labeled with a unique sequence of DNA. Then, these unique DNA identifiers from synaptically connected neurons are associated with each other using the pseudorabies virus that carries genetic material across different synapses. In the end, these barcodes from synaptically connected neurons would be joined to create a single DNA strand that would be analyzed using next-generation sequencing to gather a synaptic wiring diagram of the cortex.

Olaf Sporns, professor and associate chair in the Department of Psychological and Brain Sciences at Indiana University and a participant in the Human Connectome Project who was not involved in this study, believes the BOINC approach could offer a novel way of bypassing the time-consuming and costly nature of other current systems.

“Zador and colleagues present an intriguing new idea by converting the problem from one of untangling millions of wires to creating a connection map with the help of genetic sequencing,” explained Sporns. “If the cost is as low as anticipated in this proposal, it would allow, for the first time, [the opportunity] to study large populations of individual brains from a range of species.”

However, both Sporns and Zador note the method does have its flaws, and the approach would most likely not be able to be generalized to genetically inaccessible organisms such as humans. “On the downside, humans will remain off limits, and it won't be possible to take multiple snapshots across time or to relate structure directly to function,” said Sporns.

“Obviously, we can’t make a transgenic person, that’s a challenge,” explained Zador. “That said, what we learn in a mouse we expect to be really relevant to a person. Our expectation is that there are going to be basic circuit motifs that we understand from looking at the mouse cortex that will generalize to the cortexes of other mammals.”

References

  1. Zador AM, Dubnau J, Oyibo HK, Zhan H, Cao G, et al. 2012. Sequencing the connectome. PLoS Biol 10(10): e1001411. doi:10.1371/journal.pbio.1001411