Industrial Electronics

High Resolution Electron Microscopy Has Mapped New Parts of the Fruit Fly Brain

03 November 2017

Researchers once thought that they had completely mapped the fruit fly brain. But thanks to high-resolution electron microscopy (EM), they have discovered a new region critical for memory and learning in the brain of the fruit fly, Drosophila melanogaster. This part of the brain is developed in the larval and adult life stages. These new findings have added some unexpected neural connections, or synapses to a seemingly solved circuit.

The results highlight the need for deeply detailed brain mapping and make a case for using high-resolution electron microscopy (EM) to do it, according to Albert Cardona. Cardona is a group leader and neurobiologist at Janelia. According to him, there is still a lot more for scientists to discover about the fly brain.

A reconstruction of neurons in the adult fly mushroom body — including Kenyon cells (yellow), mushroom body output neurons (purple) and dopaminergic neurons (green) — highlights unexpected connections. Source: Takemura et al./eLife 2017A reconstruction of neurons in the adult fly mushroom body — including Kenyon cells (yellow), mushroom body output neurons (purple) and dopaminergic neurons (green) — highlights unexpected connections. Source: Takemura et al./eLife 2017

"This region of the brain had been picked over for decades, and people had already described the major circuits," says Gerry Rubin, Janelia's executive director. "The models had everything all neat and tidy; these papers say, 'Well, not so quick.'"

Scientists have studied the neural underpinnings of fly learning and memory for more than 40 years and have mapped the brain region involved using light microscopy. This technique doesn’t capture the neural nitty-gritty in the same way that electron microscopy does, according to Rubin. EM is more time-intensive but can offer much more imaging detail.

Rubin compares the current state of EM in connectomics, the mapping of synapses in the brain, to the early days of human genome sequencing. Rubin, a pioneer of gene sequencing in Drosphilia during his tenure as an HHMI investigator at the University of California, Berkeley, recalls that some scientists initially shied away from sequencing. They cited the information and deep detail as a burden. Now a similar dispute permeates the connectomics field, is an electron microscopy worth the additional effort? Or can scientists continue to rely on light microscopy?

Now the teams say that EM should be included as a key aspect of understanding the fly brain.

Both teams are part of larger efforts to map the whole Drosophila nervous system. Cardona and collaborators are focusing on larvae and the FlyEM Project’s team in adult flies. The studies employed two different EM methods: transmission electron microscopy (TEM) in the larvae and focused-ion-beam scanning electron microscopy (FIB-SEM) in the adult and specialized software that helps make sense of the immense tangle of neurons. Both studies targeted the mushroom body, the area of the brain that is responsible for associative learning.

The mushroom body consists of multiple compartments, three of which make up the “alpha lobe” in the adult. FlyEM zeroed in on this region, mapping a total of 983 neurons. Cardona’s approach differed slightly. Neurons in the larva’s nervous system are smaller compared to the adult fly so he could trace the 300 neurons of the larval mushroom bodies.

To their surprise, FIB-SEM revealed three classes of never-before-seen synapses in the mushroom body, which were observed in the larva and adult fly. The synaptic connections were formed among three neuron types: Kenyon cells, dopaminergic neurons and output neurons.

The fact that these synapses were seen in young and full-grown flies implies that the connections are a critical part of the learning and memory circuit.

"When we saw them in the larva, we weren't sure if it was just a developmental artifact – if they would go away, like the neuron version of baby teeth," he says. Janelia's FlyEM team confirmed the neurons' existence in adults, and study coauthors, Yoshi Aso, Toshi Hige, and Glenn Turner, showed that the synapses contributed to the function of the mushroom body.

The teams are continuing to map the fly and larva nervous systems in full. FlyEM, with 10-fold more neurons to chart, is taking advantage of a boost from the software side — applying the latest machine vision and AI methods in collaboration with Google, as well as computer algorithms and software that were developed in-house at Janelia. Steve Plaza, who manages the FlyEM team, speculates that the 18 months it took to complete this study could have stretched to 10 years if the computational power had not streamlined their work.

"I'm really excited about the progress in this field," Rubin says. "If you would have asked me a year ago how long it would take to map the whole fly brain, I would have said, 'Thirty years, and I'd be lucky to see it.' Now, I'd say more like five years," he says. "I think the field is really about to take off."

A paper on this research was published in Nature.

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