HHMI’s Rubin Coaxes Lessons from Fly Brains
Photo: Debbie Accame
Dr. Gerald Rubin is a fly guy. This includes the Urban Dictionary sense of “cool and awesome”—he is vice president of the Howard Hughes Medical Institute and executive director of HHMI’s Janelia Research Campus in northern Virginia and established enough to have playfully heckled NIH director Dr. Francis Collins when Collins misstated a fact during his introduction of Rubin’s Wednesday Afternoon Lecture on Jan. 30. He is also a passionate student of the fly connectome: a map of every neural circuit in the brain of Drosophila melanogaster.
“Everything that we learn in the fly, I deeply believe will also be true in humans,” said Rubin, who has studied fruit fly genetics since the 1970s.
He chose the fly as a model organism “because it is experimentally tractable, having a rather small brain of only 100,000 neurons…The small size allows for completeness. We can look at the whole brain, not just certain areas. We can define every cell type and make them genetically accessible.”
Rubin had passed on other model organisms, including the worm, whose “behavior was not interesting enough.”
Since starting at Janelia in 2003, Rubin, a molecular geneticist, has pursued fundamental knowledge about circuit neuroscience. The fly connectome allows scientists to “go in at any node and manipulate it—off and on—using sophisticated new tools,” including optogenetics.
“What we want are general principles,” he said—truths that will obtain as readily in the human brain as in the fly brain.
It turns out that flies, like humans, mice and other critters, are attracted to some smells and repelled by others. This reality can be experimentally manipulated, so that “olfactory learning” can be tracked at cell level.
A fly senses odor through its antennae, which report to the antenna lobe, then to what is known as the mushroom body (calyx); in a mouse, this scheme can be expressed as nose, to olfactory bulb, to piriform cortex.
The cells activated by odor even have a name—Kenyon cells (there was no word on whether cells excited by music are known as Oberlin cells).
“There are some 2,000 papers on olfactory learning in flies,” Rubin noted; it is a well-characterized phenomenon. Odor preference is mediated by dopamine signaling, which the HHMI team created tools to measure.
The Janelia scientists made some 7,000 transgenic animals that express genetic drivers to manipulate specific cell types and now have such tools for half the cell types in the fly brain. This includes 20 types of dopamine neurons.
Rubin showed short movies of flies moving from compartment to compartment within a dish as they responded to a pairing of light and dark with aversive and attractive stimuli, like Pavlov’s experiments with dogs.
“They learn very quickly, with short training,” Rubin noted.
To double-check whether their interpretation of neural pathway-to-behavior maps were accurate, the HHMI team used patch-clamping of specific neurons to directly measure the change in strength in the connections between specific neurons. It is such changes that store memories.
To further define the circuit boards of brain activity, the Janelia team also performs volume electron microscopy to examine synapses. Rubin said he is confident that the team is on the path to a full fly connectome by 2022.
“We had a friendly bake-off in methods,” Rubin explained, pitting a milling process with use of a diamond knife. So far, they have mapped 200,000 synapses.
“This is 100 times faster than we could do the job in 2010,” said Rubin. “It just needs to be 1,000 times faster.”
For perspective, he noted that the 156 bases that he mapped in his first published research paper in 1972 took him a year to accomplish. “In 2013, it took less than 10 nanoseconds.”
Just as in large-scale genomics, Rubin said, improvements by factors of 10 are what is required.
Photo: Credit Debbie Accame
He argued that the great pioneers of today’s industrial-scale research “are certainly not the PIs [principal investigators], but the people who do the real work”—the engineer from China who developed a high-pressure freezing technique that dramatically improved the resolution of stained fly brains, without the need for cutting; the folks who do focused ion beam milling combined with scanning electron microscopy; the guy who once worked at Janelia but has now moved to Google, whose algorithms are dramatically advancing the speed with which datasets are analyzed; the teams of proofreaders who confirm the experimental work (Janelia is ramping up to 50 of them).
“But still we need to know much more,” Rubin said, including information on transmitters, receptors and gap junctions that needs to be layered on top of what they can learn from the connectome.
Near the end of his talk, Rubin said his latest research interests—again, in flies—are the regulation of sleep and female-female aggression. Showing a brief clip of the 2004 film Mean Girls, Rubin said he told collaborator Dr. Yoshi Aso, “Yoshi, you’ve discovered the Mean Girl neuron!” To explain what he meant, Rubin then showed the audience a movie of female flies in a similar brawl induced by the optogenetic activation of a specific cell type in the fly brain.
“The brain is complicated,” concluded Rubin. “We think we have the tools to define circuits, but now we need to find out what they do…Is this enough? Can we understand from these datasets how the brain works?”
Perhaps the answer comes from the title of a 2002 film starring Mary-Kate and Ashley Olsen: Getting There.