Si Lab

Kausik Si, Ph.D.

Associate Scientific Director

Professor, Department of Molecular & Integrative Physiology
   The University of Kansas School of Medicine

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Kausik Si, Ph.D., joined the Stowers Institute as an assistant investigator in 2005, two years after he and Eric Kandel, M.D., stunned the research community with their discovery that a prion-like protein may be required for the formation of stable, long-term memories in the brain.

A neuron (shown in red) in the hippocampus, the brain's learning and memory center, expresses CPEB3, a protein with prion-like properties.

Image: Courtesy of Kausik Si.

Their findings attracted a great deal of attention because prions had earned a bad reputation for causing encephalopathies, brain disorders that include bovine spongiform encephalitis, better known as mad cow disease. Prions also have been implicated in Alzheimer's disease.

That anything resembling a prion could do something wholesome was "nothing less than extraordinary," Rockefeller University's Robert Darnell, M.D., Ph.D., wrote in a commentary that Cell published along with scientific papers about Si's and Kandel's highly innovative, groundbreaking research.  

In 1999, after being awarded the Ph.D. degree in molecular biology at Albert Einstein College of Medicine, Si joined Kandel's lab. Like his mentor, Si wanted to understand at the most basic level how memories are created in synapses, the junctions between neurons in the brain. "When I came to Eric's lab, he and other collaborators had just shown that local protein synthesis at a synapse was required for long-term facilitation," said Si, referring to biochemical changes that enable transient change in synaptic activity that become stable -- or "remembered" -- over time.

Kandel's research "suggested that those synapses must be marked to say 'I'm changed.' But what was the mark?" Si asked. While studying for his Ph.D. degree in the laboratory of Umadas Maitra, Ph.D., at Albert Einstein, Si investigated protein synthesis by cellular structures known as ribosomes. Because of his knowledge and expertise about protein synthesis, Si regarded it as feasible that messenger RNAs (mRNAs), molecules that convey genetic information from a cell's DNA to its ribosomes, would "wait" on standby at a synapse. He theorized that following neuronal stimulation, the waiting mRNAs would be rapidly translated to synthesize proteins constituting a "mark." By focusing on the waiting mRNAs, Si succeeded in identifying CPEB (Cytoplasmic Polyadenylation Element Binding) as the likely mark.

In 2003 Si and colleagues made two crucial observations from experiments with the sea slug Aplysia. The first observation was that neuronal forms of CPEB were up-regulated following excitatory stimulation, and injection of constructs that degraded CPEB in Aplysia's sensory neurons blocked the establishment of stable synaptic connections.

The second observation was that one arm of Aplysia CPEB resembled a prion and, when tested in yeast, acted like one too. That is, it morphed itself into a self-perpetuating aggregate. However, unlike the prions that characterize the brains of people with encephalopathies, the Aplysia CPEB wasn't toxic cellular "waste." Instead, it maintained the biochemical capacity to bind RNA.

Based on these and other findings, Si hypothesized that local activation of CPEB to a prion-like state at a stimulated synapse in some way facilitates long-term synaptic changes associated with memory storage.

While Si's early experiments were conducted with Aplysia, a model system for learning and memory, Si and collaborators also determined that CPEB was expressed in the memory epicenter, the hippocampus, of mice.

In a 2010 follow-up study with Aplysia, Si and his colleagues reported that synaptic activity stimulated by the neurotransmitter serotonin generated prion-like CPEB aggregates in the sea slug's nervous system. And, rather than poisoning a neuron like a prion would in a brain disease, the transformed protein stabilized activity-dependent synaptic changes.

Now an associate professor at the Stowers Institute, Si uses Drosophila, fruit flies, to test the hypothesis that CPEB is the protein mark required to form long-term memories. Prior to joining Stowers, he had not studied Drosophila. "People don't usually start a lab with a controversial topic and a new organism," he said. "But I had to test this idea either in mice or flies. I chose flies because it is faster and if I was wrong, I'd know sooner!"

In a study published in 2011, Si showed that a Drosophila version of CPEB called Orb2 binds a collection of mRNAs that facilitated synapse formation. These findings indicate that Drosophila Orb2 plays an important role in the persistence of memory. Upon stimulation, Orb2 forms amyloid-like oligomers, self-copying clusters, which are an essential ingredient for the formation of long-term memory. That team also found that disrupting Orb2 impaired the formation of long-term memory in flies.  Si's next goal is to determine whether, like Aplysia CPEB, activated Orb2 undergoes prion-like conformational changes that promote persistent expression of synaptic mRNAs favoring establishment of a "memory trace."

Born in a village in India, Si received his B.S. and M.S. degrees at the University of Calcutta. His scientific leanings were fostered by his father, a high school physics and math teacher, and his biochemistry professor Dhrubajyoti Chattopadhyay, Ph.D., now pro vice-chancellor of Calcutta University.

Si's scientific achievements and creativity have been acknowledged by a plethora of young investigator awards, including the March of Dimes Basil O'Connor Award, Klingenstein Fellowship, McKnight Fellowship, and Searle Scholar award.

But it all has not been rosy: almost three years into his career as an independent scientist at Stowers, Si lost all the flies he had engineered for his studies due to an incubator breakdown. "It took a year to get back to a functional state," Si said. "We had to go back and repeat all our experiments."

Despite the setback, Si remained determined to conduct the research required to confirm or dispute CPEB as the synaptic mark required for the maintenance of long-term memories. "An extraordinary theory demands extraordinary proof," he said. "We are still far from obtaining definitive evidence, but I cannot think of working on something else -- this idea is definitely worth pursuing."