Si Lab

Kausik Si, Ph.D.

Associate Investigator

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

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Stowers assistant investigator Kausik Si, Ph.D., admits he’s had some “crazy ideas”.  Si, a neurobiologist, uses fruit flies to study the biochemical basis of long-term memory. That is not the “crazy idea”: memory is based on a series of biochemical events that induce changes in the connection points or synapses between neurons and the fruit fly is a perfectly good system to model that in.


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 Dr. Kausik Si.

What’s “crazy” is the kind of biochemical change that has pre-occupied Si since he was a postdoc at Columbia University with Nobel laureate Eric Kandel. There, in 2003 in back-to-back Cell papers Si reported that a protein required for the formation of stable, long-term memory resembled the dreaded prion particle.

Real prions—their name a creepy combo of “protein” and “infection”—are infectious protein particles that when ingested cause encephalopathies. They became famous when bovine spongiform encephalitis, better known as mad cow disease, swept Europe in the 1990s. That anything resembling a prion could do something wholesome was, in the words of Rockefeller’s Robert Darnell, who wrote a commentary accompanying the papers, “nothing less than extraordinary.”

In part, serendipity facilitated the discovery. “When I came to Eric’s lab he had just shown that local protein synthesis at a synapse was required for long-term facilitation,” says Si, referring to biochemical changes that enable transient synaptic contacts to become stable—or “remembered”—over time. “That idea suggested that those synapses must be marked to say ‘I’m changed.’ But what was the mark?”

For his Ph.D. degree, which he earned in 1999, Si had studied ribosome biosynthesis and translational initiation with Umadas Maitra at Albert Einstein, so he knew something about protein synthesis. It seemed perfectly feasible to him that mRNAs “waiting” at a synapse might be rapidly translated following neuronal stimulation to synthesize proteins constituting a “mark”.

Si and colleagues also reported in 2003 in PNAS that an mRNA-binding protein that regulates translation called CPEB—for cytoplasmic polyadenylation element binding protein—was expressed in mouse brain in the memory epicenter, the hippocampus.

The 2003 Cell papers linked two observations. They first employed the mollusc Aplysia—a model system for learning and memory pioneered by Kandel and his colleagues—and showed that neuronal forms of CPEB were upregulated following excitatory stimulation. It also reported that injection of constructs that degraded CPEB in the mollusc’s sensory neurons blocked the establishment of stable synaptic connections.

The second showed that one arm of Aplysia CPEB resembled a prion and, when tested in yeast, acted like one, too—namely, it morphed itself into a self-perpetuating aggregate that wasn’t just toxic cellular  “waste” but maintained the biochemical capacity to bind RNA.

The conclusion? 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.

Arriving at Stowers in 2005, Si’s goal has been to test that hypothesis in the fruit fly Drosophila, a system new to him at the time. “People don’t usually start a lab with a controversial topic and a new organism,” he says. “But I had to test this idea either in mice or flies—which poison was I going to take? I chose flies because if I was wrong, I’d know sooner!”

In a 2010 follow-up in Aplysia published in Cell, Si showed that synaptic activity stimulated by the neurotransmitter serotonin generates prion-like CPEB aggregates in the mollusc’s nervous system—not just in yeast—and, rather than poisoning a neuron like a real prion would, the transformed protein stabilizes activity-dependent synaptic changes.

And in a 2011 PNAS study, Si showed that a Drosophila version of CPEB called Orb2 binds a collection mRNAs that facilitate synapse formation. His next goal is to determine whether, like Aplysia CPEB, activated Orb2 undergoes prion-like conformational changesthat promote persistent expression of synaptic mRNAs favoring establishment of a “memory trace.”

Born in a village near Calcutta, India, Si received his bachelors and masters degrees in 1993 at the University of Calcutta. His scientific leanings were fostered by his father, a high school physics and math teacher, and biochemistry professor Dhrubajyoti Chattopadhyay, now pro vice-chancellor of Calcutta University, who Si credits with steering him away from the more “acceptable” career path for budding Indian scientists at the time: chemical engineering.

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

But it all has not been rosy: almost three years into his independent career, an incubator break down knocked out the cooling system, killing all the flies Si had engineered for his studies. “It took a year to get back to a functional state,” Si says. “We had to go back and repeat all our experiments.”

Having recovered from that disaster, Si is as determined as ever to track down his synaptic “mark”. “An extraordinary claim demands extraordinary proof,” he says. “We are still far from obtaining definitive evidence, but I cannot think of working on something else—this idea is definitely worth pursuing.”