McGovern Institute for Brain Research hosts Chinese delegation

On Thursday May 12, the McGovern Institute for Brain Research at MIT hosted a visiting delegation from China, headed by the Party Secretary of Guangdong Province, Hu Chunhua (Chinese: 胡春华 ) and also including the Mayor of Shenzhen, Xu Qin (Chinese: 许勤 ), the Chinese Ambassador to the US, Cui Tiankai (Chinese: 崔天凯 ) and the Consul-General to New York, Zhang Qiyue (Chinese: 章启月 ). The visitors met with McGovern Director Robert Desimone and faculty members H. Robert Horvitz and Guoping Feng, and listened to presentations on the McGovern Institute’s collaboration with neuroscience researchers at the Shenzhen Institute of Advanced Technology (SIAT). The director of SIAT, Fan Jianping (Chinese: 樊建平 ) also attended the meeting, and they discussed the potential for future collaborations and the commercial development of new therapeutics for brain disease in Guangdong.

Robert Desimone, the McGovern Director, said “It was an honor to have Party Secretary Hu Chunhua and his delegation visit the McGovern Institute. He expressed his sincere concern for the many people suffering from brain disease, ranging from autism to Alzheimer’s disease. We believe our collaborative projects in Guangdong Province offer real hope.” The delegation later toured the MIT Media Lab and met with MIT Provost Martin Schmidt.

MIT marks 100 years in Cambridge with “Crossing the Charles” competition

They arrived via water and over land, by raft and hydrofoil, on foot and in experimental vehicles. Some paddled. Some danced. Some walked alongside robots. In all, hundreds of members of the MIT community on Saturday celebrated the 100th anniversary of the Institute’s move from Boston into Cambridge, Massachusetts with a unique procession across the Charles River, fueled by humor and creativity.

The “Crossing the Charles” parade and competition, the centerpiece of MIT’s May 7 Moving Day celebrations, took place simultaneously in the water and on the bridge that carries Massachusetts Avenue over the river.

In the river, a festive flotilla of watercraft journeyed across, including an electric hydrofoil craft, a motorized swarm of kayaks, a bamboo raft, and a pedal-powered floating platform in the shape of the dome from MIT’s main building.

Simultaneously, a colorful parade of students, faculty, staff, and alumni — plus a robotic cheetah — marched across the bridge, some with large floats in tow. Neuroscientists transported an 8-foot-high brain model, made out of plywood and set on wheels; MIT Libraries staff carried a fabric “river on sticks,” adorned with books and a laptop; undergraduates guided a “StrandBeaver,” a massive kinetic sculpture; and MIT’s Casino Rueda salsa dancers, a student club, stopped to perform. Hundreds of alumni marched across at the end of the parade.

“The diversity of the MIT community was on full display,” said John Ochsendorf, professor of civil and environmental engineering and architecture, and a faculty co-chair of the event. “You saw it all, from the brain to the bamboo.”

At an award ceremony following the crossing, MIT President L. Rafael Reif said he wanted to “thank the city of Cambridge for their generosity for 100 years” and joked that the city resembled a tolerant host enduring the visit of a long-running house guest.

“We are glad you stayed,” responded Cambridge Mayor Denise Simmons, in remarks following Reif’s comments.

Simmons also called MIT “a blessing and not a burden” and, in the spirit of the day, noted how useful it was to “keep a sense of humor” intact. Nearby, a 30-foot-high replica of a stone megalith bobbed in the river while a mechanical goose sauntered across Memorial Drive.

A noodle raft, a cheetah, and Oliver Smoot, of course

Moving Day, and the parade across the Charles River, was created in homage to MIT’s ceremonial 1916 crossing of the river, when the Institute’s charter was transported across on a barge, the Bucentaur. The 2016 celebration continued into the evening, with a multimedia extravaganza in Killian Court, followed by dance parties around campus whose themes traced 100 years of music and culture.

Moving Day is part of the series of “MIT 2016” celebrations that have been ongoing this year, commemorating MIT’s first century in Cambridge and launching the Institute’s next century of engagement with the world. MIT was founded in 1861, in Boston, before relocating to the Kendall Square area of Cambridge.

The idea behind the river-crossing event was to “let people do whatever they want and express their technical creativity,” said Annette Hosoi, a professor of mechanical engineering, and the other faculty co-chair of the event. “And people responded — really the whole community.”

Indeed, the parade and competition consisted of 26 entries on the water and 28 groups crossing the bridge. The more conventional water entries included boats from the MIT varsity sailing team and star rower Veronica Toro ’16, an Olympic hopeful. There were also folding kayaks, a “noodle raft” lashed together from pool noodles and kickboards, and a jet-powered boat from MIT’s International Design Center.

“All the watercraft stayed afloat,” Ochsendorf noted approvingly.

(For the record: Participants wore lifejackets and safety personnel were on hand.)

Up on the bridge, members of MIT’s Emergency Medical Services drove an ambulance that is dedicated to the memory of MIT police officer Sean Collier, while experimental vehicles of all kinds dotted the parade. MIT students and alumni demonstrated an aluminum-powered car, cutting-edge wheelchair designs, and a bamboo bicycle, among other entries.

Meanwhile MIT’s robotic cheetah, which can run at over 13 miles per hour, strolled across at a leisurely pace.

The parade’s grand marshal was Oliver Smoot ’62, a familiar name in local lore. As multitudes of area runners and walkers have noticed, the sidewalk over the bridge is marked in increments of “Smoots” — after a 1958 MIT prank in which Smoot’s friends got him to lie down, repeatedly, until they had crossed the entire bridge. For the record, Smoot is 5 feet 7 inches tall, and the bridge is 364.4 Smoots long.

Before the parade, Smoot reenacted lying down on the bridge’s sidewalk but noted that it had been easier for him to do so as an undergraduate. “We were faster and lighter then,” he joked.

Awards gala

A panel of six members of the MIT administration serving as judges gave out four awards to the participants, after what MIT Provost Martin A. Schmidt termed “careful deliberation.”

Brain researchers from three different MIT institutes and departments won the soon-to-be-prestigious Da Vinci Award, given for “creativity and wonder,” for their supersized brain model. Students from Course 4.032 (Design Studio: Information and Visualization) took home the Bosworth Award for “beauty and elegant design,” for their large zooplankton-motif structure, “Time Spirit and the Masquerade of Power,” which also featured printed images from MIT’s campus and history.

Researchers from MIT’s Pappalardo Lab won the Tech Pioneer Award for the “most innovative” craft in the flotilla; they transformed an obstacle course for robots from Course 2.007 (Design and Manufacturing) into a floating vessel. And the MIT Libraries team won the Beaver Spirit Award for the entry best exemplifying school spirit.

The brain researchers’ team, led by Julie Pryor of the McGovern Institute for Brain Research, built their float over two months, with 50 people participating. The plywood vehicle, called “A Beautiful Mind,” consists of 22 coronal “slices” of the brain, based on the personal data of team member Rosa Lafer-Sousa, a researcher in the Department of Brain and Cognitive Sciences (BCS).

Ben Bartelle, also of BCS, personally cut the plywood slices at MIT’s hobby shop.

“We’re MRI people,” Bartelle told MIT News. “We see slices like that all the time.”

So what is it like to see a giant plywood replica of one’s brain, on wheels, crossing the bridge over the Charles River?

“It’s pretty special,” Lafer-Sousa acknowledged. “I couldn’t sleep last night. It felt a little like Christmas.”

Mens, manus, cor: A spectacle on Killian Court

As dusk later fell over the Institute, several thousand students, faculty, staff, and friends filed into MIT’s Killian Court to witness a spectacular pageant of singing, dancing, computer art, and the embodiment of the MIT spirit.

With an illuminated MIT dome serving as a beacon for anyone within eyeshot, the event began with a procession of students bearing oars, a symbol of the 1916 river-crossing, and a parade of drummers welcoming onlookers to the fête.

Over the next hour, characters representing the living spirits of MIT’s motto, “mens et manus” (“mind and hand”) — and the two individuals on the MIT seal — guided the audience through the story of MIT from its humble beginnings in Boston through the Institute’s move to Cambridge a century ago and into the present. “Mens,” representing the theoretical, scientific, humanistic elements of MIT life, and “Manus,” representing the practical applications of these disciplines, spatted over what they thought was the most important aspect of life at MIT: theory or practice.

The two took turns making their case, bringing out, for example, human-sized bobbleheads featuring some of the most noted MIT faculty and alumni from each “side” of the mind-or-hand debate and recounting successes over the previous century — from the 19th-century application of chemical engineering to the new science of home economics by Ellen Swallow Richards to the 2015 detection of gravitational waves led by MIT Professor Emeritus Rainer Weiss. Guided by a robot voiced by MIT alumnus and “Car Talk” host Ray Magliozzi, the duo eventually realized that only with both mind and hand working in unison — and with the addition of “cor,” or “heart” — could MIT have developed into the thriving institution it is today.

Appropriately for the day’s weather — which had a distinctly wintry feel, with chilly temperatures, a brisk wind, and some rain — the event’s finale featured an undulating umbrella dance, which led, finally, into an impressive fireworks display over the Charles River. When it was all over, a roar of applause and hooting filled Killian Court, as attendees grabbed their own umbrellas and made their way to various dance parties hosted across the Institute to cap the day’s festivities.

Oliver Smoot, who has retired to Southern California, noted that he, for one, wasn’t bothered by the elements. “It’s all been great,” he said. And his friend Peter Miller ’62, who rode with Smoot in the grand marshal’s car during the afternoon parade, explained how he had ignored the cold: “From the warmth of all the people waving, and watching, and jumping up and down.”

Maia Weinstock contributed to this story.

2016 McGovern Symposium: Surya Ganguli

May 9, 2016
Surya Ganguli, Stanford University
“A theory of neural dimensionality, dynamics and measurement”

2016 McGovern Symposium: Carl Petersen

May 9, 2016
Carl Petersen, Ecole Polytechnique Federale de Lausanne
“Neural circuits for goal-directed sensorimotor transformation”

Controlling RNA in living cells

MIT researchers have devised a new set of proteins that can be customized to bind arbitrary RNA sequences, making it possible to image RNA inside living cells, monitor what a particular RNA strand is doing, and even control RNA activity.

The new strategy is based on human RNA-binding proteins that normally help guide embryonic development. The research team adapted the proteins so that they can be easily targeted to desired RNA sequences.

“You could use these proteins to do measurements of RNA generation, for example, or of the translation of RNA to proteins,” says Edward Boyden, an associate professor of biological engineering and brain and cognitive sciences at the MIT Media Lab. “This could have broad utility throughout biology and bioengineering.”

Unlike previous efforts to control RNA with proteins, the new MIT system consists of modular components, which the researchers believe will make it easier to perform a wide variety of RNA manipulations.

“Modularity is one of the core design principles of engineering. If you can make things out of repeatable parts, you don’t have to agonize over the design. You simply build things out of predictable, linkable units,” says Boyden, who is also a member of MIT’s McGovern Institute for Brain Research.

Boyden is the senior author of a paper describing the new system in the Proceedings of the National Academy of Sciences. The paper’s lead authors are postdoc Katarzyna Adamala and grad student Daniel Martin-Alarcon.

Modular code

Living cells contain many types of RNA that perform different roles. One of the best known varieties is messenger RNA (mRNA), which is copied from DNA and carries protein-coding information to cell structures called ribosomes, where mRNA directs protein assembly in a process called translation. Monitoring mRNA could tell scientists a great deal about which genes are being expressed in a cell, and tweaking the translation of mRNA would allow them to alter gene expression without having to modify the cell’s DNA.

To achieve this, the MIT team set out to adapt naturally occurring proteins called Pumilio homology domains. These RNA-binding proteins include sequences of amino acids that bind to one of the ribonucleotide bases or “letters” that make up RNA sequences — adenine (A), thymine (T), uracil (U), and guanine (G).

In recent years, scientists have been working on developing these proteins for experimental use, but until now it was more of a trial-and-error process to create proteins that would bind to a particular RNA sequence.

“It was not a truly modular code,” Boyden says, referring to the protein’s amino acid sequences. “You still had to tweak it on a case-by-case basis. Whereas now, given an RNA sequence, you can specify on paper a protein to target it.”

To create their code, the researchers tested out many amino acid combinations and found a particular set of amino acids that will bind each of the four bases at any position in the target sequence. Using this system, which they call Pumby (for Pumilio-based assembly), the researchers effectively targeted RNA sequences varying in length from six to 18 bases.

“I think it’s a breakthrough technology that they’ve developed here,” says Robert Singer, a professor of anatomy and structural biology, cell biology, and neuroscience at Albert Einstein College of Medicine, who was not involved in the research. “Everything that’s been done to target RNA so far requires modifying the RNA you want to target by attaching a sequence that binds to a specific protein. With this technique you just design the protein alone, so there’s no need to modify the RNA, which means you could target any RNA in any cell.”

RNA manipulation

In experiments in human cells grown in a lab dish, the researchers showed that they could accurately label mRNA molecules and determine how frequently they are being translated. First, they designed two Pumby proteins that would bind to adjacent RNA sequences. Each protein is also attached to half of a green fluorescent protein (GFP) molecule. When both proteins find their target sequence, the GFP molecules join and become fluorescent — a signal to the researchers that the target RNA is present.

Furthermore, the team discovered that each time an mRNA molecule is translated, the GFP gets knocked off, and when translation is finished, another GFP binds to it, enhancing the overall fluorescent signal. This allows the researchers to calculate how often the mRNA is being read.

This system can also be used to stimulate translation of a target mRNA. To achieve that, the researchers attached a protein called a translation initiator to the Pumby protein. This allowed them to dramatically increase translation of an mRNA molecule that normally wouldn’t be read frequently.

“We can turn up the translation of arbitrary genes in the cell without having to modify the genome at all,” Martin-Alarcon says.

The researchers are now working toward using this system to label different mRNA molecules inside neurons, allowing them to test the idea that mRNAs for different genes are stored in different parts of the neuron, helping the cell to remain poised to perform functions such as storing new memories. “Until now it’s been very difficult to watch what’s happening with those mRNAs, or to control them,” Boyden says.

These RNA-binding proteins could also be used to build molecular assembly lines that would bring together enzymes needed to perform a series of reactions that produce a drug or another molecule of interest.