Category: Uncategorized

Gloria Choi joins the McGovern Institute

Anne Trafton |

We are pleased to announce the appointment of Gloria Choi as a new McGovern Investigator, starting in summer 2013. She will also be an assistant professor in the MIT Department of Brain and Cognitive Sciences. Choi’s research addresses the mechanisms by which the brain learns to recognize olfactory stimuli and to associate them with appropriate behavioral responses.

Much recent work has been devoted to the question of how the binding of odorant molecules to their receptors in the olfactory epithelium leads to the perception of odors. In other sensory modalities such as vision, touch or hearing, the primary sensory cortex shows a topographical organization in which stimulus features are systematically mapped on the cortical surface. In the piriform cortex, however, no such order has been found; while individual inputs to the cortex are tuned to specific odorants, their projections within the piriform cortex appears topographically random. Consistent with this, olfactory stimuli typically activate sparse ensembles of piriform cells, with no obvious spatial pattern. Yet somehow the brain must learn to recognize these apparently arbitrary spatial patterns of activity and to endow them with behavioral significance.

Choi uses the power of rodent molecular genetics to study how this happens. Using the optogenetic molecule Channelrhodopsin2, she has been able to activate sparse arbitrarily-chosen populations of neurons within the piriform cortex using direct light stimulation. She has shown that animals can learn to recognize and distinguish these artificial “smell-like” cues, which can be flexibly associated with either rewarding or aversive stimuli to drive the appropriate behavioral responses.

In her own lab at MIT, Choi plans to dissect the brain circuits underlying this behavior, to understand how sensory representations in piriform cortex can drive downstream targets to generate learned behavioral responses. She also plans to extend her approach to study social behavior, which in rodents is strongly affected by olfactory cues. One important modulator of social behavior is the hormone oxytocin, and Choi plans to study how oxytocin may control the mechanisms by which animals learn to attribute social significance to olfactory stimuli.

Olfactory learning also provides an opportunity to study more general questions about how the brain learns to categorize sensory stimuli and to associate them with complex rule-based behaviors. Such cognitive processes have been linked to the prefrontal cortex in humans and other species, and olfactory behavior in mice may offer a new and genetically tractable system for exploring these issues.

Choi received her bachelor’s degree from University of California, Berkeley, and her Ph.D. from Caltech, where she studied with David Anderson. She is currently a postdoctoral research scientist in the laboratory of Richard Axel at Columbia University.

Editing the genome with high precision

Anne Trafton |

Researchers at MIT, the Broad Institute and Rockefeller University have developed a new technique for precisely altering the genomes of living cells by adding or deleting genes. The researchers say the technology could offer an easy-to-use, less-expensive way to engineer organisms that produce biofuels; to design animal models to study human disease; and to develop new therapies, among other potential applications.

To create their new genome-editing technique, the researchers modified a set of bacterial proteins that normally defend against viral invaders. Using this system, scientists can alter several genome sites simultaneously and can achieve much greater control over where new genes are inserted, says Feng Zhang, an assistant professor of brain and cognitive sciences at MIT and leader of the research team.

“Anything that requires engineering of an organism to put in new genes or to modify what’s in the genome will be able to benefit from this,” says Zhang, who is a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research.

Zhang and his colleagues describe the new technique in the Jan. 3 online edition of Science. Lead authors of the paper are graduate students Le Cong and Ann Ran.

Early efforts

The first genetically altered mice were created in the 1980s by adding small pieces of DNA to mouse embryonic cells. This method is now widely used to create transgenic mice for the study of human disease, but, because it inserts DNA randomly in the genome, researchers can target the newly delivered genes to replace existing ones.

In recent years, scientists have sought more precise ways to edit the genome. One such method, known as homologous recombination, involves delivering a piece of DNA that includes the gene of interest flanked by sequences that match the genome region where the gene is to be inserted. However, this technique’s success rate is very low because the natural recombination process is rare in normal cells.

More recently, biologists discovered that they could improve the efficiency of this process by adding enzymes called nucleases, which can cut DNA. Zinc fingers are commonly used to deliver the nuclease to a specific location, but zinc finger arrays can target every possible sequence of DNA, limiting their usefulness. Furthermore, assembling the proteins is a labor-intensive and expensive process.

Complexes known as transcription activator-like effector nucleases (TALENs) can also cut the genome in specific locations, but these complexes can also be expensive and difficult to assemble.

Precise targeting

The new system is much more user-friendly, Zhang says. Making use of naturally occurring bacterial protein-RNA systems that recognize and snip viral DNA, the researchers can create DNA-editing complexes that include a nuclease called Cas9 bound to short RNA sequences. These sequences are designed to target specific locations in the genome; when they encounter a match, Cas9 cuts the DNA.

This approach can be used either to disrupt the function of a gene or to replace it with a new one. To replace the gene, the researchers must also add a DNA template for the new gene, which would be copied into the genome after the DNA is cut.

Each of the RNA segments can target a different sequence. “That’s the beauty of this. You can easily program a nuclease to target one or more positions in the genome,” Zhang says.

The method is also very precise — if there is a single base-pair difference between the RNA targeting sequence and the genome sequence, Cas9 is not activated. This is not the case for zinc fingers or TALENs. The new system also appears to be more efficient than TALEN, and much less expensive.

The new system “is a significant advancement in the field of genome editing and, in its first iteration, already appears comparable in efficiency to what zinc finger nucleases and TALENs have to offer,” says Aron Geurts, an associate professor of physiology at the Medical College of Wisconsin. “Deciphering the ever-increasing data emerging on genetic variation as it relates to human health and disease will require this type of scalable and precise genome editing in model systems.”

The research team has deposited the necessary genetic components with a nonprofit called Addgene, making the components widely available to other researchers who want to use the system. The researchers have also created a website with tips and tools for using this new technique.

Engineering new therapies

Among other possible applications, this system could be used to design new therapies for diseases such as Huntington’s disease, which appears to be caused by a single abnormal gene. Clinical trials that use zinc finger nucleases to disable genes are now under way, and the new technology could offer a more efficient alternative.

The system might also be useful for treating HIV by removing patients’ lymphocytes and mutating the CCR5 receptor, through which the virus enters cells. After being put back in the patient, such cells would resist infection.

This approach could also make it easier to study human disease by inducing specific mutations in human stem cells. “Using this genome editing system, you can very systematically put in individual mutations and differentiate the stem cells into neurons or cardiomyocytes and see how the mutations alter the biology of the cells,” Zhang says.

In the Science study, the researchers tested the system in cells grown in the lab, but they plan to apply the new technology to study brain function and diseases.

The research was funded by the National Institute of Mental Health; the W.M. Keck Foundation; the McKnight Foundation; the Bill & Melinda Gates Foundation; the Damon Runyon Cancer Research Foundation; the Searle Scholars Program; and philanthropic support from MIT alumni Mike Boylan and Bob Metcalfe, as well as the newscaster Jane Pauley.

Brain Scan Cover Image: Fall 2012

Anne Trafton |

Neurons in the brain of a transgenic mouse engineered to express a protein that emits light when neurons become active. Image: Qian Chen, Guoping Feng

Satra Ghosh: Social Engineer

Anne Trafton |

Satra Ghosh is a research scientist in John Gabrieli’s lab at the McGovern Institute for Brain Research at MIT. In this video, Satra talks about his research on mild traumatic brain injury in U.S. soldiers.

[Stock footage/music: U.S. Department of Defense, Satra Ghosh, shockwave-sound.com]

McGovern Institute Magic Mug

Anne Trafton |

Our researchers and staff are an amazing bunch of individuals. To thank them for their efforts this past year, we gave them “magic mugs” — they’re quite a hit.

Video Profile: Feng Zhang

Anne Trafton |

Feng Zhang, a member of the McGovern Institute for Brain Research at MIT, is designing new molecular tools for manipulating the living brain. As a student, he played a major role in the development of optogenetics, a technology by which the brain’s electrical activity can be controlled with light-sensitive proteins. He is now working to extend this molecular engineering approach to other aspects of brain function such as gene expression, and to develop new approaches to understanding and eventually treating brain diseases.

Precisely engineering 3-D brain tissues

Anne Trafton |

Borrowing from microfabrication techniques used in the semiconductor industry, MIT and Harvard Medical School (HMS) engineers have developed a simple and inexpensive way to create three-dimensional brain tissues in a lab dish.

The new technique yields tissue constructs that closely mimic the cellular composition of those in the living brain, allowing scientists to study how neurons form connections and to predict how cells from individual patients might respond to different drugs. The work also paves the way for developing bioengineered implants to replace damaged tissue for organ systems, according to the researchers.

“We think that by bringing this kind of control and manipulation into neurobiology, we can investigate many different directions,” says Utkan Demirci, an assistant professor in the Harvard-MIT Division of Health Sciences and Technology (HST).

Demirci and Ed Boyden, associate professor of biological engineering and brain and cognitive sciences at MIT’s Media Lab and McGovern Institute,  are senior authors of a paper describing the new technique, which appears in the Nov. 27 online edition of the journal Advanced Materials. The paper’s lead author is Umut Gurkan, a postdoc at HST, Harvard Medical School and Brigham and Women’s Hospital.

‘Unique challenges’

Although researchers have had some success growing artificial tissues such as liver or kidney, “the brain presents some unique challenges,” Boyden says. “One of the challenges is the incredible spatial heterogeneity. There are so many kinds of cells, and they have such intricate wiring.”

Brain tissue includes many types of neurons, including inhibitory and excitatory neurons, as well as supportive cells such as glial cells. All of these cells occur at specific ratios and in specific locations.

To mimic this architectural complexity in their engineered tissues, the researchers embedded a mixture of brain cells taken from the primary cortex of rats into sheets of hydrogel. They also included components of the extracellular matrix, which provides structural support and helps regulate cell behavior.

Those sheets were then stacked in layers, which can be sealed together using light to crosslink hydrogels. By covering layers of gels with plastic photomasks of varying shapes, the researchers could control how much of the gel was exposed to light, thus controlling the 3-D shape of the multilayer tissue construct.

This type of photolithography is also used to build integrated circuits onto semiconductors — a process that requires a photomask aligner machine, which costs tens of thousands of dollars. However, the team developed a much less expensive way to assemble tissues using masks made from sheets of plastic, similar to overhead transparencies, held in place with alignment pins.

The tissue cubes can be made with a precision of 10 microns, comparable to the size of a single cell body. At the other end of the spectrum, the researchers are aiming to create a cubic millimeter of brain tissue with 100,000 cells and 900 million connections.

The new system is the first that includes all of the necessary features for building useful 3-D tissues: It is inexpensive, precise, and allows complex patterns to be generated, says Metin Sitti, a professor of mechanical engineering at Carnegie Mellon University. “Many people could easily use this method for creating heterogeneous, complex gel structures,” says Sitti, who was not part of the research team.

Answering fundamental questions

Because the tissues include a diverse repertoire of brain cells, occurring in the same ratios as they do in natural brain tissue, they could be used to study how neurons form the connections that allow them to communicate with each other.

“In the short term, there’s a lot of fundamental questions you can answer about how cells interact with each other and respond to environmental cues,” Boyden says.

As a first step, the researchers used these tissue constructs to study how a neuron’s environment might constrain its growth. To do this, they placed single neurons in gel cubes of different sizes, then measured the cells’ neurites, long extensions that neurons use to communicate with other cells. It turns out that under these conditions, neurons get “claustrophobic,” Demirci says. “In small gels, they don’t necessarily send out as long neurites as they would in a five-times-larger gel.”

In the long term, the researchers hope to gain a better understanding of how to design tissue implants that could be used to replace damaged tissue in patients. Much research has been done in this area, but it has been difficult to figure out whether the new tissues are correctly wiring up with existing tissue and exchanging the right kinds of information.

Another long-term goal is using the tissues for personalized medicine. One day, doctors may be able to take cells from a patient with a neurological disorder and transform them into induced pluripotent stem cells, then induce these constructs to grow into neurons in a lab dish. By exposing these tissues to many possible drugs, “you might be able to figure out if a drug would benefit that person without having to spend years giving them lots of different drugs,” Boyden says.

Other authors of the paper are Yantao Fan, a visiting graduate student at HMS and HST; Feng Xu and Emel Sokullu Urkac, postdocs at HMS and HST; Gunes Parlakgul, a visiting medical student at HMS and HST; MIT graduate students Jacob Bernstein and Burcu Erkmen; and Wangli Xing, a professor at Tsinghua University.

The research was funded by the National Science Foundation, the Paul Allen Family Foundation, the New York Stem Cell Foundation, the National Institutes of Health, the Institute of Engineering and Technology A.F. Harvey Prize, and MIT Lincoln Laboratory.

Video Profile: John Gabrieli

Anne Trafton |

John Gabrieli, a member of the McGovern Institute for Brain Research, uses brain imaging and behavioral tests to understand the organization of memory, thought, and emotion in the human brain. [Stock footage: pond5, Elekta Instrument AB]

Read more about John Gabrieli here.