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Photo Album: MRI Installation

Anne Trafton | July 30, 2013May 24, 2023

Photos: Justin Knight and Doreen Reuchsel

A crew delivers the new 3-tesla MRI scanner to the McGovern Institute on July 25 2013. Photo: Doreen Reuchsel

McGovern Institute gets new brain scanner

Anne Trafton | July 30, 2013May 24, 2023

After months of planning and construction, we are delighted to report that we have installed a new 3-tesla MRI scanner for human neuroimaging. The $2M scanner, a Siemens Magnetom Trio, was delivered to the Martinos Imaging Center on July 25, 2013.

The core of the scanner is a large electromagnet, weighing around 13 tons and containing superconducting coils that are chilled in liquid helium to within a few degrees of absolute zero. It is housed in a custom-built room, with a specially reinforced floor to support the scanner’s weight, and with some 5000 steel panels to shield the system from RF interference.

The acquisition of the new scanner was made possible by Bruce Dayton, Jeffrey and Nancy Halis, the Simons Foundation, and an anonymous donor. The scanner is expected to be fully operational by the fall, and will be used for a wide range of studies on brain function, in both children and adults.

Click here to view a photo album of the MRI installation.

Genome editing becomes more accurate

Anne Trafton | July 22, 2013June 17, 2024

Earlier this year, MIT researchers developed a way to easily and efficiently edit the genomes of living cells. Now, the researchers have discovered key factors that influence the accuracy of the system, an important step toward making it safer for potential use in humans, says Feng Zhang, leader of the research team.

With this technology, scientists can deliver or disrupt multiple genes at once, raising the possibility of treating human disease by targeting malfunctioning genes. To help with that process, Zhang’s team, led by graduate students Patrick Hsu and David Scott, has now created a computer model that can identify the best genetic sequences to target a given gene.

“Using this, you will be able to identify ways to target almost every gene. Within every gene, there are hundreds of locations that can be edited, and this will help researchers narrow down which ones are better than others,” says Zhang, an assistant professor of brain and cognitive sciences at MIT and senior author of a paper describing the new model, appearing in the July 21 online edition of Nature Biotechnology.

The genome-editing system, known as CRISPR, exploits a protein-RNA complex that bacteria use to defend themselves from infection. The complex includes short RNA sequences bound to an enzyme called Cas9, which slices DNA. These RNA 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.

This technique offers a much faster and more efficient way to create transgenic mice, which are often used to study human disease. Current methods for creating such mice require adding small pieces of DNA to mouse embryonic cells. However, the process is inefficient and time-consuming.

With CRISPR, many genes are edited at once, and the entire process can be done in three weeks, says Zhang, who is the W. M. Keck Career Development Professor in Biomedical Engineering at MIT and a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research. The system can also be used to create genetically modified cell lines for lab experiments much more efficiently.

Fine-tuning

Since Zhang and his colleagues first described the original system in January, more than 2,000 labs around the world have started using the system to generate their own genetically modified cell lines or animals. In the new paper, the researchers describe improvements in both the efficiency and accuracy of gene editing.

To modify genes using this system, an RNA “guide strand” complementary to a 20-base-pair sequence of targeted DNA is delivered to cells. After the RNA strand binds to the target DNA, it recruits the Cas9 enzyme, which snips the DNA in the correct location.

The researchers discovered they could minimize the chances of the Cas9-RNA complex accidentally cleaving the wrong site by making sure the target sequence is not too similar to other sequences found in the genome. They found that if an off-target sequence differs from the target sequence by three or fewer base pairs, the editing complex will likely also cleave that sequence, which could have deleterious effects for the cell.

The team’s new computer model can search any sequence within the mouse or human genome and identify 20-base-pair sequences within that region that have the least overlap with sequences elsewhere in the genome.

Another way to improve targeting specificity is by adjusting the dosage of the guide RNA, the researchers found. In general, decreasing the amount of RNA delivered minimizes damage to off-target sites but has a much smaller effect on cleavage of the target sequence. For each sequence, the “sweet spot” with the best balance of high on-target effects and low off-target effects can be calculated, Zhang says.

“The real value of this paper is that it does a very comprehensive and systematic analysis to understand the causes of off-target effects. That analysis suggests a lot of possible ways to eliminate or reduce off-target effects,” says Michael Terns, a professor of biochemistry and molecular biology at the University of Georgia who was not part of the research team.

Zhang and his colleagues also optimized the structure of the RNA guide needed for efficient activation of Cas9. In the January paper describing the original system, the researchers found that two separate RNA strands working together — one that binds to the target DNA and another that recruits Cas9 — produced better results than when those two strands were fused together before delivery. However, in experiments reported in the new paper, the researchers found that they could boost the efficiency of the fused RNA strand by making the strand longer. These longer RNA guide strands include a hairpin structure that may stabilize the molecules and help them interact with Cas9, Zhang says.

Zhang’s team is now working on further improving the specificity of the system, and plans to start generating cell lines and animals that could be used to study how the brain develops and builds neural circuits. By disrupting genes known to be involved in those processes, they can learn more about how they work and how they are impaired in neurological disease.

The research was funded by a National Institutes of Health Director’s Pioneer Award; an NIH Transformative R01 grant; the Keck, McKnight, Damon Runyan, Searle Scholars, Klingenstein and Simons foundations; Bob Metcalfe; and Jane Pauley.

Controlling genes with light

Anne Trafton | July 22, 2013May 24, 2023

Although human cells have an estimated 20,000 genes, only a fraction of those are turned on at any given time, depending on the cell’s needs — which can change by the minute or hour. To find out what those genes are doing, researchers need tools that can manipulate their status on similarly short timescales.

That is now possible, thanks to a new technology developed at MIT and the Broad Institute that can rapidly start or halt the expression of any gene of interest simply by shining light on the cells.

The work is based on a technique known as optogenetics, which uses proteins that change their function in response to light. In this case, the researchers adapted the light-sensitive proteins to either stimulate or suppress the expression of a specific target gene almost immediately after the light comes on.

“Cells have very dynamic gene expression happening on a fairly short timescale, but so far the methods that are used to perturb gene expression don’t even get close to those dynamics. To understand the functional impact of those gene-expression changes better, we have to be able to match the naturally occurring dynamics as closely as possible,” says Silvana Konermann, an MIT graduate student in brain and cognitive sciences.

The ability to precisely control the timing and duration of gene expression should make it much easier to figure out the roles of particular genes, especially those involved in learning and memory. The new system can also be used to study epigenetic modifications — chemical alterations of the proteins that surround DNA — which are also believed to play an important role in learning and memory.

Konermann and Mark Brigham, a graduate student at Harvard University, are the lead authors of a paper describing the technique in the July 22 online edition of Nature. The paper’s senior author is Feng Zhang, the W. M. Keck Career Development Professor in Biomedical Engineering at MIT and a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research.

Shining light on genes

The new system consists of several components that interact with each other to control the copying of DNA into messenger RNA (mRNA), which carries genetic instructions to the rest of the cell. The first is a DNA-binding protein known as a transcription activator-like effector (TALE). TALEs are modular proteins that can be strung together in a customized way to bind any DNA sequence.

Fused to the TALE protein is a light-sensitive protein called CRY2 that is naturally found in Arabidopsis thaliana, a small flowering plant. When light hits CRY2, it changes shape and binds to its natural partner protein, known as CIB1. To take advantage of this, the researchers engineered a form of CIB1 that is fused to another protein that can either activate or suppress gene copying.

After the genes for these components are delivered to a cell, the TALE protein finds its target DNA and wraps around it. When light shines on the cells, the CRY2 protein binds to CIB1, which is floating in the cell. CIB1 brings along a gene activator, which initiates transcription, or the copying of DNA into mRNA. Alternatively, CIB1 could carry a repressor, which shuts off the process.  A single pulse of light is enough to stimulate the protein binding and initiate DNA copying.

The researchers found that pulses of light delivered every minute or so are the most effective way to achieve continuous transcription for the desired period of time. Within 30 minutes of light delivery, the researchers detected an uptick in the amount of mRNA being produced from the target gene. Once the pulses stop, the mRNA starts to degrade within about 30 minutes.

In this study, the researchers tried targeting nearly 30 different genes, both in neurons grown in the lab and in living animals. Depending on the gene targeted and how much it is normally expressed, the researchers were able to boost transcription by a factor of two to 200.

   Epigenetic modifications  

An important element of gene-expression control is epigenetic modification. One major class of epigenetic effectors is chemical modification of the proteins, known as histones, that anchor chromosomal DNA and control access to the underlying genes. The researchers showed that they can also alter these epigenetic modifications by fusing TALE proteins with histone modifiers.

Epigenetic modifications are thought to play a key role in learning and forming memories, but this has not been very well explored because there are no good ways to disrupt the modifications, short of blocking histone modification of the entire genome. The new technique offers a much more precise way to interfere with modifications of individual genes.

“We want to allow people to prove the causal role of specific epigenetic modifications in the genome,” Zhang says.

So far, the researchers have demonstrated that some of the histone effector domains can be tethered to light-sensitive proteins; they are now trying to expand the types of histone modifiers they can incorporate into the system.

“It would be really useful to expand the number of epigenetic marks that we can control. At the moment we have a successful set of histone modifications, but there are a good deal more of them that we and others are going to want to be able to use this technology for,” Brigham says.

The research was funded by a Hubert Schoemaker Fellowship; a National Institutes of Health Transformative R01 Award; an NIH Director’s Pioneer Award; the Keck, McKnight, Vallee, Damon Runyon, Searle Scholars, Klingenstein and Simons foundations; and Bob Metcalfe and Jane Pauley.

Breaking habits before they start

Anne Trafton | June 27, 2013May 24, 2023

Our daily routines can become so ingrained that we perform them automatically, such as taking the same route to work every day. Some behaviors, such as smoking or biting your fingernails, become so habitual that we can’t stop even if we want to.

Although breaking habits can be hard, MIT neuroscientists have now shown that they can prevent them from taking root in the first place, in rats learning to run a maze to earn a reward. The researchers first demonstrated that activity in two distinct brain regions is necessary in order for habits to crystallize. Then, they were able to block habits from forming by interfering with activity in one of the brain regions — the infralimbic (IL) cortex, which is located in the prefrontal cortex.

The MIT researchers, led by Institute Professor Ann Graybiel, used a technique called optogenetics to block activity in the IL cortex. This allowed them to control cells of the IL cortex using light. When the cells were turned off during every maze training run, the rats still learned to run the maze correctly, but when the reward was made to taste bad, they stopped, showing that a habit had not formed. If it had, they would keep going back by habit.

“It’s usually so difficult to break a habit,” Graybiel says. “It’s also difficult to have a habit not form when you get a reward for what you’re doing. But with this manipulation, it’s absolutely easy. You just turn the light on, and bingo.”

Graybiel, a member of MIT’s McGovern Institute for Brain Research, is the senior author of a paper describing the findings in the June 27 issue of the journal Neuron. Kyle Smith, a former MIT postdoc who is now an assistant professor at Dartmouth College, is the paper’s lead author.

Patterns of habitual behavior 

Previous studies of how habits are formed and controlled have implicated the IL cortex as well as the striatum, a part of the brain related to addiction and repetitive behavioral problems, as well as normal functions such as decision-making, planning and response to reward. It is believed that the motor patterns needed to execute a habitual behavior are stored in the striatum and its circuits.

Recent studies from Graybiel’s lab have shown that disrupting activity in the IL cortex can block the expression of habits that have already been learned and stored in the striatum. Last year, Smith and Graybiel found that the IL cortex appears to decide which of two previously learned habits will be expressed.

“We have evidence that these two areas are important for habits, but they’re not connected at all, and no one has much of an idea of what the cells are doing as a habit is formed, as the habit is lost, and as a new habit takes over,” Smith says.

To investigate that, Smith recorded activity in cells of the IL cortex as rats learned to run a maze. He found activity patterns very similar to those that appear in the striatum during habit formation. Several years ago, Graybiel found that a distinctive “task-bracketing” pattern develops when habits are formed. This means that the cells are very active when the animal begins its run through the maze, are quiet during the run, and then fire up again when the task is finished.

This kind of pattern “chunks” habits into a large unit that the brain can simply turn on when the habitual behavior is triggered, without having to think about each individual action that goes into the habitual behavior.

The researchers found that this pattern took longer to appear in the IL cortex than in the striatum, and it was also less permanent. Unlike the pattern in the striatum, which remains stored even when a habit is broken, the IL cortex pattern appears and disappears as habits are formed and broken. This was the clue that the IL cortex, not the striatum, was tracking the development of the habit.

 Multiple layers of control   

The researchers’ ability to optogenetically block the formation of new habits suggests that the IL cortex not only exerts real-time control over habits and compulsions, but is also needed for habits to form in the first place.

“The previous idea was that the habits were stored in the sensorimotor system and this cortical area was just selecting the habit to be expressed. Now we think it’s a more fundamental contribution to habits, that the IL cortex is more actively making this happen,” Smith says.

This arrangement offers multiple layers of control over habitual behavior, which could be advantageous in reining in automatic behavior, Graybiel says. It is also possible that the IL cortex is contributing specific pieces of the habitual behavior, in addition to exerting control over whether it occurs, according to the researchers. They are now trying to determine whether the IL cortex and the striatum are communicating with and influencing each other, or simply acting in parallel.

The study suggests a new way to look for abnormal activity that might cause disorders of repetitive behavior, Smith says. Now that the researchers have identified the neural signature of a normal habit, they can look for signs of habitual behavior that is learned too quickly or becomes too rigid. Finding such a signature could allow scientists to develop new ways to treat disorders of repetitive behavior by using deep brain stimulation, which uses electronic impulses delivered by a pacemaker to suppress abnormal brain activity.

The research was funded by the National Institutes of Health, the Office of Naval Research, the Stanley H. and Sheila G. Sydney Fund and funding from R. Pourian and Julia Madadi.