All posts by Callum Tyndall

Berkeley researchers discover new way to boost CRISPR-Cas9 efficiency

Scientists at the University of California, Berkeley, have developed a way to increase the efficiency of the increasingly popular CRISPR-Cas9.

CRISPR-Cas9 is a gene editing technique in which the combination of a nuclease and guide RNAs allow for the cutting of a genome at a target location, enabling genes to be knocked out from human cell lines in order to discover what those genes do.

Currently the efficiency with which it disables these genes can hugely vary but, thanks to new research, the process can now operate up to five times more efficiently.

A key component in figuring out the role of genes in the body or disease is finding out what happens when said gene is disabled. CRISPR-Cas9 accelerates the process but can sometimes require scientists to screen several variations in order to find one that works.

However, the new has found that by introducing short pieces of DNA that do not match any DNA sequences in the human genome, alongside the CRISPR-Cas9 protein, into the targeted cell, the efficiency of the process is massively boosted. Notably, this efficiency increase applies to all CRISPR-Cas9s, including those that initially failed to work entirely.

Image courtesy of Ian Slaymaker, Broad Institute.

Image courtesy of Ian Slaymaker, Broad Institute.

The function of these short DNA pieces, which are called oligonucleotides, is that they interfere with DNA repair mechanisms in the targeted cell; an operation that boosts the performance of CRISPR-Cas9s, even those performing poorly, by a range of 2.5 to 5 times.

“It turns out that if you do something really simple — just feed cells inexpensive synthetic oligonucleotides that have no homology anywhere in the human genome — the rates of editing go up as much as five times,” said lead researcher Jacob Corn, the scientific director of UC Berkeley’s Innovative Genomics Initiative and an assistant adjunct professor of molecular and cell biology.

Corn’s method relied on the suspicion that the unreliability of Cas9’s efficiency stemmed from the mechanism by which DNA is repaired, given that DNA repair mechanisms are different across cells.

The idea of the oligonucleotides came from the reasoning that the introduction of random DNA into the cell could potentially confuse the repair process and thus increase the rate of a successful knockout.

Image courtesy of Ian Slaymaker, Broad Institute.

Image courtesy of Ian Slaymaker, Broad Institute.

This increased efficiency is hugely important on two fronts.

The first is understanding the role of genes, as a better chance of knockout will aid with the success rate of study. This is particularly prevalent when looking at long-lived cell lines, such as HeLa cells, as such cell lines typically have more than the regular two copies of each gene.

Increased CRISPR efficiency makes it much more likely to successfully knock at out all the copies at once.

Perhaps more importantly, though, is that gene editing is crucial to the combating of currently incurable genetic conditions, allowing for the correction of hereditary mutations.

It is speculated that genes such as those that make people susceptible to infectious diseases like AIDS could be knocked out, though it remains to be seen whether the Berkeley team’s approach is usable in a therapeutic context.

Every Brain (Scan) You Take: Scientists delve into the mind of Sting

UC Santa Barbara neurologist Scott Grafton and neuroscientist Daniel Levitin, a cognitive psychologist at McGill University, have opened a window into the mind of Police frontman Sting, using imaging analysis techniques recently developed by Grafton to map the way Sting’s brain organizes music.

Levitin, who acted as lead author on the study, says that great musicianship stems from the ability to create and manipulate highly rich representations of a desired soundscape in one’s mind. Sting, who is notable for his eclectic approach to music, therefore represents an almost ideal candidate for the study.

In fact, however, the research came about because of the musician, not the scientists. After reading Levitin’s book, Your Brain on Music, Sting requested a tour of the neuroscientist’s McGill lab and, when asked during the tour, agreed to a brain scan.

Sting stretches before being scanned. Above: Sting performing in 2008. Image courtesy of Randy Miramontez / Shutterstock.com

Sting stretches before being scanned. Above: Sting performing in 2008. Image courtesy of Randy Miramontez / Shutterstock.com

“Sting was asked to do three things while in the fMRI scanner: create music in his mind, listen to selected pieces and imagine songs,” said Grafton, a professor in UCSB’s Department of Psychological & Brain Sciences.

“The goal was to take someone who knows how to do these tasks really well and then see if there are any patterns in the brain that reflect those capabilities.”

Both functional and structural scans of Sting’s brain were taken in a single session. These scans were then analysed using multivoxel pattern analysis, in which patterns that are predictive of task conditions are identified in fMRI BOLD signal data, and representational dissimilarity analysis, which  characterizes the representation in each brain region by a representational dissimilarity matrix.

The data from these analyses identified songs that Sting found similar and those he found different by monitoring the activation of different brain regions.

Sting looks at the scans of his brain. Inline images courtesy of Owen Egan / UCSB

Sting looks at the scans of his brain. Inline images courtesy of Owen Egan / UCSB

The scan highlighted several connections between pieces of music, such as Astor Piazolla’s “Libertango” and the Beatles’ “Girl” or Sting’s own “Moon over Bourbon Street” and Booker T and the MG’s “Green Onions”. Additionally, Sting’s imaging and listening patterns were found to be similar across songs, with the exception of “Mack the Knife”, in which Levitin played the Bobby Darin version yet Sting had imagined Kurt Weil’s original composition.

“At the heart of these methods is the ability to test if patterns of brain activity are more alike for two similar styles of music compared to different styles,” Grafton explained. “This approach has never before been considered in brain imaging experiments of music.”

According to Grafton, moving forward, this research shows an approach that could well offer similar insights into the minds of other gifted individuals in different fields and how they connect thoughts or sounds that may initially seem to lack any significant connection.

For example, similar scans could find how writers connect thoughts on character and plot or how painters’ brains respond to and correlate thoughts on the usage of colour, form and space.