Carlo Piere B.

Dayao THY2
2015-01335

3D Printing of Living Cells

Date: February 1, 2018
Source: University of Twente
University of Twente. "3D printing of living cells." ScienceDaily. ScienceDaily, 1 February 2018.
<www.sciencedaily.com/releases/2018/02/180201092233.htm>

Using a new technique they call 'in-air microfluidics', University of Twente scientists succeed in printing 3D
structures with living cells. This special technique enable the fast and 'in-flight' production of micro building blocks
that are viable and can be used for repairing damaged tissue, for example.
Microfluidics is all about manipulating tiny drops of fluid with sizes between a micrometer and a millimeter. Most
often, chips with tiny fluidic channels, reactors and other components are used for this: lab-on-a-chip systems.
Although these chips offer a broad range of possibilities, in producing emulsions for example -- droplets carrying
another substance -- the speed at which droplets leave the chip is typically in the microliter per minute range. For
clinical and industrial applications, this is not fast enough: filling a volume of a cubic centimeter would take about
1000 minutes or 17 hours. The technique that is presented now, does this in a couple of minutes.
Impact of jets
Can we reach these higher speeds by not manipulating the fluids in microchannels, but in the air instead? This was
one of the questions the researchers wanted to answer. And indeed it was possible, by using two 'jets' of fluid.
From one jet, droplets are shot at the other jet. Creating the jets is relatively simple, and they move 100 to 1000
times faster than droplets from a microchip. Speed is not the only advantage. By choosing jets containing different
types of fluids that react, the collision results in new materials. Smart combinations of fluids will result in solid and
printable building blocks in one single step.
Printing tissue
In this way, it is possible to capture a living cell inside printable material. The resulting bio building blocks are
printed in a 3D structure that looks like a sponge, filled with cells and fluid. These 3D modular biomaterials have
an internal structure that is quite similar to that of natural tissue. Many 3D printing techniques are based on using
heat or UV light: both would damage living cells. The new microfluidic approach is therefore a promising technique
in tissue engineering, in which damaged tissue is repaired by using cultured cell material of the patient.
The research has been done by Tom Kamperman of the Developmental BioEngineering group of Prof Marcel
Karperien, and by Claas Willem Visser of the Physics of Fluids group of Prof Detlef Lohse. Kamperman just
recently finished his PhD on this subject, Claas Willem Visser temporarily works as a scientist at Harvard University
on a Rubicon grant. He will return to the University of Twente afterwards and become an assistant professor. Both
scientists are involved in the new IamFluidics spinoff, in which in-air microfluidics is used to create functional
particles and materials.
Carlo Piere B. Dayao THY2
2015-01335

Gene Editing Shows Promise for Alleviating Hearing Loss

Date: December 20, 2017
Source: Denworth, L. (2017, December 20). Gene Editing Shows Promise for Alleviating Hearing Loss. Retrieved February 05,
2018, from https://www.scientificamerican.com/article/gene-editing-shows-promise-for-alleviating-hearing-loss/
When David Liu first heard about a strain of mouse from his colleague Zheng-Yi Chen, he got excited. The mice
carry a gene, TMC1, with a mutation that leads to deafness over time, giving them the name Beethoven mice.
Their mutation matches one in humans that produces the same effect. The mutation is dominant; if it is present,
hearing loss is certain.
Liu, a chemical biologist at the Broad Institute, works with the noted CRISPR-Cas9 technology, which targets
and changes precise stretches of DNA. In the Beethoven mouse, he saw an ideal testing ground for the new gene
editing technology, bringing hope that it might accomplish something new: improve hearing by disrupting a
single genetic mutation. Other forms of gene modification add copies of genes, but are ineffectual if a dominant
mutation remains.
In a paper published Dec. 20 in Nature, Liu, who is also a professor at Harvard University and an investigator of
the Howard Hughes Medical Institute, and Chen, a hearing biologist at Massachusetts Eye and Ear Infirmary and
professor of otolaryngology at Harvard, along with colleagues, report that the idea worked. The mice treated
showed improved hair cell survival and hearing thresholds, and were startled by loud noises while untreated mice
weren’t. “To our knowledge, this is the first time that genome editing has been used to correct hearing loss in an
animal model of human genetic deafness,” Liu says. “There is a lot of work to do to translate these results into
patients, but there is some proof of principle here.”
Until the advent of gene editing, geneticists could catalogue mutations without being able to do much about
them. “David Liu’s work is a wonderful development in a growing trend that after all these years of trying we
have been able to do something clinically meaningful about disease-causing or disease-predisposing changes in the
genome,” says Fyodor Urnov, associate director of the Altius Institute in Seattle, Washington and a pioneer in
gene editing who wrote a commentary that accompanies the study, but wasn’t involved in the research. “This
work is exciting because it provides the first but essential step in advancing an approach like this to the clinic for
this genetic condition.”
Hearing requires the conversion of acoustic energy into electrical signals. Sound waves travel through the ear and
wash over the hair cells of the inner ear, which bend under pressure and send an electrical impulse up the
auditory nerve to the brain.
Nearly half of all cases of deafness are due in some part to genetic factors, and many of those gene mutations
affect the functioning of hair cells. The most common cause of genetic hearing loss, accounting for 20 percent of
cases, is a recessive connexin 26 mutation on the GBJ2 gene. A recessive disease mutation requires a copy of the
mutation from both parents. By contrast, one parent can pass along a dominant disease mutation like the one in
the TMC1 gene, cause of 4 to 8 percent of cases of genetic hearing loss. TMC1 creates a defect in a protein that
helps convert sounds into electrical signals, while the healthy copy of the gene is simply ignored. For people with
the condition, hearing loss begins in childhood and deafness ensues within 10 to 15 years.
Gene editing and gene therapy are not the same thing. The latter involves the insertion of a good copy of a gene
to overcome a deficiency in the copy that a patient is born with. One such clinical trial has begun for hearing loss
that aims to regenerate hair cells in patients with acquired hearing loss by injecting a new gene. “It kickstarts
supporting cells into becoming hair cells again,” says Lawrence Lustig, chair of otolaryngology at Columbia
University Medical Center, one of three sites involved in the trial. But this approach doesn’t work for dominant
mutations like the TMC1 mutation, says Lustig. “You can’t just grow new hair cells because you have the same
bad genetic background that will kill those hair cells again.” (The Food and Drug Administration approved on
December 19 a gene therapy for a rare inherited form of blindness. The treatment may cost more than $1
million.)
A technology like CRISPR-Cas9 is different. “The gene editor goes into the nucleus, finds the gene of interest and
then asks are you normal or are you mutant? If it’s normal, it largely leaves it alone. But if it’s mutant, it cuts it
and knocks it out,” says Urnov.
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Liu and his colleagues targeted the mutant TMC1 gene copies by first binding the Cas9 protein to RNA guide
molecules that program Cas9 to find and disrupt the target gene. Then they injected those protein-RNA
complexes into the ears of newborn Beethoven mice. Exquisite precision was required because the two copies of
the gene—alleles—are so similar. “You can’t get closer than differing by a single base pair,” says Liu. To avoid
disrupting healthy alleles, the team used an innovative method of delivery into the cell. Instead of the usual virus
or DNA that programs the targeted cell to generate Cas9 and the guide RNA, they used a cationic lipid to
directly deliver the Cas9 protein and the guide RNA. Liu likened the lipid to “fancy, tiny soap bubbles.” This
method allows the editing agents to naturally disappear once their work is done, minimizing unintended damage
to normal copies of the TMC1 gene. The process was roughly 10 times more precise than the viral delivery
method, so that 20 copies of the faulty gene—rather than two—were disrupted for every normal copy that was
effected.
Although Liu speculates that the number of cells that were ultimately altered was a modest fraction of those in
the inner ear, the effect was surprisingly strong. The thresholds at which the mice could detect a sound improved
from 75 or 80 decibels (the noise level of a garbage disposal, say) to 60 decibels (normal conversation). The
scientists aren’t sure why this “halo effect” protected surrounding cells, but it is an encouraging finding for the
next step of experimenting with larger animal models such as nonhuman primates, whose anatomy is more like
ours. A little bit of gene editing, it seems, can go a long way.
Because CRISPR-Cas9 can be guided to any gene, rewriting DNA with gene editing is akin to rewriting software.
Other forms of deafness attributable to an errant copy of a single gene might also be ameliorated using the same
technique. Altogether such cases amount to about 20 percent of genetic deafness.
Lustig, who works with patients with hearing loss every day, says Liu’s results are “significant” and offer hope for
gene editing as a treatment. “It’s not around the corner,” he says, “but we’re on the pathway.”
Carlo Piere B. Dayao THY2
2015-01335

Deep Learning Sharpens Views of Cells and Genes

Date: January 04, 2018
Source: Maxmen, A. (2018, January 4). Deep Learning Sharpens Views of Cells and Genes. Retrieved February 05, 2018,
from https://www.scientificamerican.com/ article/deep-learning-sharpens-views-of-cells-and-genes/
Eyes are said to be the window to the soul—but researchers at Google see them as indicators of a person’s health.
The technology giant is using deep learning to predict a person’s blood pressure, age and smoking status by
analysing a photograph of their retina. Google’s computers glean clues from the arrangement of blood vessels—
and a preliminary study suggests that the machines can use this information to predict whether someone is at risk
of an impending heart attack.
The research relied on a convolutional neural network, a type of deep-learning algorithm that is transforming
how biologists analyse images. Scientists are using the approach to find mutations in genomes and predict
variations in the layout of single cells. Google’s approach, described in a preprint in August (R.
Poplin et al. Preprint at https://arxiv.org/abs/1708.09843; 2017), is part of a wave of new deep-learning
applications that are making image processing easier and more versatile—and could even identify overlooked
biological phenomena.
“It was unrealistic to apply machine learning to many areas of biology before,” says Philip Nelson, a director of
engineering at Google Research in Mountain View, California. “Now you can—but even more exciting,
machines can now see things that humans might not have seen before.”
Convolutional neural networks allow computers to process an image efficiently and holistically, without splitting
it into parts. The approach took off in the tech sector around 2012, enabled by advances in computer power and
storage; for example, Facebook uses this type of deep learning to identify faces in photo-graphs. But scientists
struggled to apply the networks to biology, in part because of cultural differences between fields. “Take a group
of smart biologists and put them in a room of smart computer scientists and they will talk two different languages
to each other, and have different mindsets,” says Daphne Koller, chief computing officer at Calico—a
biotechnology company in San Francisco, California, that is backed by Google’s parent, Alphabet.
Scientists also had to identify which types of study could be conducted using networks that must be trained with
huge sets of images before they can start making predictions. When Google wanted to use deep learning to find
mutations in genomes, its scientists had to convert strands of DNA letters into images that computers could
recognize. Then they trained their network on DNA snippets that had been aligned with a reference genome, and
whose mutations were known. The end result was DeepVariant, a tool released in December that can find small
variations in DNA sequences. In tests, DeepVariant performed at least as well as conventional tools.
Cell biologists at the Allen Institute for Cell Science in Seattle, Washington, are using convolutional neural
networks to convert flat, grey images of cells captured with light microscopes into 3D images in which some of a
cell’s organelles are labelled in colour. The approach eliminates the need to stain cells—a process that requires
more time and a sophisticated lab, and can damage the cell. Last month, the group published details of an
advanced technique that can predict the shape and location of even more cell parts using just a few pieces of
data—such as the cell’s outline (G. R. Johnson et al. Preprint at bioRxiv http://doi.org/chwv; 2017).
“What you’re seeing now is an unprecedented shift in how well machine learning can accomplish biological tasks
that have to do with imaging,” says Anne Carpenter, director of the Imaging Platform at the Broad Institute of
MIT and Harvard in Cambridge, Massachusetts. In 2015, her interdisciplinary team began to process cell images
using convolutional neural networks; now, Carpenter says, the networks process about 15% of image data at her
centre. She predicts that the approach will become the centre’s main mode of processing in a few years.
Others are most excited by the idea that analysing images with convolutional neural networks could inadvertently
reveal subtle biological phenomena, prompting biologists to ask questions they might not have considered before.
“The most interesting phrase in science isn’t ‘Eureka!’, but ‘That’s weird—what’s going on?’” Nelson says.
Such serendipitous discoveries could help to advance disease research, says Rick Horwitz, the Allen Institute’s
executive director. If deep learning can reveal subtle markers of cancer in an individual cell, he says, it could help
to improve how researchers classify tumour progression. That could in turn trigger new hypotheses about how
cancer spreads.
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Other machine-learning connoisseurs in biology have set their sights on new frontiers, now that convolutional
neural networks are taking flight for image processing. “Imaging is important, but so is chemistry and molecular
data,” says Alex Wolf, a computational biologist at the German Research Center for Environmental Health in
Neuherberg. Wolf hopes to tweak neural networks so that they can analyse gene expression. “I think there will
be a very big breakthrough in the next few years,” he says, “that allows biologists to apply neural networks much
more broadly.”