#Erasing a genetic mutation Using a new gene-editing system based on bacterial proteins MIT researchers have cured mice of a rare liver disorder caused by a single genetic mutation.
The findings described in the March 30 issue of Nature Biotechnology offer the first evidence that this gene-editing technique known as CRISPR can reverse disease symptoms in living animals.
CRISPR which offers an easy way to snip out mutated DNA and replace it with the correct sequence holds potential for treating many genetic disorders according to the research team.
What s exciting about this approach is that we can actually correct a defective gene in a living adult animal says Daniel Anderson the Samuel A. Goldblith Associate professor of Chemical engineering at MIT a member of the Koch Institute for Integrative Cancer Research
and the senior author of the paper. The recently developed CRISPR system relies on cellular machinery that bacteria use to defend themselves from viral infection.
Researchers have copied this cellular system to create gene-editing complexes that include a DNA-cutting enzyme called Cas9 bound to a short RNA guide strand that is programmed to bind to a specific genome sequence telling Cas9 where to make its cut.
At the same time the researchers also deliver a DNA template strand. When the cell repairs the damage produced by Cas9 it copies from the template introducing new genetic material into the genome.
Scientists envision that this kind of genome editing could one day help treat diseases such as hemophilia Huntington s disease
and others that are caused by single mutations. Scientists have developed other gene-editing systems based on DNA-slicing enzymes also known as nucleases
but those complexes can be expensive and difficult to assemble. The CRISPR system is very easy to configure
and customize says Anderson who is also a member of MIT s Institute for Medical Engineering and Science.
He adds that other systems can potentially be used in a similar way to the CRISPR system but with those it is much harder to make a nuclease that s specific to your target of interest.
Disease correctionfor this study the researchers designed three GUIDE RNA strands that target different DNA sequences near the mutation that causes type I tyrosinemia in a gene that codes for an enzyme called FAH.
Patients with this disease which affects about 1 in 100000 people cannot break down the amino acid tyrosine
which accumulates and can lead to liver failure. Current treatments include a low-protein diet and a drug called NTCB
which disrupts tyrosine production. In experiments with adult mice carrying the mutated form of the FAH enzyme the researchers delivered RNA guide strands
along with the gene for Cas9 and a 199-nucleotide DNA template that includes the correct sequence of the mutated FAH gene.
Using this approach the correct gene was inserted in about one of every 250 hepatocytes the cells that make up most of the liver.
Over the next 30 days those healthy cells began to proliferate and replace diseased liver cells eventually accounting for about one-third of all hepatocytes.
This was enough to cure the disease allowing the mice to survive after being taken off the NCTB drug.
We can do a onetime treatment and totally reverse the condition says Hao Yin a postdoc at the Koch Institute
and one of the lead authors of the Nature Biotechnology paper. This work shows that CRISPR can be used successfully in adults
and also identifies several of the challenges that will need to be addressed moving forward to the development of human therapies says Charles Gersbach an assistant professor of biomedical engineering at Duke university who was not part of the research team.
In particular the authors note that the efficiency of gene editing will need to improve significantly to be relevant for most diseases
and other delivery methods need to be explored to extend the approach to humans. Nevertheless this work is an exciting first step to using modern gene-editing tools to correct the devastating genetic diseases for
which there are currently no options for affected patients. To deliver the CRISPR components the researchers employed a technique known as high-pressure injection
which uses a high-powered syringe to rapidly discharge the material into a vein. This approach delivers material successfully to liver cells
but Anderson envisions that better delivery approaches are possible. His lab is now working on methods that may be safer
and more efficient including targeted nanoparticles. Wen Xue a senior postdoc at the Koch Institute is also a lead author of the paper.
Other authors are Institute Professor Phillip Sharp; Tyler Jacks director of the Koch Institute; postdoc Sidi Chen;
senior postdoc Roman Bogorad; Eric Benedetti and Markus Grompe of the Oregon Stem Cell Center;
The research was funded by the National Cancer Institute the National institutes of health and the Marie D. and Pierre Casimir-Lambert Fund u
This new approach could ultimately lead to advances in solar photovoltaics, detectors for telescopes and microscopes,
and privacy filters for display screens. The work is described in a paper appearing this week in the journal Science,
written by MIT graduate student Yichen Shen, professor of physics Marin Soljacic, and four others. e are excited about this,
Soljacic says, ecause it is a very fundamental building block in our ability to control light.
The new structure consists of a stack of ultrathin layers of two alternating materials where the thickness of each layer is controlled precisely. hen you have two materials
Previous work had demonstrated ways of selectively reflecting light except for one precise angle, but those approaches were limited to a narrow range of colors of light.
his could have great applications in energy, and especially in solar thermophotovoltaicsharnessing solar energy by using it to heat a material,
That light emission can then be harnessed using a photovoltaic cell tuned to make maximum use of that color of light.
But for this approach to work it is essential to limit the heat and light lost to reflections,
The filtering could also be applied to display screens on phones or computers so only those viewing from directly in front could see them.
John Pendry, a professor at Imperial College London who was connected not to this research, calls this an ngenious application. n a macroscopic scale this is equivalent to observing the world through a set of louvers that allow light to enter from one direction only,
associate professor of mathematics Steven Johnson; John Joannopoulos, the Francis Wright Davis Professor of Physics; and Dexin Ye of Zhejiang University in China.
The work was supported in part by the Army Research Office, through MIT Institute for Soldier Nanotechnologies,
and the U s. Department of energy, through the MIT S3tec Energy Research Frontier Center r
#Seeking a parts list for the retina New technique classifies retinal neurons into 15 categories,
including some previously unknown types. As we scan a scene, many types of neurons in our retinas interact to analyze different aspects of what we see
and form a cohesive image. Each type is specialized to respond to a particular variety of visual input for example, light or darkness, the edges of an object,
Using a computer algorithm that traces the shapes of neurons and groups them based on structural similarity,
the researchers sorted more than 350 mouse retinal neurons into 15 types, including six that were unidentified previously.
Sebastian Seung, a former MIT professor of brain and cognitive sciences and physics who is now at Princeton university,
When light strikes the retina, it first encounters photoreceptor cells, which relay visual input through several layers of neurons in the retina.
Using a computer algorithm, they traced along the many branches, known as dendrites, that extend from each cell to connect with other cells.
These dendrites form clusters called arbors which were the key to the researchersclassification system. After each neuron arbor was diagrammed,
the researchers used a computer program to align and condense each one so that the arbors were represented by smaller,
but still distinctive, shapes. By comparing these shapes, the computer program correctly classified all of the known neurons.
Among the randomly selected neurons, some ended up being grouped with the known types, while others formed six new clusters yet to be identified.
This approach is an important contribution to efforts to create a arts listfor the retina,
says Constance Cepko, a professor of genetics at Harvard Medical school. Previous efforts have focused on analyzing only a small number of cell types at a time,
who was involved not in this research. hat nice here is that this is a comprehensive approach to try to get a good amount of data on many different cells.
The researchers believe there may be still more types of neurons that did not appear in their data set
In future work, they hope to examine larger sets of neurons in hopes of finding some of these other neuron types.
The research was funded by the Harvard Neurodiscovery Center, the Howard hughes medical institute, the Gatsby Charitable Foundation, and the Human Frontier Science Program
#Engineers design living materials Inspired by natural materials such as bone a matrix of minerals and other substances including living cells MIT engineers have coaxed bacterial cells to produce biofilms that can incorporate nonliving materials such as gold nanoparticles and quantum dots.
These living materials combine the advantages of live cells which respond to their environment produce complex biological molecules
and span multiple length scales with the benefits of nonliving materials which add functions such as conducting electricity or emitting light.
The new materials represent a simple demonstration of the power of this approach which could one day be used to design more complex devices such as solar cells self-healing materials
or diagnostic sensors says Timothy Lu an assistant professor of electrical engineering and biological engineering. Lu is the senior author of a paper describing the living functional materials in the March 23 issue of Nature Materials.
Our idea is to put the living and the nonliving worlds together to make hybrid materials that have living cells in them
The paper s lead author is Allen Chen an MIT-Harvard MD-Phd student. Other authors are postdocs Zhengtao Deng Amanda Billings Urartu Seker and Bijan Zakeri;
and graduate student Robert Citorik. Self-assembling materialslu and his colleagues chose to work with the bacterium E coli
because it naturally produces biofilms that contain so-called curli fibers amyloid proteins that help E coli attach to surfaces.
Each curli fiber is made from a repeating chain of identical protein subunits called Csga which can be modified by adding protein fragments called peptides.
These peptides can capture nonliving materials such as gold nanoparticles incorporating them into the biofilms. By programming cells to produce different types of curli fibers under certain conditions the researchers were able to control the biofilms properties
and create gold nanowires conducting biofilms and films studded with quantum dots or tiny crystals that exhibit quantum mechanical properties.
They also engineered the cells so they could communicate with each other and change the composition of the biofilm over time.
First the MIT team disabled the bacterial cells natural ability to produce Csga then replaced it with an engineered genetic circuit that produces Csga
but only under certain conditions specifically when a molecule called AHL is present. This puts control of curli fiber production in the hands of the researchers who can adjust the amount of AHL in the cells environment.
When AHL is present the cells secrete Csga which forms curli fibers that coalesce into a biofilm coating the surface where the bacteria are growing.
The researchers then engineered E coli cells to produce Csga tagged with peptides composed of clusters of the amino acid histidine
The two types of engineered cells can be grown together in a colony allowing researchers to control the material composition of the biofilm by varying the amounts of AHL and atc in the environment.
If both are present the film will contain a mix of tagged and untagged fibers.
If gold nanoparticles are added to the environment the histidine tags will grab onto them creating rows of gold nanowires and a network that conducts electricity.
Cells that talk to each other The researchers also demonstrated that the cells can coordinate with each other to control the composition of the biofilm.
To add quantum dots to the curli fibers the researchers engineered cells that produce curli fibers
along with a different peptide tag called Spytag which binds to quantum dots that are coated with Spycatcher a protein that is Spytag s partner.
along with the bacteria that produce histidine-tagged fibers resulting in a material that contains both quantum dots and gold nanoparticles.
These hybrid materials could be worth exploring for use in energy applications such as batteries and solar cells Lu says.
The researchers are interested also in coating the biofilms with enzymes that catalyze the breakdown of cellulose
which could be useful for converting agricultural waste to biofuels. Other potential applications include diagnostic devices and scaffolds for tissue engineering.
I think this is really fantastic work that represents a great integration of synthetic biology and materials engineering says Lingchong You an associate professor of biomedical engineering at Duke university who was not part of the research team.
The research was funded by the Office of Naval Research the Army Research Office the National Science Foundation the Hertz Foundation the Department of defense the National institutes of health and the Presidential Early Career Award for Scientists and Engineers s
#Brighter future for bacteria detection Ever wonder why fruits and vegetables sometimes hit the shelves contaminated by pathogenic bacteria such as listeria, E coli, and salmonella?
According to Tim Lu, an assistant professor of electrical engineering and biological engineering at MIT, it boils down to the inefficient bacteria-detection assays used in the food industry.
In some cases, these aren accurate or speedy enough sometimes taking several days to catch contaminated produce.
Based on Lu graduate school research at MIT, the assay uses biological particles called bacteriophages, or phages,
wait for the phages to do their work, and run the sample through a machine that detects any light emitted.
Results can be plugged into the company software, which tracks contaminated products and can provide analytics on
The aim is to mitigate the millions of illnesses caused each year by contaminated food in the United states,
along with costly recalls for food producers. But the assay simplicity should also promote better sanitation practices
or polymerase chain reactions (PCR, which copies DNA) may be efficient in one area, but lacking in the other two.
injected by the phage into the pathogen, to cause the bacteria to shine very brightly,
making it, according to Sample6, the world first nrichment-free pathogen diagnostic system. For instance if one strain of a pathogen needs identification, roducers usually grow the bacteria out to large numbers before they can detect it,
Lu says. his is slow, and obviously not ideal for the food industry. All these improvements contribute to the assay speed,
Lu says. asically, wee producing enough signal to detect a few specific cells quickly, which gets you really rapid sensors,
he says. A diagnostic pivot The assay is used today strictly for detection of bacteria. But it started as a potential therapeutic,
when Lu was an MD/Phd student in the MIT-Harvard Health Sciences and Technology program in the mid-2000s.
In a lab at Boston University Lu engineered phages that could break apart antibiotic-resistant biofilms coatings where bacteria live
and thrive by injecting bacteria with certain enzymes to make the biofilms self-destruct. This discovery would earn Lu the $30, 000 Lemelson-MIT Student Prize, in 2008,
and a spot on Technology Review 2010 list of top innovators under 35. Seeing phages as better antimicrobial treatments than antibiotics to which biofilms and bacteria can build immunity Lu, Sample6 cofounder and now vice president of operations Michael Koeris,
and other colleagues bootstrapped to commercialize the technology. They funded their company, then called Novophage
through university business-plan competitions across the country, and outfitted nearly an entire lab with reused equipment from MIT and auctions.
Faced with the financial crisis and challenges in commercializing therapeutics, they pivoted to diagnostics. They shopped their phages to bacteria-plagued industries such as oil and water treatment,
where biofilms build up in pipelines before seeing firsthand that the food industry as in desperate need of new detection technologies.
Most food manufacturers were still using traditional assays, Lu says, with some still using pen and paper or spreadsheets to track contamination hich makes it nearly impossible to gather large amounts of data,
he says. In an incubator at the University of Massachusetts at Boston, the renamed Sample6 tailored the product for the food industry before relocating to its current headquarters in Boston Seaport District,
where a 15-person team now works on research and development and small-scale manufacturing. After leading the startup through technological implementation,
Lu took a position in 2012 on its board, where he continues advising. ourcing from naturetoday,
Sample6 assay detects listeria and is used solely by the food industry. But it a platform technology, Lu says,
that can be used to detect other pathogenic bacteria, such as E coli and salmonella, and for other means across other industries. hages are the most abundant biological particle On earth.
Since they have coevolved with bacteria for eons, nature provides a rich database of phages
which target desired bacteria. Thus, by sourcing from nature, we can adapt the platform to other pathogens and applications,
he says. The phages could be modified, for instance, to break apart the biofilms that build up and corrode oil pipelines,
or to detect the pathogenic bacteria that sometimes cause oil to sour by changing its composition.
The next practical application however, is most likely in health care, with the potential for clinical diagnostics or rapid detection of contamination in hospital rooms with the aim of decreasing the 1. 7 million cases of hospital-associated infections recorded in the United states each year.
With the assay, Lu says Sample6 hopes to bring synthetic biology, and specifically phages, to microbial detection across many fields.
Further down the road, he says, a goal is to transform diagnostics into something more accessible to the public perhaps even leading to at home diagnostics. undamentally,
I see this assay as an enabler for many more applications. We want ultimately to democratize the use of synthetic biology in the real world
he says i
#Fast synthesis could boost drug development Small protein fragments, also called peptides, are promising as drugs
an assistant professor of chemistry and leader of the research team. eptides are ubiquitous. Theye used in therapeutics,
theye found in hydrogels, and theye used to control drug delivery. Theye also used as biological probes to image cancer and to study processes inside cells,
Pentelute says. ecause you can get these really fast now, you can start to do things you couldn do before.
a graduate student in Pentelute lab. Other authors include Klavs Jensen, head of MIT Department of Chemical engineering,
Accelerated manufacturing Therapeutic peptides usually consist of a chain of 30 to 40 amino acids, the building blocks of proteins.
Many universities, including MIT, have facilities to manufacture these peptides, but the process usually takes two to six weeks,
an associate professor of chemistry at the Scripps Research Institute who was not part of the research team. hat
and rapidly test new peptides to treat cancer and other diseases, as well as more effective variants of existing peptides, such as insulin, Pentelute says.
they created an antibody mimic that has 130 amino acids, as well as a 113-amino-acid enzyme produced by bacteria.
Chemistry graduate students Surin Mong and Alexander Vinogradov are lead authors of that paper along with Simon. The researchers have patented the technology,
Pentelute envisions that the technology could have an impact on synthetic biology comparable to rapid synthesis of short strands of DNA and RNA.
Lai Fellowship, an Astrazeneca Distinguished Graduate student Fellowship, the National Institute of General Medical sciences, and the National institutes of health M
Now, a team of MIT researchers wants to make plants even more useful by augmenting them with nanomaterials that could enhance their energy production
and give them completely new functions, such as monitoring environmental pollutants. In a new Nature Materials paper, the researchers report boosting plantsability to capture light energy by 30 percent by embedding carbon nanotubes in the chloroplast,
the plant organelle where photosynthesis takes place. Using another type of carbon nanotube, they also modified plants to detect the gas nitric oxide.
Together these represent the first steps in launching a scientific field the researchers have dubbed lant nanobionics. lants are very attractive as a technology platform,
says Michael Strano, the Carbon P. Dubbs Professor of Chemical engineering and leader of the MIT research team. hey repair themselves, theye environmentally stable outside,
they survive in harsh environments, and they provide their own power source and water distribution.
Strano and the paper lead author, postdoc and plant biologist Juan Pablo Giraldo, envision turning plants into self-powered, photonic devices such as detectors for explosives or chemical weapons.
The researchers are also working on incorporating electronic devices into plants. he potential is really endless Strano says.
Supercharged photosynthesis The idea for nanobionic plants grew out of a project in Strano lab to build self-repairing solar cells modeled on plant cells.
As a next step, the researchers wanted to try enhancing the photosynthetic function of chloroplasts isolated from plants, for possible use in solar cells.
Chloroplasts host all of the machinery needed for photosynthesis, which occurs in two stages. During the first stage, pigments such as chlorophyll absorb light,
which excites electrons that flow through the thylakoid membranes of the chloroplast. The plant captures this electrical energy
and uses it to power the second stage of photosynthesis building sugars. Chloroplasts can still perform these reactions
when removed from plants, but after a few hours, they start to break down because light and oxygen damage the photosynthetic proteins.
the researchers embedded them with cerium oxide nanoparticles, also known as nanoceria. These particles are very strong antioxidants that scavenge oxygen radicals
and other highly reactive molecules produced by light and oxygen, protecting the chloroplasts from damage.
the researchers also embedded semiconducting carbon nanotubes, coated in negatively charged DNA, into the chloroplasts. Plants typically make use of only about 10 percent of the sunlight available to them,
but carbon nanotubes could act as artificial antennae that allow chloroplasts to capture wavelengths of light not in their normal range, such as ultraviolet, green,
With carbon nanotubes appearing to act as a rosthetic photoabsorber photosynthetic activity measured by the rate of electron flow through the thylakoid membranes was 49 percent greater than that in isolated chloroplasts without embedded nanotubes.
When nanoceria and carbon nanotubes were delivered together, the chloroplasts remained active for a few extra hours. The researchers then turned to living plants
and used a technique called vascular infusion to deliver nanoparticles into Arabidopsis thaliana, a small flowering plant.
Using this method, the researchers applied a solution of nanoparticles to the underside of the leaf,
where it penetrated tiny pores known as stomata, which normally allow carbon dioxide to flow in and oxygen to flow out.
the nanotubes moved into the chloroplast and boosted photosynthetic electron flow by about 30 percent.
What is the impact of nanoparticles on the production of chemical fuels like glucose? Giraldo says.
Lean green machines The researchers also showed that they could turn Arabidopsis thaliana plants into chemical sensors by delivering carbon nanotubes that detect the gas nitric oxide,
an environmental pollutant produced by combustion. Strano lab has developed previously carbon nanotube sensors for many different chemicals,
including hydrogen peroxide, the explosive TNT, and the nerve gas sarin. When the target molecule binds to a polymer wrapped around the nanotube,
it alters the tube fluorescence. e could someday use these carbon nanotubes to make sensors that detect in real time, at the single-particle level,
free radicals or signaling molecules that are at very low-concentration and difficult to detect, Giraldo says. his is a marvelous demonstration of how nanotechnology can be coupled with synthetic biology to modify
and enhance the function of living organisms in this case, plants, says James Collins, a professor of biomedical engineering at Boston University who was involved not in the research. he authors nicely show that self-assembling nanoparticles can be used to enhance the photosynthetic capacity of plants,
as well as serve as plant-based biosensors and stress reducers. By adapting the sensors to different targets,
the researchers hope to develop plants that could be used to monitor environmental pollution, pesticides, fungal infections, or exposure to bacterial toxins.
They are also working on incorporating electronic nanomaterials, such as graphene, into plants. ight now, almost no one is working in this emerging field,
Giraldo says. t an opportunity for people from plant biology and the chemical engineering nanotechnology community to work together in an area that has a large potential.
The research was funded primarily by the U s. Department of energy
#Soft robotic fish moves like the real thing Soft robots which don t just have soft exteriors
but are powered also by fluid flowing through flexible channels have become a sufficiently popular research topic that they now have their own journal Soft Robotics.
In the first issue of that journal out this month MIT researchers report the first self-contained autonomous soft robot capable of rapid body motion:
a fish that can execute an escape maneuver convulsing its body to change direction in just a fraction of a second
We re excited about soft robots for a variety of reasons says Daniela Rus a professor of computer science
and engineering director of MIT s Computer science and Artificial intelligence Laboratory and one of the researchers who designed
In most robotic motion-planning systems avoiding collisions with the environment is the highest priority.
With soft robots collision poses little danger to either the robot or the environment. In some cases it is actually advantageous for these robots to bump into the environment
because they can use these points of contact as means of getting to the destination faster Rus says.
Escape velocitythe robotic fish was built by Andrew Marchese a graduate student in MIT s Department of Electrical engineering
and Computer science and lead author on the new paper where he s joined by Rus and postdoc Cagdas D. Onal.
In experiments Marchese found that the angle at which the fish changes direction which can be as extreme as 100 degrees is determined almost entirely by the duration of inflation
That decoupling of the two parameters he says is something that biologists had observed in real fish.
That points to yet another possible application of soft robotics Rus says in biomechanics If you build an artificial creature with a particular bio-inspired behavior perhaps the solution for the engineered behavior could serve as a hypothesis for understanding
He used the lab s 3-D printer to build the mold in which he cast the fish s tail
and the polymer ring that protects the electronics in the fish s guts. The long haulthe fish can perform 20
But the comparatively simple maneuver of swimming back and forth across a tank drains the canister quickly.
and building something that s compromised on performance a little bit but increases longevity. A new version of the fish that should be able to swim continuously for around 30 minutes will use pumped water instead of carbon dioxide to inflate the channels
Video Melanie Gonick All of our algorithms and control theory are designed pretty much with the idea that we ve got rigid systems with defined joints says Barry Trimmer a biology professor at Tufts University who specializes in biomimetic soft robots.
That works really really well as long as the world is pretty predictable. If you re in a world that is not which to be honest is everywhere outside a factory situation then you start to lose some of your advantage.
The premise of soft robotics Trimmer says is that if we learn how to incorporate all these other sorts of materials
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