Scaling up synthetic-biology innovation

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Gen9's BioFab platform synthesizes small DNA fragments on silicon chips and uses other technologies to build longer DNA constructs from those fragments. Done in a parallel, this produces hundreds to thousands of DNA constructs simultaneously. Shown here is an automated liquid-handling instrument that dispenses DNA onto the chips. Courtesy of Gen9

MIT professor’s startup makes synthesizing genes many times more cost effective.
Inside and outside of the classroom, MIT professor Joseph Jacobson has become a prominent figure in — and advocate for — the emerging field of synthetic biology.

As head of the Molecular Machines group at the MIT Media Lab, Jacobson’s work has focused on, among other things, developing technologies for the rapid fabrication of DNA molecules. In 2009, he spun out some of his work into .Gen9, which aims to boost synthetic-biology innovation by offering scientists more cost-effective tools and resources.
Headquartered in Cambridge, Massachusetts, Gen9 has developed a method for synthesizing DNA on silicon chips, which significantly cuts costs and accelerates the creation and testing of genes. Commercially available since 2013, the platform is now being used by dozens of scientists and commercial firms worldwide.
Synthetic biologists synthesize genes by combining strands of DNA. These new genes can be inserted into microorganisms such as yeast and bacteria. Using this approach, scientists can tinker with the cells’ metabolic pathways, enabling the microbes to perform new functions, including testing new antibodies, sensing chemicals in an environment, or creating biofuels.

But conventional gene-synthesizing methods can be time-consuming and costly. Chemical-based processes, for instance, cost roughly 20 cents per base pair — DNA’s key building block — and produce one strand of DNA at a time. This adds up in time and money when synthesizing genes comprising 100,000 base pairs.

Gen9’s chip-based DNA, however, drops the price to roughly 2 cents per base pair, Jacobson says. Additionally, hundreds of thousands of base pairs can be tested and compiled in parallel, as opposed to testing and compiling each pair individually through conventional methods.

This means faster testing and development of new pathways — which usually takes many years — for applications such as advanced therapeutics, and more effective enzymes for detergents, food processing, and biofuels, Jacobson says. “If you can build thousands of pathways on a chip in parallel, and can test them all at once, you get to a working metabolic pathway much faster,” he says.

Over the years, Jacobson and Gen9 have earned many awards and honors. In November, Jacobson was also inducted into the National Inventors Hall of Fame for co-inventing E Ink, the electronic ink used for Amazon’s Kindle e-reader display.

Scaling gene synthesizing Throughout the early-and mid-2000s, a few important pieces of research came together to allow for the scaling up of gene synthesis, which ultimately led to Gen9.

First, Jacobson and his students Chris Emig and Brian Chow began developing chips with thousands of “spots,” which each contained about 100 million copies of a different DNA sequence.

Then, Jacobson and another student, David Kong, created a process that used a certain enzyme as a catalyst to assemble those small DNA fragments into larger DNA strands inside microfluidics devices — “which was the first microfluidics assembly of DNA ever,” Jacobson says.

Despite the novelty, however, the process still wasn’t entirely cost effective. On average, it produced a 99 percent yield, meaning that about 1 percent of the base pairs didn’t match when constructing larger strands. That’s not so bad for making genes with 100 base pairs. “But if you want to make something that’s 10,000 or 100,000 bases long, that’s no good anymore,” Jacobson says.

Around 2004, Jacobson and then-postdoc Peter Carr, along with several other students, found a way to drastically increase yields by taking a cue from a natural error-correcting protein, Mut-S, which recognizes mismatches in DNA base pairing that occur when two DNA strands form a double helix. For synthetic DNA, the protein can detect and extract mismatches arising in base pairs synthesized on the chip, improving yields. In a paper published that year in Nucleic Acids Research, the researchers wrote that this process reduces the frequency of errors, from one in every 100 base pairs to around one in every 10,000.

With these innovations, Jacobson launched Gen9 with two co-founders: George Church of Harvard University, who was also working on synthesizing DNA on microchips, and Drew Endy of Stanford University, a world leader in synthetic-biology innovations.

Together with employees, they created a platform called BioFab and several other tools for synthetic biologists. Today, clients use an online portal to order gene sequences. Then Gen9 designs and fabricates those sequences on chips and delivers them to customers. Recently, the startup updated the portal to allow drag-and-drop capabilities and options for editing and storing gene sequences.

This allows users to “make these very extensive libraries that have been inaccessible previously,” Jacobson says.

Fueling big ideas

Many published studies have already used Gen9’s tools, several of which are posted to the startup’s website. Notable ones, Jacobson says, include designing proteins for therapeutics. In those cases, the researcher needs to make 10 million or 100 million versions of a protein, each comprising maybe 50,000 pieces of DNA, to see which ones work best.

Instead of making and testing DNA sequences one at a time with conventional methods, Gen9 lets researchers test hundreds of thousands of sequences at once on a chip. This should increase chances of finding the right protein, more quickly. “If you just have one shot you’re very unlikely to hit the target,” Jacobson says. “If you have thousands or tens of thousands of shots on a goal, you have a much better chance of success.”

Currently, all the world’s synthetic-biology methods produce only about 300 million bases per year. About 10 of the chips Gen9 uses to make DNA can hold the same amount of content, Jacobson says. In principle, he says, the platform used to make Gen9’s chips — based on collaboration with manufacturing firm Agilent — could produce enough chips to cover about 200 billion bases. This is about the equivalent capacity of GenBank, an open-access database of DNA bases and gene sequences that has been constantly updated since the 1980s.

Such technology could soon be worth a pretty penny: According to a study published in November by MarketsandMarkets, a major marketing research firm, the market for synthesizing short DNA strands is expected to reach roughly $1.9 billion by 2020.

Still, Gen9 is pushing to drop costs for synthesis to under 1 cent per base pair, Jacobson says. Additionally, for the past few years, the startup has hosted an annual G-Prize Competition, which awards 1 million base pairs of DNA to researchers with creative synthetic-biology ideas. That’s a prize worth roughly $100,000.

The aim, Jacobson says, is to remove cost barriers for synthetic biologists to boost innovation. “People have lots of ideas but are unable to try out those ideas because of cost,” he says. “This encourages people to think about bigger and bigger ideas.”

ORIGINAL: .MIT News

Rob Matheson | MIT News Office
December 10, 2015

Bio-Powered Chips Might One Day Fit Inside Cells

Illustration: Trevor Finney and Jared Roseman/Columbia Engineering

For the first time, researchers have developed a microchip that is powered by the same energy-rich molecules that fuel living cells, researchers say. This advance could one day lead to devices that are implanted within cells and harvest biological energy to operate.

The molecule adenosine triphosphate (.ATP) stores chemical energy and is used inside cells to ferry energy from where it is generated to where it is consumed. The new microchip relies on enzymes known as sodium-potassium ATPases. These molecules break down ATP to release energy the enzymes use to pump sodium and potassium ions across membranes, generating an electrical potential during the process.

“Ion pumps are electronics-like components in living systems,” says study senior author .Ken Shepard, an electrical engineer at Columbia University in New York. Shepard and his colleagues detailed .their findings in the 7 December edition of the journal Nature Communications.

The researchers embedded sodium-potassium ATPases taken from pig brains in artificial fatty membranes. There were more than 2 million of these molecules active per square millimeter of the membranes, about 5 percent of the density naturally occurring in mammalian nerve fibers.

In the presence of ATP, these ion pumps generated 78 millivolts. A “biocell” of two membranes provides enough of a voltage to operate a CMOS integrated circuit. The ion pumps have a chemical-to-electrical energy conversion efficiency of of 14.9 percent.

“These ion pumps generated an electrical field that we harnessed to power a solid-state system,” Shepard says.

Since ATP is only really found within cells and not in the bloodstream, Shepard cautions that this new system is not a way to power conventional implantable medical devices such as pacemakers.

“However, such a system might power an implant small enough to sit inside a cell,” Shepard says. “Solid-state materials are already used in nanoparticles for various therapeutic and imaging purposes in the body, but those are all just passive materials. Our idea is to make something that would have the ability to compute and act, to make decisions and then actuate in some way.”

Future research could also incorporate other membrane proteins into electronics, such as those responsible for taste and .smell, Shepard says. "There could be many ways to couple solid-state systems with the biological machinery of cells," he says.

ORIGINAL: .IEEE Spectrum

By Charles Q. Choi

Posted 9 Dec 2015

Stanford engineers create artificial skin that can send pressure sensation to brain cell

Stanford engineers have created a plastic skin-like material that can detect pressure and deliver a Morse code-like signal directly to a living brain cell. The work takes a big step toward adding a sense of touch to prosthetic limbs.

Stanford chemical engineering Professor Zhenan Bao and her team have created a skin-like material that can tell the difference between a soft touch and a firm handshake. The device on the golden “fingertip” is the skin-like sensor developed by Stanford engineers. (Bao Lab)

Stanford engineers have created a plastic "skin" that can detect how hard it is being pressed and generate an electric signal to deliver this sensory input directly to a living brain cell.

Zhenan Bao, a professor of chemical engineering at Stanford, has spent a decade trying to develop a material that mimics skin's ability to flex and heal, while also serving as the sensor net that sends touch, temperature and pain signals to the brain. Ultimately she wants to create a flexible electronic fabric embedded with sensors that could cover a prosthetic limb and replicate some of skin's sensory functions.

Bao's work, reported today in Science, takes another step toward her goal by replicating one aspect of touch, the sensory mechanism that enables us to distinguish the pressure difference between a limp handshake and a firm grip.

"This is the first time a flexible, skin-like material has been able to detect pressure and also transmit a signal to a component of the nervous system," said Bao, who led the 17-person research team responsible for the achievement.

Benjamin Tee, a recent doctoral graduate in electrical engineering; Alex Chortos, a doctoral candidate in materials science and engineering; and Andre Berndt, a postdoctoral scholar in bioengineering, were the lead authors on the Science paper.

DIGITIZING TOUCH

The heart of the technique is a two-ply plastic construct: the top layer creates a sensing mechanism and the bottom layer acts as the circuit to transport electrical signals and translate them into biochemical stimuli compatible with nerve cells. The top layer in the new work featured a sensor that can detect pressure over the same range as human skin, from a light finger tap to a firm handshake.

Five years ago, Bao's team members first described how to use plastics and rubbers as pressure sensors by measuring the natural springiness of their molecular structures. They then increased this natural pressure sensitivity by indenting a waffle pattern into the thin plastic, which further compresses the plastic's molecular springs.

To exploit this pressure-sensing capability electronically, the team scattered billions of carbon nanotubes through the waffled plastic. Putting pressure on the plastic squeezes the nanotubes closer together and enables them to conduct electricity.

This allowed the plastic sensor to mimic human skin, which transmits pressure information to the brain as short pulses of electricity, similar to Morse code. Increasing pressure on the waffled nanotubes squeezes them even closer together, allowing more electricity to flow through the sensor, and those varied impulses are sent as short pulses to the sensing mechanism. Remove pressure, and the flow of pulses relaxes, indicating light touch. Remove all pressure and the pulses cease entirely.

The team then hooked this pressure-sensing mechanism to the second ply of their artificial skin, a flexible electronic circuit that could carry pulses of electricity to nerve cells.

IMPORTING THE SIGNAL

Bao's team has been developing flexible electronics that can bend without breaking. For this project, team members worked with researchers from PARC, a Xerox company, which has a technology that uses an inkjet printer to deposit flexible circuits onto plastic. Covering a large surface is important to making artificial skin practical, and the PARC collaboration offered that prospect.

Finally the team had to prove that the electronic signal could be recognized by a biological neuron. It did this by adapting a technique developed by Karl Deisseroth, a fellow professor of bioengineering at Stanford who pioneered a field that combines genetics and optics, called optogenetics. Researchers bioengineer cells to make them sensitive to specific frequencies of light, then use light pulses to switch cells, or the processes being carried on inside them, on and off.

For this experiment the team members engineered a line of neurons to simulate a portion of the human nervous system. They translated the electronic pressure signals from the artificial skin into light pulses, which activated the neurons, proving that the artificial skin could generate a sensory output compatible with nerve cells.

Optogenetics was only used as an experimental proof of concept, Bao said, and other methods of stimulating nerves are likely to be used in real prosthetic devices. Bao's team has already worked with Bianxiao Cui, an associate professor of chemistry at Stanford, to show that direct stimulation of neurons with electrical pulses is possible.

Bao's team envisions developing different sensors to replicate, for instance, the ability to distinguish corduroy versus silk, or a cold glass of water from a hot cup of coffee. This will take time. There are six types of biological sensing mechanisms in the human hand, and the experiment described in Science reports success in just one of them.

But the current two-ply approach means the team can add sensations as it develops new mechanisms. And the inkjet printing fabrication process suggests how a network of sensors could be deposited over a flexible layer and folded over a prosthetic hand.

"We have a lot of work to take this from experimental to practical applications," Bao said. "But after spending many years in this work, I now see a clear path where we can take our artificial skin."

ORIGINAL: Stanford

By Tom Abate

Bio-Computing near as MIT Programs Bacteria to Treat Diseases

If you’ve been a reader of Serious Wonder for sometime now, you’ve surely heard of the technology known as nanobots . It’s a technology in which consists of nanoscaled robotics that’ll swim through the bloodstream to deliver drugs and repair any organ damage throughout the body. But what if we can treat diseases, such as colon cancer and immune disorders, by transforming the bacteria in our bodies into bio-cybernetic carriers within our digestive system?

According to a new study published in the journal Cell Systems , researchers at MIT have  achieved just that by using gene expression and genome editing tools, such as CRISPR/Cas9, to modify and enhance gut bacteria, known as Bacteroides thetaiotaomicron, to attain a series of sensors, memory switches, and circuits!

By applying these basic computing elements, MIT has taken one extra step towards a future of bio-computing. Like previous attempts in building genetic circuits inside of organisms such as E. coli, researchers have targeted the gut bacterium B. thetaiotaomicron as a means of figuring out novel ways in delivering drugs throughout the body. However, unlike previous attempts in building genetic circuits, gut bacteria like B. thetaiotaomicron is much more preferable over E. coli, given the bacteria’s abundance in the human gut. For now, researchers are using mice, with long-haul expectations of human deliveries soon after. 

(PHOTO CREDIT:  JANET IWASA )

“We achieve up to 10,000- fold range in constitutive gene expression and 100- fold regulation of gene expression with inducible promoters and use these parts to record DNA-encoded memory in the genome. We use CRISPR interference (CRISPRi) for regulated knockdown of recombinant and endogenous gene expression to alter the metabolic capacity of B. thetaiotaomicronand its resistance to antimicrobial peptides. 

Finally, we show that inducible CRISPRi and recombinase systems can function in B. thetaiotaomicron colonizing the mouse gut. These results provide a blueprint for engineering new chassis and a resource to engineer Bacteroides for surveillance of or therapeutic delivery to the gut microbiome.” –  Cell Systems Study by MIT

FUTURE IMPLICATIONS

The future of margin: 20px;bio-computing may not be fully comprehensible, given the fact that we’re still not entirely sure about the ins and outs of our own biological substrate, but one can surely agree that bio-computing will forever change the way we not only view our own biology, but subsequently how we use it as well. We are on a path towards merging “man” and “machine,” and with MIT’s latest attempts at engineering bio-cybernetic hybrids using our own gut bacteria, one can be rest assured that a future of bio-computing is closer than ever before! What applications can you think of in which we’ll use bio-computing in the next few decades?

Photo Credit: MIT

About the author

B.J. Murphy is the Editor and Social Media Manager of Serious Wonder. He is a futurist, philosopher, activist, author and poet. B.J. is an Advisory Board Member for the NGO nonprofit Lifeboat Foundation and a writer for the Institute for Ethics and Emerging Technologies (IEET).

ORIGIN: Serious Wonder

BY B.J. MURPHY

July 14, 2015

Harvard Creates Half-Man Cyborg Flesh

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Bioengineers at Harvard University have created the first examples of cyborg tissue: 

• Neurons, 
• heart cells, 
• muscle, and 
• blood vessels 

that are interwoven by nanowires and transistors.

These cyborg tissues are half living cells, half electronics. As far as the cells are concerned, they’re just normal cells that behave normally — but the electronic side actually acts as a sensor network, allowing a computer to interface directly with the cells. In the case of cyborg heart tissue, the researchers have already used the embedded nanowires to measure the contractions (heart rate) of the cells.

To create cyborg flesh, you start with a three-dimensional scaffold that encourages cells to grow around them. These scaffolds are generally made of collagen, which makes up the connective tissue in almost every animal. The Harvard engineers basically took normal collagen, and wove nanowires and transistors into the matrix to create nanoelectric scaffolds (nanoES). The neurons, heart cells, muscle, and blood vessels were then grown as normal, creating cyborg tissue with a built-in sensor network.

Cardiac cells, with a nanoelectroic electrode highlighted

So far the Havard team has mostly grown rat tissues, but they have also succeeded in growing a 1.5-centimeter (0.6in) cyborg human blood vessel. They’ve also only used the nanoelectric scaffolds to read data from the cells — but according to lead researcher Charles Lieber, the next step is to find a way of talking to the individual cells, to “wire up tissue and communicate with it in the same way a biological system does.”

A computer chip, containing a sample of nanoES tissue

Suffice it to say, if you can use a digital computer to read and write data to your body’s cells, there are some awesome applications. If you need a quick jolt of adrenaline, you would simply tap a button on your smartphone, which is directly connected to your sympathetic nervous system. You could augment your existing physiology with patches — a patch of nanoelectric heart cells, for example, that integrates with your heart and reports back if you experience any problems. When we eventually put nanobots into our bloodstream, small pulses of electricity emitted by the cells could be used as guidance to damaged areas. In the case of blood vessels and other organs, the nanoelectric sensor network could detect if there’s inflammation, blockage, or tumors.

Realistically, though, we’re a long way away from such applications. In the short term, though, these cyborg tissues could be used to create very accurate organs-on-a-chip — lab-grown human organs that are encased within computer chips and then used to test drugs or substance toxicity, without harming a single bunny or bonobo.

Read: Nanotech: will it kill us all?, and Stanford’s wireless, implantable “Innerspace” medical device

Research paper: doi:10.1038/nmat3404 (paywalled)


ORIGINAL: ExtremeTech

By Sebastian Anthony 

August 29, 2012 at 6:54 am

Scientists Just Invented the Neural Lace

Images via Charles Lieber

In the Culture novels by Iain M. Banks, futuristic post-humans install devices on their brains called a “neural lace.” A mesh that grows with your brain, it’s essentially a wireless brain-computer interface. But it’s also a way to program your neurons to release certain chemicals with a thought. And now, there’s a neural lace prototype in real life.

A group of chemists and engineers who work with nanotechnology published a paper this month in Nature Nanotechnology about an ultra-fine mesh that can merge into the brain to create what appears to be a seamless interface between machine and biological circuitry. Called “mesh electronics,” the device is so thin and supple that it can be injected with a needle — they’ve already tested it on mice, who survived the implantation and are thriving. The researchers describe their device as “syringe-injectable electronics,” and say it has a number of uses, including 

• monitoring brain activity, 
• delivering treatment for degenerative disorders like Parkinson’s, and 
• even enhancing brain capabilities.

Writing about the paper in Smithsonian magazine, Devin Powell says a number of groups are investing in this research, including the military:

[Study researcher Charles Lieber’s] backers include Fidelity Biosciences, a venture capital firm interested in new ways to treat neurodegenerative disorders such as Parkinson’s disease. The military has also taken an interest, providing support through the U.S. Air Force’s Cyborgcell program, which focuses on small-scale electronics for the “performance enhancement” of cells.

For now, the mice with this electronic mesh are connected by a wire to computer — but in the future, this connection could become wireless. The most amazing part about the mesh is that the mouse brain cells grew around it, forming connections with the wires, essentially welcoming a mechanical component into a biochemical system.

A 3D microscope image of the mesh merging with brain cells

Lieber and his colleagues do hope to begin testing it on humans as soon as possible, though realistically that’s many years off. Still, this could be the beginning of the first true human internet, where brain-to-brain interfaces are possible via injectable electronics that pass your mental traffic through the cloud. What could go wrong?


[Read the scientific article in Nature Nanotechnology]



ORIGINAL: Gizmodo
Annalee Newitz
6/15/15

Contact the author at annalee@gizmodo.com.
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