#ScienceHack: Violacien Factory Design Automation with OpenTrons

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Yesterday Genspace hosted the second #ScienceHack. It was awesome to participate in a new type of peer-to-peer syn-bio research and design event. And, there was a robot!!!

The format of a #ScienceHack, designed by the awesome team at Synbiota, brings labs across the world together to work on optimizing a genetic circuit. We are focused on the circuit to produce violacein, an anti-cancer and anti-parasite drug that currently costs more than $360K per gram. The #sciencehack uses the Genomikon system to re-design genetic circuits with the hope of bringing this cost down significantly. Genomikon is a biological prototyping platform that modularizes DNA building blocks so that snapping together a novel genetic design is easier than ever.

G_rulesbA diagram broadly describing the Genomikon plasmid assembly process.

While the six gene pathway to produce violacein is known, it remains mysterious. For example, it is unclear where the promotor sequence that initiates the pathway’s expression is located. In order to optimize design, then, we need to use the old trial and error strategy, producing and testing as many different designs as possible. That is why the distributed nature of a #ScienceHack is so great — with people across the world collaborating, it is possible to make a design that drastically lowers the cost of this violacein without millions of dollars to pay lab fees.

Vio-1This is the chemical process to make Violacein and the genes associated with each step.

Synbiota provides an amazing platform for sharing data and protocols, making it the basic collaboration tool for open science projects. And we were lucky to have Connor Dickie, CEO of Synbiota and one of the main developers of the open source genetic design software GENtle, at the event to show us how to design DNA in silico. Check out everyone’s genetic designs here at the event’s Synbiota project page. And this PDF provides information on the different strategies teams used to optimize violacein production.

Affordable lab robotics is another way to pump out violacein factory designs to test and accelerate the pace of optimization. Actually designing the pathway is the crucial part, but it takes hours of lab work to produce an e. coli strain in order to test a design and see how good it is. If a robot can do the time consuming genetic assemblies, individuals can spend more time problem solving and designing and less time pipetting and waiting. Is am a part of the team, also including Chiu Chau and Nick Wagner, developing OpenTrons, an affordable open automation platform well on its way to doing synthetic biology.

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The OpenTron BETA

The whole OpenTrons team came to the #sciencehack to show off the assembly for automating the magnetic bead wash step — the most time consuming part of the Genomikon protocol — that Chiu and Nick designed over the weekend. It uses a custom 3D printed holder for the vial, and a magnetic tip that the pipette can use repeatedly to move the wash magnet back and forth. You can see it in action in the video above.

magnetBeadHolderA 3D printed magnet stand Chiu made for Genspace classes that use the Genomikon kit.

I teamed up with Christal Gordon to design the simplest deoxyviolacein pathway on GENtle and begin the process of automating the DNA assembly. But once the protocol is complete, we will share it so that other OpenTrons users can download and repeat it to assemble their own violacein factory designs.

toolboxAlpha1The prototype lab suitcase, my pipette, and the Genomikon violacein factory kit.

The OpenTrons team was also excited to show off our new Android controlled, modular, portable synthetic biology kit prototype. Its a lab in a box! Heating, cooling, and centrifuge all included, with a vortex soon to be added. Next, it will be re-designed to work with the automation platform.

The #sciencehack is a great format, and it was a pleasure to experiment with such cool and capable tools as Synbiota, Genomikon, and OpenTrons. I have a feeling these three have quite a future together! Watch this space for updates on how our violacein factory designs preform, and please be in touch with any questions or to be involved (opentronsinfo |at| gmail |dot| com).

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Genspace in China!

By Pia-Kelsey O’Neill

“Will someone who knows about DNA make the monsters that we see in cartoons?” a young girl worried aloud at the Zhejiang Museum of Science and Technology (ZJSTM), located in Hangzhou, China. Hers was among the many thoughtful questions we received last week during a presentation that Oliver Medvedik and I gave on the past, present, and future of DIY biology. The audience of about two hundred included middle school students and adult professionals from the city.

We had been invited to Hangzhou by the non-profit organization, Zhejiang Association of Science and Technology (ZAST), a branch of the national Association of Science and Technology (AST). Enacted by the legislature of the People’s Republic of China, AST is expected to create programs that will popularize scientific knowledge. Bing Zhu, Deputy Director of the International Department of ZAST, first wrote to us in January explaining that a major goal of the organization is to reach especially young audiences. “Presentations of science [in China] are usually thought to be a plainly force-fed process,” he wrote. He hoped that during our visit, we could begin to introduce more hands-on methods of presenting science and art to the public, as well as to consult with the ZJSTM staff about setting up their own community biotechnology lab for teaching purposes. “We want [the public] to realize that it is ever more important that they look at science not from a single-minded point of view, but rather a cross-boundary view.” Through numerous emails, conference calls and even a personal visit to Genspace by Ms. Phyllis Tang Yifei, the Project Coordinator of ZAST, we hashed out a detailed agenda for our visit. The plan was for us to run two workshops for the ZAST staff similar to those we offer at Genspace and to hold an open seminar in order to demonstrate to the public the variety of projects-from laboratory equipment to bio design-that Genspace and others in the DIY movement have thus far created.

Upon arriving in Shanghai, Oliver and I were promptly greeted by Bing who was ready with friendly questions about each of us, our research and about Genspace. That night, he treated us to dinner at a waterfront restaurant along the Huangpu River with a spectacular view of the Bund; a sparkling cityscape just beyond our tabletop. As we were unfamiliar with the Shanghai cuisine, Bing took it upon himself to select a feast of colorful and tasty dishes, which were presented to us in the traditional Chinese manner: cold dishes first, followed by hot dishes and finally, soup. His warmth, and that of the entire ZAST staff, was maintained throughout our visit.

The headquarters of ZAST is in Hangzhou, a bustling city in the Zhejiang province, set on the idyllic West Lake. As Bing and many of the staff are natives of Hangzhou, they were very knowledgeable about the city’s long history and local culture. Between our teaching engagements, they took special care to make arrangements so that we could experience the unique attributes of the city firsthand. One afternoon we were rowed on a traditional wooden boat through the peaceful channels of the West Lake where we admired the surrounding willow trees, their long branches sweeping with the breeze along the water surface. One of the translators introduced us to the ozymandias tree, which is found throughout Hangzhou and produces tiny aromatic flowers, exuding a sweet fragrance over the entire city. We sat down another afternoon to an extended cup of Longjing tea in the hills above Hangzhou where these tea bushes are famously tended, in ancient times by monks.

On Tuesday, we went to see the ZJSTM Science Center where we would be teaching in the main hall. The enormity of the space was at first overwhelming, with an immense replica of the moon serving as the backdrop to our preparations. Our workshops went off without a hitch, thanks in no small part to the ZAST staff for providing us with crucial pieces of equipment that we had requested. Among the items were a high speed microcentrifuge, a PCR machine for amplifying DNA, a new gel imaging and documentation system for DNA analysis and a set of high quality Eppendorf pipettors, still in their boxes. The equipment was certainly much nicer than what one would find in use in many university labs.

Over the next two days Oliver and I ran the two workshops we had planned, on genotyping and neuroscience, for the museum and ZAST staff. The participants arrived early each day, in business attire, and were clearly eager to start the activities. Oliver first demonstrated how to use a pipettor and after a little practice, the group began their first hands-on experiment: to extract and genotype DNA from meat used in food. Using cow and chicken primers and meat from the local market, they successfully identified one from the other with the extracted DNA.

With another group, I held a workshop in basic neuroscience and electrophysiology. Using Spikerboxes obtained from Backyard Brains, we were able to record action potentials in Chinese fighting crickets and earthworms obtained from the local chicken coops.

On Friday morning, we then presented a series of demonstrations for two groups of fifth grade classes who were visiting the museum. We started first with our ever popular home DNA extraction procedure, which we love to apply to strawberries. Since strawberries weren’t in season we made do with oranges and tangerines which also gave great yields of fluffy chromosomal DNA. The children were first a bit reserved, though quite attentive. But soon, after asking for volunteers, the kids threw themselves into activities with enthusiasm. We finished the series with a very messy, and very fun demonstration of building Winogradsky columns, basically a self-contained ecosystem within a pop bottle using mud from lake sediments that contain naturally occurring bacteria. When we asked for help in mashing hard-boiled egg yolks (they supply the sulfur for certain microbes) into the sticky mud, such a rush of waving hands shot into the air – it was difficult to choose just a few.

Before our final “TED-style” presentation on Friday night, we had the opportunity to sit down with Mr. Li, the director of the ZJSTM Science Center, and his staff to have a deep discussion regarding the possibility of future collaborations between Genspace and ZJSTM. He reiterated to us what Bing had expressed in our initial conversations, that the museum is keen on engaging the public in science. Though the universities teach scientific topics, Mr. Li said, there is not much opportunity for the type of public exploration in science that is possible at a community space such as Genspace. He seemed quite open as to how collaborations between Genspace and the museum would progress. For the remainder of this year, they plan to set up a teaching lab within the museum and then, with our guidance next year, they hope to learn how to organize and run biological workshops, including the ones we had done during this trip. Although the concept for an interactive science museum originated with the Exploratorium in San Francisco during the late 1960’s, the Science Center in Zhejiang has a vision to take interactivity to the next level. Progressing beyond workshops, the goal would be to have longer term research projects carried out by students, schools and citizen scientists within a community laboratory situated at the museum.

Overall, it was an exceptionally positive experience for both Oliver and myself to work with the members of ZAST and ZJSTM. We’d like to thank everyone we’ve met there for such a rewarding and thought-provoking week. Many thanks also goes to Dan Grushkin for establishing our initial correspondence with ZAST. This introduction has the potential to develop into the first long term international collaboration for Genspace and we are excited to see how it progresses.

Left to Right: Ms. Zhao Xin (Deputy Curator of ZJSTM), Ms. Jackie, Pia, Oliver, Mr. Li (Director of ZJSTM), Bing Zhu (Secretary General of ZAST), Mr Hueng, Ms. Wendy (Assistant to Ms. Zhao)

Left to Right: Ms. Zhao Xin (Deputy Curator of ZJSTM), Ms. Jackie, Pia (Genspace Instructor) , Oliver (Scientific Director, Genspace), Mr. Li (Director of ZJSTM), Bing Zhu (Deputy Director of the International Division of ZAST), Mr Hueng, Ms. Wendy (Assistant to Ms. Zhao)

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Bacterial Photography: Creating Photosynthetic Images Using Living Microorganisms

By Karen Ingram

Dark and early one winter morning in New York, Wythe Marschall and I embarked on a quest to find a microorganism—a genetically engineered chimaera—that could turn itself into a living photograph. We intended to join Dr. Natalie Kuldell’s bacterial photography class at MIT. Undaunted by a 3:45am departure time from the Port Authority, unhalted by a bus wreck in Connecticut, and aided by four cups of coffee we arrived just in time for the 11am class.

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Natalie Kuldell

On the chalkboard, Natalie rapidly outlined the design principles we would be exploring to create the living photographs. First she drew an electrical circuit. She explained that these design principles were a simple, electronics-derived way of depicting the series of biochemical reactions that would occur within the living photograph.  Essentially, we would introduce a light sensitive gene (from photosynthetic blue-green algae) into a strain of  E.coli that cause the bacteria to create a black pigment. Red light would activate the mechanism, and bacteria in areas of the dark areas of the photo would digest a certain kind of sugar (S-gal®) that would cause a blackish color to be produced from the bacteria.

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Now it was time for the hands-on portion of the class. To further support the biology-as-electronics analogy, the class used a breadboard and LEDs to show how the bio chemical reactions would create the circuits. Natalie mused, “If only biology were are predictable as electronics.”

MIT students creating a simulation of the biological circuitry using breadboards.

MIT students creating a simulation of the biological circuitry using breadboards.

After everyone had tested their breadboards, it was time to create the actual bacterial photographs. Using pipettes we followed the protocols that had been outlined to create the photoreceptive E.coli. Each Petri dish’s bacteria was suspended in liquid agar to assure adequate distribution, creating a lawn for the bacteria to grow evenly.

A little about the development of these protocols: photosynthetic bacteria created from a dual biological circuit system designed by Dr. Chris Voigt, then an assistant chemistry professor at the University of California, San Francisco (UCSF), now also at MIT. The idea further developed by a group of students at the University of Texas at Austin, as part of the iGEM (intercollegiate Genetically Engineered Machine) competition in 2005 at MIT. (http://2006.igem.org/wiki/index.php/University_of_Texas_2006)

Pouring the agar into the Petri dish

Pouring the agar into the Petri dish

Petri dishes in hand, we selected images to be printed on transparencies. This creates a shaded area that allows the bacteria beneath to activate and produce the sugar-digesting enzyme (beta-galactosidase) that creates the darks in the Petri dish. The UT students explained it nicely (http://www.utexas.edu/features/2005/bacteria/index.html), “When the bacteria grow in dark parts of the Petri dish, they digest the sugar and produce black pigment. Those in the light don’t produce the sugar-digesting enzyme and the film remains clear.”

Students selected a penguin, the Taj Mahal, even a petite handlebar mustache. Wythe selected an octopus rendering from the legendary botanist and artist Ernest Haeckel, and I pulled a dotted unicorn that I had created on my computer. After all images had been loaded onto the thumb drive, Wythe and I accompanied Natalie to the lab where her bacterial darkroom was located.

My unicorn and Wythe’s octopus transparencies taped on top of our Petri dishes

My unicorn and Wythe’s octopus transparencies taped on top of our Petri dishes

Natalie experimented many years to create the perfect “darkroom” for the bacterial cultures. Identifying the combination of the perfect distance and light intensity was no speedy feat. Her darkroom is constructed in a refrigerator outfitted with a red light and shelving for the Petri dishes to sit on. The outside of the refrigerator is covered with post cards from distant places; monuments to great achievements in beauty and construction from both humans and nature. The gothic Duomo di Milano, the majestic Grand Canyon, a gorgeous selection of Central and South American coastlines… even a Texan cowboy, perhaps a nod to the UT students. Our octopus and unicorn petri dishes safely tucked into the bacterial darkroom, we thanked Natalie and bid her farewell.

The bacterial photography darkroom

The bacterial photography darkroom

Simultaneously exhausted and enlivened, Wythe and I boarded the bus back to New York, chatting the entire journey back about the wonders of biotechnology.

Two days later we received an email from Natalie with several photos of bacterial photography from the class. There, imprinted in the agar were the students’ selections; the Taj Mahal, the penguin, the mustache. Sadly though, we were not bacteria-whispers. Our little microbes precipitated neither fish nor fauna… no octopus, no unicorn. So what had happened? Somewhere we made an error; a fine measurement in the protocols was off—perhaps we had too much of one thing and not enough of another. Who knows? We’ll get it next time!

Successful bacterial photographs created by MIT students with original transparency images

Successful bacterial photographs created by MIT students with original transparency images

About bacterial photography
http://www.utexas.edu/features/2005/bacteria/index.html
http://2006.igem.org/wiki/index.php/University_of_Texas_2006

About Natalie:
http://web.mit.edu/be/people/kuldell.shtml
http://www.biobuilder.org/

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TED Video of Stranger Visions

This is a great video about Heather Dewey-Hagborg’s project, Stranger Visions.

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Member Project: Vivian Xu’s Living Devices

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In a world where computer systems have the capacity to learn and resemble living systems, where we can clone our own meat and grow our own clothes, what then differentiates the organic from the artificial and the living from the dead?  - Vivian Xu

Vivian Xu refined a technique for dispersing charges through an E. coli growth medium, causing the bacteria to grow in the pattern of electrical waves. A bio-artist from Bejing, she created these beautiful living devices at Genspace’s lab as part of her thesis project at Parson’s Design and Technology MFA program.

In the tradition of scientists and DIYers alike, Vivian provided extensive documentation, giving her project real methodological and theoretical rigor. Cant wait to see where she takes her art/science next.

Devices from Jacques de Vaucanson’s Mechanical Duck, 1739 (image below)—a mechanism that could flap, squawk, even eat and poop like a duck—to modern bio-memetic robots and computer learning algorithms blur the lines between the organic and technological. Xu blurs them one step further.

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Bacteria and other organisms like ants are known to have an unexplained affinity for electrical fields. She uses this scientific mystery as a point of departure for her art. Vivian’s results are, to say the least, intricately visually stunning.

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