Biofabricate: Genspace Pop Up Lab

Genspace_Biofabricate_imgGenspace set up a pop-up DIYBio LAB at ‘BIOFABRICATE’,  The world’s first summit dedicated to biofabrication for future industrial and consumer products, organized by Suzanne Lee of Biocouture in partnership with Synbiobeta.

The event featured a full day of speakers and keynote talks from pioneering biomaterial, biotech and biofabrication start-ups along with key researchers, designers, thought leaders and academics, as well as multiple workshops, a design lab and the pop up lab.

The pop up lab was a space for people to come and ‘Grow Your Own Scoby’ and make necklaces filled with culture to take home, interact with the material in a living, grown, and dried state, check out slime mold and mycelium under the microscope, or learn how to pipette, while chatting with members about Genspace and biofabrication! People could come and interact with some of the materials discussed throughout the day, and learn how a DIY lab could support them in their projects. A few Genspace members projects were displayed along with the pop up lab as well as in the design lab, and multiple members spoke throughout the day.

IMG_8687the Pop Up Lab
IMG_8691the lab and some members projects
IMG_8683GYOS: grow your own scoby!IMG_8669scoby: living, wet and dry culturesIMG_8680the pipetting stationIMG_8689Some members projects featured in the Pop Up lab

Featuring members projects:

Heather Dewey-Hagborg, Stranger Visions, exploring the traces of the DNA you leave behind; Ali Schachtschneider, Fungal Shoes, Bacterial Textiles and Garmentobject exploring the bodies interaction with biomaterial technology through the growth of cellulose, mycelium and bacterial materials; Fabiola Einhorn, 174 Magazine, exploring how Synthetic Biology and bio-tech fabrications will integrate into our everyday life and citizens access to its making; And at the Design Lab: Genspace 2012 iGEM team collaboration with Terreform One, Gen2Seat, a biodegradable Genetic Generation sitting Module; Sylvia Saborio, Vee Vo, creating wall papers tiles using traditional print making techniques and engineered bacteria; and Genspace co-founder Nurit Bar-Shai, Objectivity [tentative], exploring how bacteria communication and network systems might inform smarter design.
IMG_8724 Projects in the Design LabIMG_8725


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Genspace wins gold medal at 2014 iGEM competition!


igem goldAh, success! After working our butts off for months, we participated in the iGEM Giant Jamboree and won a gold medal (the second time Genspace has done so, but this time we could compete under our own name in the new Community Lab Track!).

20141101_092048Jonathan Badal at the podium during our presentation.

20141102_191358Explaining our project to the iGEM judges…

20141102_194449…and to other participants.

20141101_202150The team relaxes after the presentation is over at a local bar…

20141102_001505…and meets some old friends.

20141103_140754At the awards ceremony, seeing out name on the list of gold medal winners!

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Genspace co-founder Dr. Ellen Jorgensen gives keynote speech at Maker Faire Rome event.

Watch Make Cells Dance- Ellen’s Maker Faire presentation

UntitledMaker Faire Rome is even bigger than World Make Faire in New York! It was held at the beautiful Auditorium Parco della Musica and it took days to see it all. There were makers from all over the world exhibiting their creations. Everything from 3D food printing to giant robot musicians. It was fabulous, as befits the incredible city of Rome. There was an exhibit spotlighting the history Italian innovation that included an Olivetti Programma 101, the first ‘portable’ computer and one that Ellen has fond memories of from high school. She had a great time hanging out with friends too.





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#ScienceHack: Violacien Factory Design Automation with OpenTrons


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.

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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