Monday, November 28, 2011

Do-It-Yourself Neuroscience

By Moheb CostandiNovember 28, 2011

Traditionally, scientific research was the preserve of the wealthy and today the situation is not much different—while researchers need not be rich, almost all of them work in institutional laboratories using equipment that can be very expensive.
Recently, however, a do-it-yourself biology movement has emerged, and a symposium held at the 41st annual meeting of the Society for Neuroscience in Washington, DC, earlier this month described several innovative projects aimed at minimizing the cost of brain research and making it accessible to everyone.

“If astronomy were like neuroscience, you’d need a Ph.D. to look through a telescope,” says Tim Marzullo, who chaired the symposium. “It’s ridiculous—the technology for recording nervous impulses is 90 years old and there’s no reason why it can’t be brought into schools.”

Marzullo and his colleague Greg Gage are doing just that. Three years ago, they founded Backyard Brains, a small company that manufactures neuroscience kits out of cheap off-the-shelf electronics purchased from outlets such as Radio Shack and distributes them to high schools and colleges, with the help of grant funding from the National Institutes of Health.

“I come from a family of teachers,” says Marzullo. “Backyard Brains came out of my love of neuroscience, education and building things. We see ourselves as part of a broader movement of DIY hackers who are trying to build just-good-enough versions of gear to reduce the barrier to entry.”

Monday, October 24, 2011

Michael Pollan Calls for Open Source Genetic Engineering

Try this at home by Daniel Grushkin

The next big scientific breakthrough may come from a garage, not a lab, with do-it-yourself biologists popping up everywhere. Genetic tinkerer Daniel Grushkin has a message for the curious: go ahead, try this at home. 
In the scientific journals, we’ve been labeled biotech hobbyists, citizen scientists, even biohackers.
Last December, seven of us opened the first community lab, called Genspace. Though it’s a fully functional lab, it has a decidedly hacked-together aesthetic. We built it in a Brooklyn, N.Y., warehouse that was converted into a workspace for architects and designers. At the center of the floor sits a glass cube made of found objects. The walls are created from windows and sliding glass doors saved from demo sites. The lab benches are stainless steel tables salvaged from industrial kitchens. Most of the equipment was donated by a biotech company that downsized during the economic crisis.
We incorporated Genspace as a nonprofit to serve as a shared lab, a nursery for biotech tinkerers. Our members include an entrepreneur with great ideas but a miniscule budget, an artist employing single-celled organisms for an experimental design palette, a molecular biologist with a penchant for mentorship, and folks like me, who want to learn by creating novel organisms.

Wednesday, October 12, 2011

DIY Bio: Growing Movement takes On Aging

Article by H+ Magazine

A movement is growing quietly, steadily, and with great speed. In basements, attics, garages, and living rooms, amateurs and professionals alike are moving steadily towards disparate though unified goals. They come home from work or school and transform into biologists: do-it-yourself biologists, to be exact.

DIYbiology (“DIYbio”) is a homegrown synthesis of software, hardware, and wetware. In the tradition of homebrew computing and in the spirit of the Make space (best typified by o‘Reilly‘s Make Magazine), these DIYers hack much more than software and electronics. These biohackers build their own laboratory equipment, write their own code (computer and genetic) and design their own biological systems. They engineer tissue, purify proteins, extract nucleic acids and alter the genome itself. Whereas typical laboratory experiments can run from tens-of-thousands to millions of dollars, many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist‘s budget. As the movement evolves, cooperatives are also springing up where hobbyists are pooling resources and creating “hacker spaces” and clubs to further reduce costs, share knowledge and boost morale.

The Pearl Gel Box and Creative Commons

Open Hardware for Molecular Biology Experiments

Sure it takes years of training to become a world class biologist, but now you can have fun with their equipment without slaving away in academia. Pearl Biotech is selling an electrophoresis gel box, an instrument used in the separation and characterization of DNA online. Electrophoresis is a safe procedure that is useful to molecular biologists but can be enjoyed by anyone. It’s a standard experiment in high school labs. The Pearl Gel Box is an open hardware device which means that anyone is free to build or adapt it as along as they share their modifications in a similar manner. Pearl Biotech sells a fully assembled version for $200. By providing a cheap entry level tool for genetics Pearl is helping generate interest in the field and supporting the do it yourself community.

Mammalian synthetic biology: engineering of sophisticated gene networks

J Biotechnol. 2007 Jul 15;130(4):329-45. Epub 2007 May 24.

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With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess "memory" so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.

Programmable cells: Interfacing natural and engineered gene networks

Article From Proceedings of the National Academy of Sciences of the United States of America.

(Full-text available)


Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of “plug-and-play” genetic circuitry that can be used to create cells with programmable behaviors.

Here is a fine discussion of the above article from an Openwetware blog.